[M::bwa_idx_load_from_disk] read 0 ALT contigs
[M::process] read 556256 sequences (80000269 bp)...
[M::process] read 556344 sequences (80000087 bp)...
[M::mem_process_seqs] Processed 556256 reads in 171.244 CPU sec, 21.357 real sec
[M::process] read 556306 sequences (80000214 bp)...
[M::mem_process_seqs] Processed 556344 reads in 173.721 CPU sec, 21.368 real sec
[M::process] read 556230 sequences (80000177 bp)...
[M::mem_process_seqs] Processed 556306 reads in 176.987 CPU sec, 21.750 real sec
[M::process] read 459857 sequences (66125527 bp)...
[M::mem_process_seqs] Processed 556230 reads in 174.485 CPU sec, 21.412 real sec
[M::mem_process_seqs] Processed 459857 reads in 146.039 CPU sec, 18.046 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_435\tSM:MontereyBayCA_435\tPL:Illumina reference.fasta MontereyBayCA_435.R1.fq.gz
[main] Real time: 108.303 sec; CPU: 845.360 sec