[M::bwa_idx_load_from_disk] read 0 ALT contigs
[M::process] read 556588 sequences (80000018 bp)...
[M::process] read 556584 sequences (80000214 bp)...
[M::mem_process_seqs] Processed 556588 reads in 141.832 CPU sec, 17.649 real sec
[M::process] read 556568 sequences (80000179 bp)...
[M::mem_process_seqs] Processed 556584 reads in 145.770 CPU sec, 17.951 real sec
[M::process] read 556584 sequences (80000109 bp)...
[M::mem_process_seqs] Processed 556568 reads in 145.601 CPU sec, 17.840 real sec
[M::process] read 52079 sequences (7483811 bp)...
[M::mem_process_seqs] Processed 556584 reads in 146.153 CPU sec, 18.050 real sec
[M::mem_process_seqs] Processed 52079 reads in 16.621 CPU sec, 1.966 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_Q243\tSM:DabobBayWA_Q243\tPL:Illumina reference.fasta DabobBayWA_Q243.R1.fq.gz
[main] Real time: 76.352 sec; CPU: 598.246 sec