[M::bwa_idx_load_from_disk] read 0 ALT contigs
[M::process] read 556106 sequences (80000086 bp)...
[M::process] read 555950 sequences (80000146 bp)...
[M::mem_process_seqs] Processed 556106 reads in 167.304 CPU sec, 20.840 real sec
[M::process] read 470679 sequences (67741116 bp)...
[M::mem_process_seqs] Processed 555950 reads in 176.048 CPU sec, 21.677 real sec
[M::mem_process_seqs] Processed 470679 reads in 148.232 CPU sec, 18.312 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:MontereyBayCA_449\tSM:MontereyBayCA_449\tPL:Illumina reference.fasta MontereyBayCA_449.R1.fq.gz
[main] Real time: 65.875 sec; CPU: 494.641 sec