build_ref: set -o verbose;/prepare_inputs.sh;python3 /prepare_fasta.py;/kaiju/bin/mkbwt -n $thread -a ACDEFGHIKLMNPQRSTVWY -o /bbx/reference/$reference /bbx/tmp/train.faa || true;/kaiju/bin/mkfmi /bbx/reference/$reference;cp /bbx/input/training/*.dmp /bbx/reference/;
analysis: set -o verbose;ls /bbx/tmp;gunzip -c /bbx/input/testing/reads.1.fq.gz >  /bbx/tmp/reads.1.fq;gunzip -c /bbx/input/testing/reads.2.fq.gz >  /bbx/tmp/reads.2.fq;/kaiju/bin/kaiju -z $thread -t /bbx/reference/nodes.dmp -f /bbx/reference/$reference.fmi -i /bbx/tmp/reads.1.fq -j /bbx/tmp/reads.2.fq -o /bbx/tmp/kaiju.out;/kaiju/bin/kaijuReport -i /bbx/tmp/kaiju.out -o /bbx/tmp/abundance -t /bbx/reference/nodes.dmp -n /bbx/reference/names.dmp -r $taxlevel;/extract_taxid.sh;python3 /prepare_results.py;mv /bbx/output/profile.tsv /bbx/output/profile.$taxlevel.tsv;mv /bbx/output/bins.tsv /bbx/output/bins.$taxlevel.tsv;
