Fri Jun  4 10:15:29 2021

/usr/bin/breseq-0.35.4-Linux-x86_64/bin/breseq -p -j 2 --consensus-frequency-cutoff=0.75 --require-match-fraction=0.95 -o breseq_processes/0 -r /var/data/NC_000964_BS168_ref.gbk -r /var/data/pSIJ663_pHT315.gb /var/alemutpipe-outputs/good/JADR40_R1_A5_F60_I0_R1_S73_L001_R1_001.good.fq.gz /var/alemutpipe-outputs/good/JADR40_R1_A5_F60_I0_R1_S73_L001_R2_001.good.fq.gz /var/alemutpipe-outputs/good/JADR40_R1_A5_F60_I0_R1_S73_L002_R1_001.good.fq.gz /var/alemutpipe-outputs/good/JADR40_R1_A5_F60_I0_R1_S73_L002_R2_001.good.fq.gz /var/alemutpipe-outputs/good/JADR40_R1_A5_F60_I0_R1_S73_L003_R1_001.good.fq.gz /var/alemutpipe-outputs/good/JADR40_R1_A5_F60_I0_R1_S73_L003_R2_001.good.fq.gz /var/alemutpipe-outputs/good/JADR40_R1_A5_F60_I0_R1_S73_L004_R1_001.good.fq.gz /var/alemutpipe-outputs/good/JADR40_R1_A5_F60_I0_R1_S73_L004_R2_001.good.fq.gz