[M::bwa_idx_load_from_disk] read 0 ALT contigs
[M::process] read 555906 sequences (80000081 bp)...
[M::process] read 555962 sequences (80000077 bp)...
[M::mem_process_seqs] Processed 555906 reads in 186.325 CPU sec, 23.241 real sec
[M::process] read 555868 sequences (80000281 bp)...
[M::mem_process_seqs] Processed 555962 reads in 192.790 CPU sec, 23.694 real sec
[M::process] read 555896 sequences (80000139 bp)...
[M::mem_process_seqs] Processed 555868 reads in 194.055 CPU sec, 23.852 real sec
[M::process] read 59970 sequences (8629800 bp)...
[M::mem_process_seqs] Processed 555896 reads in 193.195 CPU sec, 23.902 real sec
[M::mem_process_seqs] Processed 59970 reads in 24.048 CPU sec, 2.845 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_429\tSM:MontereyBayCA_429\tPL:Illumina reference.fasta MontereyBayCA_429.R1.fq.gz
[main] Real time: 100.862 sec; CPU: 792.698 sec