[M::bwa_idx_load_from_disk] read 0 ALT contigs
[M::process] read 556150 sequences (80000052 bp)...
[M::process] read 555912 sequences (80000258 bp)...
[M::mem_process_seqs] Processed 556150 reads in 163.987 CPU sec, 20.405 real sec
[M::process] read 555946 sequences (80000203 bp)...
[M::mem_process_seqs] Processed 555912 reads in 168.442 CPU sec, 20.708 real sec
[M::process] read 555844 sequences (80000041 bp)...
[M::mem_process_seqs] Processed 555946 reads in 168.519 CPU sec, 20.698 real sec
[M::process] read 1538 sequences (221363 bp)...
[M::mem_process_seqs] Processed 555844 reads in 166.504 CPU sec, 20.599 real sec
[M::mem_process_seqs] Processed 1538 reads in 0.791 CPU sec, 0.092 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_449-SEQREP\tSM:MontereyBayCA_449-SEQREP\tPL:Illumina reference.fasta MontereyBayCA_449-SEQREP.R1.fq.gz
[main] Real time: 87.896 sec; CPU: 671.547 sec