[M::bwa_idx_load_from_disk] read 0 ALT contigs
[M::process] read 556694 sequences (80000218 bp)...
[M::process] read 556682 sequences (80000028 bp)...
[M::mem_process_seqs] Processed 556694 reads in 149.028 CPU sec, 18.514 real sec
[M::process] read 556696 sequences (80000126 bp)...
[M::mem_process_seqs] Processed 556682 reads in 152.025 CPU sec, 18.651 real sec
[M::process] read 268711 sequences (38610926 bp)...
[M::mem_process_seqs] Processed 556696 reads in 151.439 CPU sec, 18.657 real sec
[M::mem_process_seqs] Processed 268711 reads in 76.723 CPU sec, 9.396 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_Q244\tSM:DabobBayWA_Q244\tPL:Illumina reference.fasta DabobBayWA_Q244.R1.fq.gz
[main] Real time: 68.506 sec; CPU: 531.430 sec