[M::bwa_idx_load_from_disk] read 0 ALT contigs
[M::process] read 555968 sequences (80000254 bp)...
[M::process] read 556046 sequences (80000096 bp)...
[M::mem_process_seqs] Processed 555968 reads in 174.392 CPU sec, 21.713 real sec
[M::process] read 556036 sequences (80000063 bp)...
[M::mem_process_seqs] Processed 556046 reads in 177.164 CPU sec, 21.803 real sec
[M::process] read 555930 sequences (80000228 bp)...
[M::mem_process_seqs] Processed 556036 reads in 178.096 CPU sec, 21.881 real sec
[M::process] read 555952 sequences (80000114 bp)...
[M::mem_process_seqs] Processed 555930 reads in 179.758 CPU sec, 22.074 real sec
[M::process] read 127648 sequences (18366328 bp)...
[M::mem_process_seqs] Processed 555952 reads in 177.728 CPU sec, 21.947 real sec
[M::mem_process_seqs] Processed 127648 reads in 45.323 CPU sec, 5.405 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_412\tSM:MontereyBayCA_412\tPL:Illumina reference.fasta MontereyBayCA_412.R1.fq.gz
[main] Real time: 117.681 sec; CPU: 934.343 sec