build_ref: set -o xtrace && sleep 5 && alias python=python3 && mkdir /bbx/tmp/results && /prepare_inputs.sh && cat /bbx/input/training/mapping.tsv | grep -v "@" | grep -v "#" | awk '{split($0,a,"\t") ; print a[5]"\t"a[1]}' > /bbx/tmp/conversion.tsv && centrifuge-build -p 12 -a --bmax 1342177280 --conversion-table /bbx/tmp/conversion.tsv --taxonomy-tree /bbx/input/training/nodes.dmp --name-table /bbx/input/training/names.dmp /bbx/tmp/bench.fa /bbx/reference/$reference;
analysis: set -o xtrace;sleep 5;alias python=python3;cp /bbx/input/testing/*.fq.gz /bbx/tmp/;gunzip /bbx/tmp/*.fq.gz;centrifuge -p $thread -x /bbx/reference/$reference -1 /bbx/tmp/reads.1.fq -2 /bbx/tmp/reads.2.fq --report-file bench_report.txt -S /bbx/tmp/classification.tmp;cp /empty_out.tsv /bbx/output/classification.tsv;tail -n+2 classification.tmp | cut -f1,3 >> /bbx/output/classification.tsv ;head /bbx/output/classification.tsv;cat bench_report.txt;pwd;cat /bbx/tmp/reads.1.fq | wc -l > /bbx/tmp/total.txt;python3 /prepare_results.py;cp /empty_out.tsv /bbx/output/bins.$taxlevel.tsv;tail -n+2 classification.tmp | cut -f1,3 | grep -v -P "\t0$" >> /bbx/output/bins.$taxlevel.tsv;mv /bbx/output/profile.tsv /bbx/output/profile.$taxlevel.tsv
