[M::bwa_idx_load_from_disk] read 0 ALT contigs
[M::process] read 556828 sequences (80000074 bp)...
[M::process] read 556818 sequences (80000004 bp)...
[M::mem_process_seqs] Processed 556828 reads in 148.446 CPU sec, 18.485 real sec
[M::process] read 556848 sequences (80000094 bp)...
[M::mem_process_seqs] Processed 556818 reads in 151.467 CPU sec, 18.580 real sec
[M::process] read 556760 sequences (80000052 bp)...
[M::mem_process_seqs] Processed 556848 reads in 150.659 CPU sec, 18.472 real sec
[M::process] read 438328 sequences (62973232 bp)...
[M::mem_process_seqs] Processed 556760 reads in 150.801 CPU sec, 18.522 real sec
[M::mem_process_seqs] Processed 438328 reads in 117.971 CPU sec, 14.562 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_FG228\tSM:DabobBayWA_FG228\tPL:Illumina reference.fasta DabobBayWA_FG228.R1.fq.gz
[main] Real time: 92.711 sec; CPU: 722.177 sec