[M::bwa_idx_load_from_disk] read 0 ALT contigs
[M::process] read 556038 sequences (80000222 bp)...
[M::process] read 556096 sequences (80000154 bp)...
[M::mem_process_seqs] Processed 556038 reads in 172.312 CPU sec, 21.479 real sec
[M::process] read 555936 sequences (80000163 bp)...
[M::mem_process_seqs] Processed 556096 reads in 175.589 CPU sec, 21.584 real sec
[M::process] read 555960 sequences (80000150 bp)...
[M::mem_process_seqs] Processed 555936 reads in 177.941 CPU sec, 21.876 real sec
[M::process] read 84941 sequences (12220829 bp)...
[M::mem_process_seqs] Processed 555960 reads in 176.491 CPU sec, 21.841 real sec
[M::mem_process_seqs] Processed 84941 reads in 30.502 CPU sec, 3.622 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_425\tSM:MontereyBayCA_425\tPL:Illumina reference.fasta MontereyBayCA_425.R1.fq.gz
[main] Real time: 92.747 sec; CPU: 734.685 sec