[M::bwa_idx_load_from_disk] read 0 ALT contigs
[M::process] read 556576 sequences (80000278 bp)...
[M::process] read 556550 sequences (80000014 bp)...
[M::mem_process_seqs] Processed 556576 reads in 152.358 CPU sec, 18.972 real sec
[M::process] read 556574 sequences (80000168 bp)...
[M::mem_process_seqs] Processed 556550 reads in 156.354 CPU sec, 19.200 real sec
[M::process] read 556504 sequences (80000047 bp)...
[M::mem_process_seqs] Processed 556574 reads in 155.873 CPU sec, 19.101 real sec
[M::process] read 336964 sequences (48431454 bp)...
[M::mem_process_seqs] Processed 556504 reads in 155.887 CPU sec, 19.185 real sec
[M::mem_process_seqs] Processed 336964 reads in 95.152 CPU sec, 11.686 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_Q242\tSM:DabobBayWA_Q242\tPL:Illumina reference.fasta DabobBayWA_Q242.R1.fq.gz
[main] Real time: 91.746 sec; CPU: 718.136 sec