[M::bwa_idx_load_from_disk] read 0 ALT contigs
[M::process] read 555890 sequences (80000087 bp)...
[M::process] read 555894 sequences (80000039 bp)...
[M::mem_process_seqs] Processed 555890 reads in 187.942 CPU sec, 23.438 real sec
[M::process] read 555840 sequences (80000129 bp)...
[M::mem_process_seqs] Processed 555894 reads in 193.058 CPU sec, 23.777 real sec
[M::process] read 99691 sequences (14346071 bp)...
[M::mem_process_seqs] Processed 555840 reads in 191.076 CPU sec, 23.611 real sec
[M::mem_process_seqs] Processed 99691 reads in 39.510 CPU sec, 4.680 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_438\tSM:MontereyBayCA_438\tPL:Illumina reference.fasta MontereyBayCA_438.R1.fq.gz
[main] Real time: 77.686 sec; CPU: 613.132 sec