[M::bwa_idx_load_from_disk] read 0 ALT contigs
[M::process] read 555960 sequences (80000170 bp)...
[M::process] read 555984 sequences (80000261 bp)...
[M::mem_process_seqs] Processed 555960 reads in 177.611 CPU sec, 22.152 real sec
[M::process] read 555942 sequences (80000188 bp)...
[M::mem_process_seqs] Processed 555984 reads in 182.450 CPU sec, 22.450 real sec
[M::process] read 94421 sequences (13586221 bp)...
[M::mem_process_seqs] Processed 555942 reads in 181.534 CPU sec, 22.435 real sec
[M::mem_process_seqs] Processed 94421 reads in 36.525 CPU sec, 4.307 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_436\tSM:MontereyBayCA_436\tPL:Illumina reference.fasta MontereyBayCA_436.R1.fq.gz
[main] Real time: 73.707 sec; CPU: 579.893 sec