[M::bwa_idx_load_from_disk] read 0 ALT contigs
[M::process] read 556064 sequences (80000268 bp)...
[M::process] read 555908 sequences (80000007 bp)...
[M::mem_process_seqs] Processed 556064 reads in 162.645 CPU sec, 20.244 real sec
[M::process] read 555842 sequences (80000159 bp)...
[M::mem_process_seqs] Processed 555908 reads in 169.142 CPU sec, 20.806 real sec
[M::process] read 62508 sequences (8997573 bp)...
[M::mem_process_seqs] Processed 555842 reads in 167.629 CPU sec, 20.714 real sec
[M::mem_process_seqs] Processed 62508 reads in 22.034 CPU sec, 2.619 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_426\tSM:MontereyBayCA_426\tPL:Illumina reference.fasta MontereyBayCA_426.R1.fq.gz
[main] Real time: 67.412 sec; CPU: 523.753 sec