[M::bwa_idx_load_from_disk] read 0 ALT contigs
[M::process] read 556662 sequences (80000043 bp)...
[M::process] read 556660 sequences (80000146 bp)...
[M::mem_process_seqs] Processed 556662 reads in 153.224 CPU sec, 19.100 real sec
[M::process] read 211019 sequences (30323177 bp)...
[M::mem_process_seqs] Processed 556660 reads in 154.491 CPU sec, 19.091 real sec
[M::mem_process_seqs] Processed 211019 reads in 60.071 CPU sec, 7.295 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_Q358\tSM:DabobBayWA_Q358\tPL:Illumina reference.fasta DabobBayWA_Q358.R1.fq.gz
[main] Real time: 48.220 sec; CPU: 369.708 sec