Fri Jun  4 10:17:06 2021

/usr/bin/breseq-0.35.4-Linux-x86_64/bin/breseq -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_R2_A6_F61_I1_R1_S58_L001_R1_001.good.fq.gz /var/alemutpipe-outputs/good/JADR40_R2_A6_F61_I1_R1_S58_L001_R2_001.good.fq.gz /var/alemutpipe-outputs/good/JADR40_R2_A6_F61_I1_R1_S58_L002_R1_001.good.fq.gz /var/alemutpipe-outputs/good/JADR40_R2_A6_F61_I1_R1_S58_L002_R2_001.good.fq.gz /var/alemutpipe-outputs/good/JADR40_R2_A6_F61_I1_R1_S58_L003_R1_001.good.fq.gz /var/alemutpipe-outputs/good/JADR40_R2_A6_F61_I1_R1_S58_L003_R2_001.good.fq.gz /var/alemutpipe-outputs/good/JADR40_R2_A6_F61_I1_R1_S58_L004_R1_001.good.fq.gz /var/alemutpipe-outputs/good/JADR40_R2_A6_F61_I1_R1_S58_L004_R2_001.good.fq.gz