[M::bwa_idx_load_from_disk] read 0 ALT contigs
[M::process] read 556216 sequences (80000063 bp)...
[M::process] read 555942 sequences (80000123 bp)...
[M::mem_process_seqs] Processed 556216 reads in 171.343 CPU sec, 21.353 real sec
[M::process] read 555950 sequences (80000078 bp)...
[M::mem_process_seqs] Processed 555942 reads in 179.596 CPU sec, 22.090 real sec
[M::process] read 555908 sequences (80000253 bp)...
[M::mem_process_seqs] Processed 555950 reads in 181.199 CPU sec, 22.308 real sec
[M::process] read 555844 sequences (80000039 bp)...
[M::mem_process_seqs] Processed 555908 reads in 179.702 CPU sec, 22.057 real sec
[M::process] read 178360 sequences (25671817 bp)...
[M::mem_process_seqs] Processed 555844 reads in 179.057 CPU sec, 22.129 real sec
[M::mem_process_seqs] Processed 178360 reads in 63.836 CPU sec, 7.698 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_424\tSM:MontereyBayCA_424\tPL:Illumina reference.fasta MontereyBayCA_424.R1.fq.gz
[main] Real time: 120.587 sec; CPU: 956.722 sec