[M::bwa_idx_load_from_disk] read 0 ALT contigs
[M::process] read 556886 sequences (80000009 bp)...
[M::process] read 556850 sequences (80000032 bp)...
[M::mem_process_seqs] Processed 556886 reads in 151.796 CPU sec, 18.896 real sec
[M::process] read 556824 sequences (80000143 bp)...
[M::mem_process_seqs] Processed 556850 reads in 155.912 CPU sec, 19.136 real sec
[M::process] read 295189 sequences (42402168 bp)...
[M::mem_process_seqs] Processed 556824 reads in 154.812 CPU sec, 19.031 real sec
[M::mem_process_seqs] Processed 295189 reads in 84.302 CPU sec, 10.328 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_Q363\tSM:DabobBayWA_Q363\tPL:Illumina reference.fasta DabobBayWA_Q363.R1.fq.gz
[main] Real time: 70.557 sec; CPU: 549.083 sec