[M::bwa_idx_load_from_disk] read 0 ALT contigs
[M::process] read 555736 sequences (80000198 bp)...
[M::process] read 555684 sequences (80000016 bp)...
[M::mem_process_seqs] Processed 555736 reads in 171.711 CPU sec, 21.389 real sec
[M::process] read 555656 sequences (80000077 bp)...
[M::mem_process_seqs] Processed 555684 reads in 177.197 CPU sec, 21.828 real sec
[M::process] read 97553 sequences (14045566 bp)...
[M::mem_process_seqs] Processed 555656 reads in 177.279 CPU sec, 21.926 real sec
[M::mem_process_seqs] Processed 97553 reads in 36.335 CPU sec, 4.310 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_428\tSM:MontereyBayCA_428\tPL:Illumina reference.fasta MontereyBayCA_428.R1.fq.gz
[main] Real time: 72.072 sec; CPU: 564.356 sec