[M::bwa_idx_load_from_disk] read 0 ALT contigs
[M::process] read 556296 sequences (80000284 bp)...
[M::process] read 556380 sequences (80000023 bp)...
[M::mem_process_seqs] Processed 556296 reads in 168.008 CPU sec, 20.924 real sec
[M::process] read 556316 sequences (80000229 bp)...
[M::mem_process_seqs] Processed 556380 reads in 172.682 CPU sec, 21.202 real sec
[M::process] read 556266 sequences (80000067 bp)...
[M::mem_process_seqs] Processed 556316 reads in 175.118 CPU sec, 21.526 real sec
[M::process] read 463200 sequences (66600897 bp)...
[M::mem_process_seqs] Processed 556266 reads in 172.358 CPU sec, 21.198 real sec
[M::mem_process_seqs] Processed 463200 reads in 143.176 CPU sec, 17.685 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_406\tSM:MontereyBayCA_406\tPL:Illumina reference.fasta MontereyBayCA_406.R1.fq.gz
[main] Real time: 107.448 sec; CPU: 834.420 sec