[M::bwa_idx_load_from_disk] read 0 ALT contigs
[M::process] read 556520 sequences (80000030 bp)...
[M::process] read 556522 sequences (80000216 bp)...
[M::mem_process_seqs] Processed 556520 reads in 149.297 CPU sec, 18.584 real sec
[M::process] read 556480 sequences (80000271 bp)...
[M::mem_process_seqs] Processed 556522 reads in 152.726 CPU sec, 18.762 real sec
[M::process] read 556478 sequences (80000144 bp)...
[M::mem_process_seqs] Processed 556480 reads in 152.116 CPU sec, 18.661 real sec
[M::process] read 184619 sequences (26539337 bp)...
[M::mem_process_seqs] Processed 556478 reads in 151.465 CPU sec, 18.686 real sec
[M::mem_process_seqs] Processed 184619 reads in 54.527 CPU sec, 6.631 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_Q238\tSM:DabobBayWA_Q238\tPL:Illumina reference.fasta DabobBayWA_Q238.R1.fq.gz
[main] Real time: 83.906 sec; CPU: 661.993 sec