[M::bwa_idx_load_from_disk] read 0 ALT contigs
[M::process] read 555560 sequences (80000161 bp)...
[M::process] read 555562 sequences (80000277 bp)...
[M::mem_process_seqs] Processed 555560 reads in 176.567 CPU sec, 22.017 real sec
[M::process] read 555562 sequences (80000257 bp)...
[M::mem_process_seqs] Processed 555562 reads in 182.293 CPU sec, 22.444 real sec
[M::process] read 555560 sequences (80000191 bp)...
[M::mem_process_seqs] Processed 555562 reads in 184.844 CPU sec, 22.668 real sec
[M::process] read 555560 sequences (80000235 bp)...
[M::mem_process_seqs] Processed 555560 reads in 182.453 CPU sec, 22.411 real sec
[M::process] read 555560 sequences (80000238 bp)...
[M::mem_process_seqs] Processed 555560 reads in 180.911 CPU sec, 22.237 real sec
[M::process] read 210959 sequences (30377931 bp)...
[M::mem_process_seqs] Processed 555560 reads in 180.390 CPU sec, 22.242 real sec
[M::mem_process_seqs] Processed 210959 reads in 72.277 CPU sec, 8.796 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_FG202\tSM:DabobBayWA_FG202\tPL:Illumina reference.fasta DabobBayWA_FG202.R1.fq.gz
[main] Real time: 145.594 sec; CPU: 1161.748 sec