[M::bwa_idx_load_from_disk] read 0 ALT contigs
[M::process] read 555560 sequences (80000222 bp)...
[M::process] read 555560 sequences (80000234 bp)...
[M::mem_process_seqs] Processed 555560 reads in 174.001 CPU sec, 21.698 real sec
[M::process] read 555562 sequences (80000151 bp)...
[M::mem_process_seqs] Processed 555560 reads in 176.322 CPU sec, 21.701 real sec
[M::process] read 555560 sequences (80000199 bp)...
[M::mem_process_seqs] Processed 555562 reads in 177.010 CPU sec, 21.764 real sec
[M::process] read 555560 sequences (80000196 bp)...
[M::mem_process_seqs] Processed 555560 reads in 178.524 CPU sec, 21.951 real sec
[M::process] read 555560 sequences (80000230 bp)...
[M::mem_process_seqs] Processed 555560 reads in 176.643 CPU sec, 21.743 real sec
[M::process] read 555558 sequences (80000013 bp)...
[M::mem_process_seqs] Processed 555560 reads in 176.086 CPU sec, 21.664 real sec
[M::process] read 356622 sequences (51353360 bp)...
[M::mem_process_seqs] Processed 555558 reads in 178.160 CPU sec, 21.967 real sec
[M::mem_process_seqs] Processed 356622 reads in 115.772 CPU sec, 14.269 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_FG211\tSM:DabobBayWA_FG211\tPL:Illumina reference.fasta DabobBayWA_FG211.R1.fq.gz
[main] Real time: 170.845 sec; CPU: 1355.331 sec