[M::bwa_idx_load_from_disk] read 0 ALT contigs
[M::process] read 555814 sequences (80000161 bp)...
[M::process] read 555880 sequences (80000024 bp)...
[M::mem_process_seqs] Processed 555814 reads in 164.350 CPU sec, 20.489 real sec
[M::process] read 555890 sequences (80000205 bp)...
[M::mem_process_seqs] Processed 555880 reads in 164.714 CPU sec, 20.263 real sec
[M::process] read 555754 sequences (80000163 bp)...
[M::mem_process_seqs] Processed 555890 reads in 168.807 CPU sec, 20.735 real sec
[M::process] read 555756 sequences (80000089 bp)...
[M::mem_process_seqs] Processed 555754 reads in 166.776 CPU sec, 20.504 real sec
[M::process] read 326750 sequences (47029594 bp)...
[M::mem_process_seqs] Processed 555756 reads in 165.605 CPU sec, 20.440 real sec
[M::mem_process_seqs] Processed 326750 reads in 99.585 CPU sec, 12.220 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_407\tSM:MontereyBayCA_407\tPL:Illumina reference.fasta MontereyBayCA_407.R1.fq.gz
[main] Real time: 118.683 sec; CPU: 932.308 sec