[M::bwa_idx_load_from_disk] read 0 ALT contigs
[M::process] read 556180 sequences (80000151 bp)...
[M::process] read 556212 sequences (80000207 bp)...
[M::mem_process_seqs] Processed 556180 reads in 165.786 CPU sec, 20.661 real sec
[M::process] read 556084 sequences (80000004 bp)...
[M::mem_process_seqs] Processed 556212 reads in 168.959 CPU sec, 20.725 real sec
[M::process] read 320734 sequences (46131626 bp)...
[M::mem_process_seqs] Processed 556084 reads in 169.296 CPU sec, 20.790 real sec
[M::mem_process_seqs] Processed 320734 reads in 101.077 CPU sec, 12.395 real sec
[main] Version: 0.7.17-r1188
[main] CMD: bwa mem -L 20,5 -t 8 -a -M -T 10 -A 1 -B 4 -O 6 -R @RG\tID:MontereyBayCA_410\tSM:MontereyBayCA_410\tPL:Illumina reference.fasta MontereyBayCA_410.R1.fq.gz
[main] Real time: 78.400 sec; CPU: 607.721 sec