[M::bwa_idx_load_from_disk] read 0 ALT contigs
[M::process] read 555934 sequences (80000230 bp)...
[M::process] read 555956 sequences (80000270 bp)...
[M::mem_process_seqs] Processed 555934 reads in 184.745 CPU sec, 23.025 real sec
[M::process] read 555920 sequences (80000236 bp)...
[M::mem_process_seqs] Processed 555956 reads in 191.814 CPU sec, 23.560 real sec
[M::process] read 137754 sequences (19820809 bp)...
[M::mem_process_seqs] Processed 555920 reads in 188.440 CPU sec, 23.272 real sec
[M::mem_process_seqs] Processed 137754 reads in 49.949 CPU sec, 6.001 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_413\tSM:MontereyBayCA_413\tPL:Illumina reference.fasta MontereyBayCA_413.R1.fq.gz
[main] Real time: 78.226 sec; CPU: 616.591 sec