[M::bwa_idx_load_from_disk] read 0 ALT contigs
[M::process] read 555882 sequences (80000133 bp)...
[M::process] read 555764 sequences (80000110 bp)...
[M::mem_process_seqs] Processed 555882 reads in 161.411 CPU sec, 20.112 real sec
[M::process] read 555750 sequences (80000003 bp)...
[M::mem_process_seqs] Processed 555764 reads in 172.076 CPU sec, 21.146 real sec
[M::process] read 555730 sequences (80000268 bp)...
[M::mem_process_seqs] Processed 555750 reads in 170.858 CPU sec, 20.997 real sec
[M::process] read 555696 sequences (80000178 bp)...
[M::mem_process_seqs] Processed 555730 reads in 170.410 CPU sec, 20.930 real sec
[M::process] read 171592 sequences (24704018 bp)...
[M::mem_process_seqs] Processed 555696 reads in 168.739 CPU sec, 20.857 real sec
[M::mem_process_seqs] Processed 171592 reads in 56.190 CPU sec, 6.783 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_421\tSM:MontereyBayCA_421\tPL:Illumina reference.fasta MontereyBayCA_421.R1.fq.gz
[main] Real time: 113.482 sec; CPU: 901.513 sec