[M::bwa_idx_load_from_disk] read 0 ALT contigs
[M::process] read 555558 sequences (80000083 bp)...
[M::process] read 555560 sequences (80000251 bp)...
[M::mem_process_seqs] Processed 555558 reads in 176.959 CPU sec, 22.021 real sec
[M::process] read 555560 sequences (80000235 bp)...
[M::mem_process_seqs] Processed 555560 reads in 180.015 CPU sec, 22.118 real sec
[M::process] read 555560 sequences (80000265 bp)...
[M::mem_process_seqs] Processed 555560 reads in 180.054 CPU sec, 22.139 real sec
[M::process] read 555558 sequences (80000023 bp)...
[M::mem_process_seqs] Processed 555560 reads in 179.650 CPU sec, 22.108 real sec
[M::process] read 555558 sequences (80000106 bp)...
[M::mem_process_seqs] Processed 555558 reads in 179.456 CPU sec, 22.070 real sec
[M::process] read 555558 sequences (80000063 bp)...
[M::mem_process_seqs] Processed 555558 reads in 181.952 CPU sec, 22.363 real sec
[M::process] read 555558 sequences (80000072 bp)...
[M::mem_process_seqs] Processed 555558 reads in 180.661 CPU sec, 22.174 real sec
[M::process] read 320604 sequences (46166794 bp)...
[M::mem_process_seqs] Processed 555558 reads in 178.669 CPU sec, 22.028 real sec
[M::mem_process_seqs] Processed 320604 reads in 105.093 CPU sec, 12.915 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_FG205\tSM:DabobBayWA_FG205\tPL:Illumina reference.fasta DabobBayWA_FG205.R1.fq.gz
[main] Real time: 193.587 sec; CPU: 1545.121 sec