[M::bwa_idx_load_from_disk] read 0 ALT contigs
[M::process] read 556412 sequences (80000142 bp)...
[M::process] read 556418 sequences (80000014 bp)...
[M::mem_process_seqs] Processed 556412 reads in 157.001 CPU sec, 19.553 real sec
[M::process] read 556386 sequences (80000226 bp)...
[M::mem_process_seqs] Processed 556418 reads in 159.237 CPU sec, 19.534 real sec
[M::process] read 556382 sequences (80000000 bp)...
[M::mem_process_seqs] Processed 556386 reads in 161.999 CPU sec, 19.903 real sec
[M::process] read 152428 sequences (21913623 bp)...
[M::mem_process_seqs] Processed 556382 reads in 157.937 CPU sec, 19.475 real sec
[M::mem_process_seqs] Processed 152428 reads in 46.492 CPU sec, 5.614 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_Q233\tSM:DabobBayWA_Q233\tPL:Illumina reference.fasta DabobBayWA_Q233.R1.fq.gz
[main] Real time: 86.623 sec; CPU: 684.635 sec