[M::bwa_idx_load_from_disk] read 0 ALT contigs
[M::process] read 556106 sequences (80000249 bp)...
[M::process] read 556078 sequences (80000118 bp)...
[M::mem_process_seqs] Processed 556106 reads in 186.364 CPU sec, 23.255 real sec
[M::process] read 279537 sequences (40213404 bp)...
[M::mem_process_seqs] Processed 556078 reads in 192.612 CPU sec, 23.770 real sec
[M::mem_process_seqs] Processed 279537 reads in 98.947 CPU sec, 12.123 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_437\tSM:MontereyBayCA_437\tPL:Illumina reference.fasta MontereyBayCA_437.R1.fq.gz
[main] Real time: 62.471 sec; CPU: 480.113 sec