[M::bwa_idx_load_from_disk] read 0 ALT contigs
[M::process] read 556074 sequences (80000024 bp)...
[M::process] read 555942 sequences (80000248 bp)...
[M::mem_process_seqs] Processed 556074 reads in 165.143 CPU sec, 20.579 real sec
[M::process] read 429307 sequences (61788870 bp)...
[M::mem_process_seqs] Processed 555942 reads in 167.621 CPU sec, 20.640 real sec
[M::mem_process_seqs] Processed 429307 reads in 134.329 CPU sec, 16.580 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_427\tSM:MontereyBayCA_427\tPL:Illumina reference.fasta MontereyBayCA_427.R1.fq.gz
[main] Real time: 62.288 sec; CPU: 470.025 sec