[M::bwa_idx_load_from_disk] read 0 ALT contigs
[M::process] read 556134 sequences (80000021 bp)...
[M::process] read 556216 sequences (80000229 bp)...
[M::mem_process_seqs] Processed 556134 reads in 164.943 CPU sec, 20.550 real sec
[M::process] read 556152 sequences (80000067 bp)...
[M::mem_process_seqs] Processed 556216 reads in 168.159 CPU sec, 20.693 real sec
[M::process] read 556134 sequences (80000000 bp)...
[M::mem_process_seqs] Processed 556152 reads in 172.794 CPU sec, 21.239 real sec
[M::process] read 282789 sequences (40670296 bp)...
[M::mem_process_seqs] Processed 556134 reads in 170.605 CPU sec, 21.017 real sec
[M::mem_process_seqs] Processed 282789 reads in 89.610 CPU sec, 10.992 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_442\tSM:MontereyBayCA_442\tPL:Illumina reference.fasta MontereyBayCA_442.R1.fq.gz
[main] Real time: 97.702 sec; CPU: 768.246 sec