build_ref: set -o verbose && python3 /prepare_inputs_CCM.py && kma index -NI -Sparse $parameter -i /bbx/tmp/all.fna -o /bbx/reference/$reference
analysis: set -o verbose && kma -ipe /bbx/input/testing/reads.1.fq.gz /bbx/input/testing/reads.2.fq.gz -o sample_out_kma -t_db /bbx/reference/$reference -t $thread -1t1 -mem_mode -and -apm f && CCMetagen.py -i sample_out_kma.res -o /bbx/output/results --depth_unit kma && python3 /prepare_results_ccm.py && mv /bbx/output/profile.tsv /bbx/output/profile.$taxlevel.tsv && touch /bbx/output/bins.$taxlevel.tsv
