[M::bwa_idx_load_from_disk] read 0 ALT contigs
[M::process] read 555916 sequences (80000004 bp)...
[M::process] read 555924 sequences (80000053 bp)...
[M::mem_process_seqs] Processed 555916 reads in 167.417 CPU sec, 20.847 real sec
[M::process] read 555806 sequences (80000206 bp)...
[M::mem_process_seqs] Processed 555924 reads in 171.095 CPU sec, 21.027 real sec
[M::process] read 287249 sequences (41340606 bp)...
[M::mem_process_seqs] Processed 555806 reads in 174.587 CPU sec, 21.532 real sec
[M::mem_process_seqs] Processed 287249 reads in 93.710 CPU sec, 11.462 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_416\tSM:MontereyBayCA_416\tPL:Illumina reference.fasta MontereyBayCA_416.R1.fq.gz
[main] Real time: 78.431 sec; CPU: 609.024 sec