[M::bwa_idx_load_from_disk] read 0 ALT contigs
[M::process] read 556412 sequences (80000038 bp)...
[M::process] read 556410 sequences (80000192 bp)...
[M::mem_process_seqs] Processed 556412 reads in 146.722 CPU sec, 18.257 real sec
[M::process] read 556410 sequences (80000220 bp)...
[M::mem_process_seqs] Processed 556410 reads in 151.314 CPU sec, 18.597 real sec
[M::process] read 556388 sequences (80000226 bp)...
[M::mem_process_seqs] Processed 556410 reads in 149.270 CPU sec, 18.313 real sec
[M::process] read 556418 sequences (80000040 bp)...
[M::mem_process_seqs] Processed 556388 reads in 151.509 CPU sec, 18.605 real sec
[M::process] read 10674 sequences (1534488 bp)...
[M::mem_process_seqs] Processed 556418 reads in 149.664 CPU sec, 18.535 real sec
[M::mem_process_seqs] Processed 10674 reads in 4.237 CPU sec, 0.498 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_Q239\tSM:DabobBayWA_Q239\tPL:Illumina reference.fasta DabobBayWA_Q239.R1.fq.gz
[main] Real time: 97.104 sec; CPU: 755.576 sec