[M::bwa_idx_load_from_disk] read 0 ALT contigs
[M::process] read 555836 sequences (80000188 bp)...
[M::process] read 555900 sequences (80000021 bp)...
[M::mem_process_seqs] Processed 555836 reads in 174.431 CPU sec, 21.743 real sec
[M::process] read 555888 sequences (80000057 bp)...
[M::mem_process_seqs] Processed 555900 reads in 178.998 CPU sec, 21.989 real sec
[M::process] read 555770 sequences (80000080 bp)...
[M::mem_process_seqs] Processed 555888 reads in 181.763 CPU sec, 22.324 real sec
[M::process] read 555772 sequences (80000261 bp)...
[M::mem_process_seqs] Processed 555770 reads in 183.337 CPU sec, 22.556 real sec
[M::process] read 190992 sequences (27488521 bp)...
[M::mem_process_seqs] Processed 555772 reads in 178.929 CPU sec, 22.079 real sec
[M::mem_process_seqs] Processed 190992 reads in 66.663 CPU sec, 8.087 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_401\tSM:MontereyBayCA_401\tPL:Illumina reference.fasta MontereyBayCA_401.R1.fq.gz
[main] Real time: 122.134 sec; CPU: 966.393 sec