[M::bwa_idx_load_from_disk] read 0 ALT contigs
[M::process] read 555560 sequences (80000235 bp)...
[M::process] read 555560 sequences (80000212 bp)...
[M::mem_process_seqs] Processed 555560 reads in 174.668 CPU sec, 21.786 real sec
[M::process] read 555560 sequences (80000169 bp)...
[M::mem_process_seqs] Processed 555560 reads in 177.316 CPU sec, 21.832 real sec
[M::process] read 555560 sequences (80000287 bp)...
[M::mem_process_seqs] Processed 555560 reads in 177.845 CPU sec, 21.869 real sec
[M::process] read 555558 sequences (80000087 bp)...
[M::mem_process_seqs] Processed 555560 reads in 176.871 CPU sec, 21.774 real sec
[M::process] read 555560 sequences (80000262 bp)...
[M::mem_process_seqs] Processed 555558 reads in 178.565 CPU sec, 21.919 real sec
[M::process] read 555558 sequences (80000050 bp)...
[M::mem_process_seqs] Processed 555560 reads in 176.323 CPU sec, 21.687 real sec
[M::process] read 219615 sequences (31624412 bp)...
[M::mem_process_seqs] Processed 555558 reads in 178.769 CPU sec, 22.042 real sec
[M::mem_process_seqs] Processed 219615 reads in 74.238 CPU sec, 9.079 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_FG201\tSM:DabobBayWA_FG201\tPL:Illumina reference.fasta DabobBayWA_FG201.R1.fq.gz
[main] Real time: 164.933 sec; CPU: 1316.681 sec