[M::bwa_idx_load_from_disk] read 0 ALT contigs
[M::process] read 557170 sequences (80000210 bp)...
[M::process] read 557212 sequences (80000006 bp)...
[M::mem_process_seqs] Processed 557170 reads in 148.567 CPU sec, 18.511 real sec
[M::process] read 557196 sequences (80000059 bp)...
[M::mem_process_seqs] Processed 557212 reads in 149.636 CPU sec, 18.389 real sec
[M::process] read 557212 sequences (80000094 bp)...
[M::mem_process_seqs] Processed 557196 reads in 150.341 CPU sec, 18.415 real sec
[M::process] read 557142 sequences (80000003 bp)...
[M::mem_process_seqs] Processed 557212 reads in 150.101 CPU sec, 18.375 real sec
[M::process] read 166352 sequences (23882128 bp)...
[M::mem_process_seqs] Processed 557142 reads in 147.989 CPU sec, 18.261 real sec
[M::mem_process_seqs] Processed 166352 reads in 49.328 CPU sec, 5.945 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_FG223\tSM:DabobBayWA_FG223\tPL:Illumina reference.fasta DabobBayWA_FG223.R1.fq.gz
[main] Real time: 100.455 sec; CPU: 797.883 sec