[M::bwa_idx_load_from_disk] read 0 ALT contigs
[M::process] read 557474 sequences (80000109 bp)...
[M::process] read 557582 sequences (80000049 bp)...
[M::mem_process_seqs] Processed 557474 reads in 149.664 CPU sec, 18.619 real sec
[M::process] read 557526 sequences (80000139 bp)...
[M::mem_process_seqs] Processed 557582 reads in 150.661 CPU sec, 18.475 real sec
[M::process] read 557472 sequences (80000052 bp)...
[M::mem_process_seqs] Processed 557526 reads in 151.561 CPU sec, 18.604 real sec
[M::process] read 557412 sequences (80000121 bp)...
[M::mem_process_seqs] Processed 557472 reads in 152.182 CPU sec, 18.647 real sec
[M::process] read 432312 sequences (62027399 bp)...
[M::mem_process_seqs] Processed 557412 reads in 151.511 CPU sec, 18.611 real sec
[M::mem_process_seqs] Processed 432312 reads in 115.389 CPU sec, 14.237 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:DabobBayWA_Q231\tSM:DabobBayWA_Q231\tPL:Illumina reference.fasta DabobBayWA_Q231.R1.fq.gz
[main] Real time: 111.129 sec; CPU: 873.678 sec