build_ref: set -o xtrace && cd /CLARKSCV1.2.6.1 && alias python=python3 && mkdir -p /bbx/reference/$reference/$reference/Custom/ && mkdir -p /bbx/reference/$reference/$reference/taxonomy && cp /taxonomy/* /bbx/reference/$reference/$reference/taxonomy && /prepare_inputs.sh && touch /bbx/reference/$reference/$reference/.taxondata && yes | ./resetCustomDB.sh && set_targets.sh /bbx/reference/$reference/$reference custom --$taxlevel && classify_metagenome.sh --light -n $thread -P /tmp/reads.1.fq /tmp/reads.2.fq -R /bbx/tmp/blank_run
analysis: set -o xtrace && cd /CLARKSCV1.2.6.1 && alias python=python3 && gunzip -c /bbx/input/testing/reads.1.fq.gz > /bbx/tmp/reads.1.fq && gunzip -c /bbx/input/testing/reads.2.fq.gz > /bbx/tmp/reads.2.fq && set_targets.sh /bbx/reference/$reference/$reference custom --$taxlevel && classify_metagenome.sh --light -n $thread -P /bbx/tmp/reads.1.fq /bbx/tmp/reads.2.fq -R /bbx/tmp/bench && head /bbx/tmp/bench.csv && estimate_abundance.sh -F /bbx/tmp/bench.csv -D /bbx/reference/$reference/$reference > /bbx/tmp/abu.txt && tail -n +2 /bbx/tmp/abu.txt | cut -f2,5 -d"," | grep -v "UNKNOWN"> /bbx/tmp/abundance.tsv&& python /time100.py && python /prepare_results.py $taxlevel && mv /bbx/output/profile.tsv /bbx/output/profile.$taxlevel.tsv && mv /bbx/output/bins.tsv /bbx/output/bins.$taxlevel.tsv
