[M::bwa_idx_load_from_disk] read 0 ALT contigs
[M::process] read 556128 sequences (80000233 bp)...
[M::process] read 556194 sequences (80000123 bp)...
[M::mem_process_seqs] Processed 556128 reads in 176.531 CPU sec, 22.000 real sec
[M::process] read 556146 sequences (80000068 bp)...
[M::mem_process_seqs] Processed 556194 reads in 181.739 CPU sec, 22.369 real sec
[M::process] read 556138 sequences (80000051 bp)...
[M::mem_process_seqs] Processed 556146 reads in 184.101 CPU sec, 22.640 real sec
[M::process] read 293967 sequences (42278371 bp)...
[M::mem_process_seqs] Processed 556138 reads in 179.951 CPU sec, 22.181 real sec
[M::mem_process_seqs] Processed 293967 reads in 98.442 CPU sec, 12.087 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_403\tSM:MontereyBayCA_403\tPL:Illumina reference.fasta MontereyBayCA_403.R1.fq.gz
[main] Real time: 104.907 sec; CPU: 823.216 sec