[M::bwa_idx_load_from_disk] read 0 ALT contigs
[M::process] read 555816 sequences (80000266 bp)...
[M::process] read 555718 sequences (80000046 bp)...
[M::mem_process_seqs] Processed 555816 reads in 165.389 CPU sec, 20.603 real sec
[M::process] read 555704 sequences (80000177 bp)...
[M::mem_process_seqs] Processed 555718 reads in 173.607 CPU sec, 21.362 real sec
[M::process] read 555666 sequences (80000269 bp)...
[M::mem_process_seqs] Processed 555704 reads in 173.270 CPU sec, 21.268 real sec
[M::process] read 275472 sequences (39661015 bp)...
[M::mem_process_seqs] Processed 555666 reads in 171.301 CPU sec, 21.099 real sec
[M::mem_process_seqs] Processed 275472 reads in 89.006 CPU sec, 10.909 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_433\tSM:MontereyBayCA_433\tPL:Illumina reference.fasta MontereyBayCA_433.R1.fq.gz
[main] Real time: 98.967 sec; CPU: 775.004 sec