[M::bwa_idx_load_from_disk] read 0 ALT contigs
[M::process] read 556044 sequences (80000100 bp)...
[M::process] read 556122 sequences (80000117 bp)...
[M::mem_process_seqs] Processed 556044 reads in 182.879 CPU sec, 22.810 real sec
[M::process] read 555984 sequences (80000208 bp)...
[M::mem_process_seqs] Processed 556122 reads in 186.468 CPU sec, 22.974 real sec
[M::process] read 556032 sequences (80000229 bp)...
[M::mem_process_seqs] Processed 555984 reads in 188.485 CPU sec, 23.175 real sec
[M::process] read 34409 sequences (4949937 bp)...
[M::mem_process_seqs] Processed 556032 reads in 185.988 CPU sec, 22.996 real sec
[M::mem_process_seqs] Processed 34409 reads in 13.571 CPU sec, 1.622 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_404\tSM:MontereyBayCA_404\tPL:Illumina reference.fasta MontereyBayCA_404.R1.fq.gz
[main] Real time: 98.020 sec; CPU: 760.289 sec