[M::bwa_idx_load_from_disk] read 0 ALT contigs
[M::process] read 556302 sequences (80000125 bp)...
[M::process] read 556072 sequences (80000238 bp)...
[M::mem_process_seqs] Processed 556302 reads in 163.843 CPU sec, 20.423 real sec
[M::process] read 555924 sequences (80000052 bp)...
[M::mem_process_seqs] Processed 556072 reads in 169.360 CPU sec, 20.801 real sec
[M::process] read 555934 sequences (80000225 bp)...
[M::mem_process_seqs] Processed 555924 reads in 172.631 CPU sec, 21.251 real sec
[M::process] read 556022 sequences (80000039 bp)...
[M::mem_process_seqs] Processed 555934 reads in 173.599 CPU sec, 21.288 real sec
[M::process] read 555918 sequences (80000207 bp)...
[M::mem_process_seqs] Processed 556022 reads in 171.068 CPU sec, 21.031 real sec
[M::process] read 555862 sequences (80000223 bp)...
[M::mem_process_seqs] Processed 555918 reads in 174.252 CPU sec, 21.416 real sec
[M::process] read 532979 sequences (76707160 bp)...
[M::mem_process_seqs] Processed 555862 reads in 171.209 CPU sec, 21.057 real sec
[M::mem_process_seqs] Processed 532979 reads in 167.644 CPU sec, 20.748 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_447\tSM:MontereyBayCA_447\tPL:Illumina reference.fasta MontereyBayCA_447.R1.fq.gz
[main] Real time: 173.561 sec; CPU: 1367.210 sec