[M::bwa_idx_load_from_disk] read 0 ALT contigs
[M::process] read 555784 sequences (80000021 bp)...
[M::process] read 555736 sequences (80000014 bp)...
[M::mem_process_seqs] Processed 555784 reads in 166.751 CPU sec, 20.786 real sec
[M::process] read 555694 sequences (80000014 bp)...
[M::mem_process_seqs] Processed 555736 reads in 168.272 CPU sec, 20.712 real sec
[M::process] read 555688 sequences (80000029 bp)...
[M::mem_process_seqs] Processed 555694 reads in 168.959 CPU sec, 20.752 real sec
[M::process] read 555680 sequences (80000147 bp)...
[M::mem_process_seqs] Processed 555688 reads in 169.642 CPU sec, 20.840 real sec
[M::process] read 555660 sequences (80000095 bp)...
[M::mem_process_seqs] Processed 555680 reads in 169.506 CPU sec, 20.823 real sec
[M::process] read 555654 sequences (80000066 bp)...
[M::mem_process_seqs] Processed 555660 reads in 172.619 CPU sec, 21.208 real sec
[M::process] read 311209 sequences (44806731 bp)...
[M::mem_process_seqs] Processed 555654 reads in 167.464 CPU sec, 20.637 real sec
[M::mem_process_seqs] Processed 311209 reads in 98.389 CPU sec, 12.081 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_446\tSM:MontereyBayCA_446\tPL:Illumina reference.fasta MontereyBayCA_446.R1.fq.gz
[main] Real time: 162.277 sec; CPU: 1284.511 sec