build_ref:set -o verbose && mkdir -p /bbx/tmp/input/ && mkdir -p /bbx/reference/ && mkdir -p /bbx/reference/$reference/library/ && mkdir -p /bbx/reference/$reference/taxonomy/ && cp /bbx/input/training/*.dmp /bbx/reference/$reference/taxonomy/ && cd /metacache && /prepare_inputs1.sh && python3 /prepare_inputs.py && /prepare_inputs2.sh && /clean.sh  && ./metacache build /bbx/reference/$reference/library/bench /bbx/tmp/bench.fna -taxonomy /bbx/reference/$reference/taxonomy/ -taxpostmap /bbx/tmp/acc2taxid -kmerlen $(echo $parameter | cut -f1 -d",") && rm /bbx/tmp/bench.fna

analysis: set -o verbose && mkdir -p /bbx/tmp/results && gunzip /bbx/input/testing/reads.1.fq.gz -c > /bbx/tmp/reads.1.fq && gunzip /bbx/input/testing/reads.2.fq.gz -c > /bbx/tmp/reads.2.fq && /metacache/metacache query /bbx/reference/$reference/library/bench /bbx/tmp/reads.1.fq /bbx/tmp/reads.2.fq -pairfiles -out /bbx/tmp/bench.out -lowest $taxlevel -mapped-only -taxids -separate-cols -threads $thread -abundances /bbx/tmp/abundances.txt -abundance-per ${taxlevel} && /prepare_profiles.sh ${taxlevel} && python3 /prepare_profiles.py && cp /bins.header /bbx/output/bins.tsv && python3 /prepare_outputs.py && mv /bbx/output/bins.tsv /bbx/output/bins.$taxlevel.tsv && cp /bbx/input/training/mapping.tsv /bbx/tmp/mapping.tsv && mv /bbx/output/profile.tsv /bbx/output/profile.$taxlevel.tsv && rm /bbx/tmp/*.fq
