[M::bwa_idx_load_from_disk] read 0 ALT contigs
[M::process] read 556638 sequences (80000106 bp)...
[M::process] read 556694 sequences (80000219 bp)...
[M::mem_process_seqs] Processed 556638 reads in 157.880 CPU sec, 19.679 real sec
[M::process] read 556698 sequences (80000197 bp)...
[M::mem_process_seqs] Processed 556694 reads in 160.519 CPU sec, 19.735 real sec
[M::process] read 556654 sequences (80000118 bp)...
[M::mem_process_seqs] Processed 556698 reads in 162.032 CPU sec, 19.911 real sec
[M::process] read 556760 sequences (80000154 bp)...
[M::mem_process_seqs] Processed 556654 reads in 160.590 CPU sec, 19.722 real sec
[M::process] read 556566 sequences (80000202 bp)...
[M::mem_process_seqs] Processed 556760 reads in 160.040 CPU sec, 19.666 real sec
[M::process] read 556722 sequences (80000229 bp)...
[M::mem_process_seqs] Processed 556566 reads in 165.176 CPU sec, 20.304 real sec
[M::process] read 556630 sequences (80000026 bp)...
[M::mem_process_seqs] Processed 556722 reads in 160.178 CPU sec, 19.661 real sec
[M::process] read 556616 sequences (80000047 bp)...
[M::mem_process_seqs] Processed 556630 reads in 162.287 CPU sec, 19.901 real sec
[M::process] read 556722 sequences (80000234 bp)...
[M::mem_process_seqs] Processed 556616 reads in 160.622 CPU sec, 19.721 real sec
[M::process] read 228850 sequences (32885866 bp)...
[M::mem_process_seqs] Processed 556722 reads in 159.682 CPU sec, 19.705 real sec
[M::mem_process_seqs] Processed 228850 reads in 68.239 CPU sec, 8.339 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_Q360\tSM:DabobBayWA_Q360\tPL:Illumina reference.fasta DabobBayWA_Q360.R1.fq.gz
[main] Real time: 209.543 sec; CPU: 1679.551 sec