[M::bwa_idx_load_from_disk] read 0 ALT contigs
[M::process] read 555970 sequences (80000108 bp)...
[M::process] read 556060 sequences (80000106 bp)...
[M::mem_process_seqs] Processed 555970 reads in 167.403 CPU sec, 20.873 real sec
[M::process] read 556114 sequences (80000241 bp)...
[M::mem_process_seqs] Processed 556060 reads in 168.926 CPU sec, 20.740 real sec
[M::process] read 555934 sequences (80000155 bp)...
[M::mem_process_seqs] Processed 556114 reads in 170.153 CPU sec, 20.925 real sec
[M::process] read 555936 sequences (80000018 bp)...
[M::mem_process_seqs] Processed 555934 reads in 169.628 CPU sec, 20.868 real sec
[M::process] read 445641 sequences (64116133 bp)...
[M::mem_process_seqs] Processed 555936 reads in 170.725 CPU sec, 21.013 real sec
[M::mem_process_seqs] Processed 445641 reads in 140.220 CPU sec, 17.325 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_408\tSM:MontereyBayCA_408\tPL:Illumina reference.fasta MontereyBayCA_408.R1.fq.gz
[main] Real time: 126.590 sec; CPU: 990.019 sec