[M::bwa_idx_load_from_disk] read 0 ALT contigs
[M::process] read 556924 sequences (80000092 bp)...
[M::process] read 556920 sequences (80000185 bp)...
[M::mem_process_seqs] Processed 556924 reads in 147.833 CPU sec, 18.404 real sec
[M::process] read 556946 sequences (80000171 bp)...
[M::mem_process_seqs] Processed 556920 reads in 151.754 CPU sec, 18.623 real sec
[M::process] read 556878 sequences (80000238 bp)...
[M::mem_process_seqs] Processed 556946 reads in 153.481 CPU sec, 18.786 real sec
[M::process] read 505673 sequences (72637496 bp)...
[M::mem_process_seqs] Processed 556878 reads in 152.481 CPU sec, 18.729 real sec
[M::mem_process_seqs] Processed 505673 reads in 137.297 CPU sec, 16.982 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_FG229\tSM:DabobBayWA_FG229\tPL:Illumina reference.fasta DabobBayWA_FG229.R1.fq.gz
[main] Real time: 95.740 sec; CPU: 745.509 sec