[M::bwa_idx_load_from_disk] read 0 ALT contigs
[M::process] read 555956 sequences (80000156 bp)...
[M::process] read 555904 sequences (80000250 bp)...
[M::mem_process_seqs] Processed 555956 reads in 180.541 CPU sec, 22.475 real sec
[M::process] read 209631 sequences (30164538 bp)...
[M::mem_process_seqs] Processed 555904 reads in 185.647 CPU sec, 22.933 real sec
[M::mem_process_seqs] Processed 209631 reads in 74.366 CPU sec, 9.051 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_432\tSM:MontereyBayCA_432\tPL:Illumina reference.fasta MontereyBayCA_432.R1.fq.gz
[main] Real time: 57.685 sec; CPU: 442.847 sec