[M::bwa_idx_load_from_disk] read 0 ALT contigs
[M::process] read 556410 sequences (80000074 bp)...
[M::process] read 556412 sequences (80000048 bp)...
[M::mem_process_seqs] Processed 556410 reads in 151.222 CPU sec, 18.832 real sec
[M::process] read 556414 sequences (80000128 bp)...
[M::mem_process_seqs] Processed 556412 reads in 153.825 CPU sec, 18.904 real sec
[M::process] read 556420 sequences (80000196 bp)...
[M::mem_process_seqs] Processed 556414 reads in 153.795 CPU sec, 18.862 real sec
[M::process] read 556382 sequences (80000228 bp)...
[M::mem_process_seqs] Processed 556420 reads in 154.194 CPU sec, 18.948 real sec
[M::process] read 163839 sequences (23555808 bp)...
[M::mem_process_seqs] Processed 556382 reads in 151.247 CPU sec, 18.690 real sec
[M::mem_process_seqs] Processed 163839 reads in 47.327 CPU sec, 5.724 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_Q402\tSM:MontereyBayCA_Q402\tPL:Illumina reference.fasta MontereyBayCA_Q402.R1.fq.gz
[main] Real time: 102.513 sec; CPU: 813.566 sec