[M::bwa_idx_load_from_disk] read 0 ALT contigs
[M::process] read 555966 sequences (80000285 bp)...
[M::process] read 556016 sequences (80000230 bp)...
[M::mem_process_seqs] Processed 555966 reads in 166.690 CPU sec, 20.770 real sec
[M::process] read 555936 sequences (80000205 bp)...
[M::mem_process_seqs] Processed 556016 reads in 170.283 CPU sec, 20.922 real sec
[M::process] read 519343 sequences (74730347 bp)...
[M::mem_process_seqs] Processed 555936 reads in 171.682 CPU sec, 21.107 real sec
[M::mem_process_seqs] Processed 519343 reads in 157.608 CPU sec, 19.495 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_415\tSM:MontereyBayCA_415\tPL:Illumina reference.fasta MontereyBayCA_415.R1.fq.gz
[main] Real time: 86.903 sec; CPU: 669.076 sec