[M::bwa_idx_load_from_disk] read 0 ALT contigs
[M::process] read 557368 sequences (80000211 bp)...
[M::process] read 557342 sequences (80000255 bp)...
[M::mem_process_seqs] Processed 557368 reads in 146.486 CPU sec, 18.223 real sec
[M::process] read 557354 sequences (80000250 bp)...
[M::mem_process_seqs] Processed 557342 reads in 152.312 CPU sec, 18.675 real sec
[M::process] read 557284 sequences (80000106 bp)...
[M::mem_process_seqs] Processed 557354 reads in 149.721 CPU sec, 18.364 real sec
[M::process] read 550381 sequences (79000258 bp)...
[M::mem_process_seqs] Processed 557284 reads in 148.885 CPU sec, 18.257 real sec
[M::mem_process_seqs] Processed 550381 reads in 146.729 CPU sec, 18.125 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_Q237\tSM:DabobBayWA_Q237\tPL:Illumina reference.fasta DabobBayWA_Q237.R1.fq.gz
[main] Real time: 96.820 sec; CPU: 747.395 sec