[M::bwa_idx_load_from_disk] read 0 ALT contigs
[M::process] read 555802 sequences (80000081 bp)...
[M::process] read 555732 sequences (80000096 bp)...
[M::mem_process_seqs] Processed 555802 reads in 156.124 CPU sec, 19.453 real sec
[M::process] read 555700 sequences (80000116 bp)...
[M::mem_process_seqs] Processed 555732 reads in 162.096 CPU sec, 19.883 real sec
[M::process] read 555688 sequences (80000236 bp)...
[M::mem_process_seqs] Processed 555700 reads in 161.753 CPU sec, 19.869 real sec
[M::process] read 555672 sequences (80000092 bp)...
[M::mem_process_seqs] Processed 555688 reads in 161.582 CPU sec, 19.798 real sec
[M::process] read 555654 sequences (80000188 bp)...
[M::mem_process_seqs] Processed 555672 reads in 161.607 CPU sec, 19.853 real sec
[M::process] read 286976 sequences (41317835 bp)...
[M::mem_process_seqs] Processed 555654 reads in 160.840 CPU sec, 19.780 real sec
[M::mem_process_seqs] Processed 286976 reads in 86.421 CPU sec, 10.583 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_420\tSM:MontereyBayCA_420\tPL:Illumina reference.fasta MontereyBayCA_420.R1.fq.gz
[main] Real time: 132.518 sec; CPU: 1052.737 sec