[M::bwa_idx_load_from_disk] read 0 ALT contigs
[M::process] read 556268 sequences (80000067 bp)...
[M::process] read 556006 sequences (80000109 bp)...
[M::mem_process_seqs] Processed 556268 reads in 167.690 CPU sec, 20.909 real sec
[M::process] read 555988 sequences (80000245 bp)...
[M::mem_process_seqs] Processed 556006 reads in 178.813 CPU sec, 22.001 real sec
[M::process] read 555996 sequences (80000004 bp)...
[M::mem_process_seqs] Processed 555988 reads in 176.603 CPU sec, 21.693 real sec
[M::process] read 555894 sequences (80000224 bp)...
[M::mem_process_seqs] Processed 555996 reads in 175.618 CPU sec, 21.569 real sec
[M::process] read 340919 sequences (49064138 bp)...
[M::mem_process_seqs] Processed 555894 reads in 176.209 CPU sec, 21.705 real sec
[M::mem_process_seqs] Processed 340919 reads in 111.277 CPU sec, 13.671 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_445\tSM:MontereyBayCA_445\tPL:Illumina reference.fasta MontereyBayCA_445.R1.fq.gz
[main] Real time: 125.464 sec; CPU: 988.995 sec