[M::bwa_idx_load_from_disk] read 0 ALT contigs
[M::process] read 556134 sequences (80000054 bp)...
[M::process] read 556222 sequences (80000136 bp)...
[M::mem_process_seqs] Processed 556134 reads in 158.037 CPU sec, 19.693 real sec
[M::process] read 556112 sequences (80000216 bp)...
[M::mem_process_seqs] Processed 556222 reads in 163.015 CPU sec, 20.028 real sec
[M::process] read 546172 sequences (78563754 bp)...
[M::mem_process_seqs] Processed 556112 reads in 162.530 CPU sec, 19.970 real sec
[M::mem_process_seqs] Processed 546172 reads in 157.349 CPU sec, 19.458 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_414\tSM:MontereyBayCA_414\tPL:Illumina reference.fasta MontereyBayCA_414.R1.fq.gz
[main] Real time: 83.970 sec; CPU: 643.992 sec