[M::bwa_idx_load_from_disk] read 0 ALT contigs
[M::process] read 556082 sequences (80000046 bp)...
[M::process] read 556152 sequences (80000136 bp)...
[M::mem_process_seqs] Processed 556082 reads in 175.834 CPU sec, 21.947 real sec
[M::process] read 556122 sequences (80000114 bp)...
[M::mem_process_seqs] Processed 556152 reads in 178.195 CPU sec, 21.925 real sec
[M::process] read 556098 sequences (80000050 bp)...
[M::mem_process_seqs] Processed 556122 reads in 178.562 CPU sec, 21.966 real sec
[M::process] read 556136 sequences (80000215 bp)...
[M::mem_process_seqs] Processed 556098 reads in 178.263 CPU sec, 21.922 real sec
[M::process] read 40398 sequences (5810901 bp)...
[M::mem_process_seqs] Processed 556136 reads in 176.929 CPU sec, 21.913 real sec
[M::mem_process_seqs] Processed 40398 reads in 15.896 CPU sec, 1.874 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_441\tSM:MontereyBayCA_441\tPL:Illumina reference.fasta MontereyBayCA_441.R1.fq.gz
[main] Real time: 115.012 sec; CPU: 906.064 sec