[M::bwa_idx_load_from_disk] read 0 ALT contigs
[M::process] read 555928 sequences (80000238 bp)...
[M::process] read 555976 sequences (80000135 bp)...
[M::mem_process_seqs] Processed 555928 reads in 170.400 CPU sec, 21.229 real sec
[M::process] read 555910 sequences (80000127 bp)...
[M::mem_process_seqs] Processed 555976 reads in 175.934 CPU sec, 21.611 real sec
[M::process] read 555874 sequences (80000276 bp)...
[M::mem_process_seqs] Processed 555910 reads in 178.026 CPU sec, 21.891 real sec
[M::process] read 286646 sequences (41247788 bp)...
[M::mem_process_seqs] Processed 555874 reads in 176.309 CPU sec, 21.707 real sec
[M::mem_process_seqs] Processed 286646 reads in 92.918 CPU sec, 11.395 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_411\tSM:MontereyBayCA_411\tPL:Illumina reference.fasta MontereyBayCA_411.R1.fq.gz
[main] Real time: 101.147 sec; CPU: 796.023 sec