[M::bwa_idx_load_from_disk] read 0 ALT contigs
[M::process] read 556014 sequences (80000267 bp)...
[M::process] read 555790 sequences (80000054 bp)...
[M::mem_process_seqs] Processed 556014 reads in 153.901 CPU sec, 19.168 real sec
[M::process] read 555758 sequences (80000133 bp)...
[M::mem_process_seqs] Processed 555790 reads in 164.588 CPU sec, 20.246 real sec
[M::process] read 555716 sequences (80000029 bp)...
[M::mem_process_seqs] Processed 555758 reads in 161.970 CPU sec, 19.873 real sec
[M::process] read 44459 sequences (6400849 bp)...
[M::mem_process_seqs] Processed 555716 reads in 158.440 CPU sec, 19.556 real sec
[M::mem_process_seqs] Processed 44459 reads in 15.065 CPU sec, 1.768 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_FG220\tSM:DabobBayWA_FG220\tPL:Illumina reference.fasta DabobBayWA_FG220.R1.fq.gz
[main] Real time: 84.285 sec; CPU: 656.139 sec