[M::bwa_idx_load_from_disk] read 0 ALT contigs
[M::process] read 556048 sequences (80000072 bp)...
[M::process] read 556158 sequences (80000218 bp)...
[M::mem_process_seqs] Processed 556048 reads in 175.066 CPU sec, 21.822 real sec
[M::process] read 556180 sequences (80000030 bp)...
[M::mem_process_seqs] Processed 556158 reads in 180.140 CPU sec, 22.163 real sec
[M::process] read 556076 sequences (80000266 bp)...
[M::mem_process_seqs] Processed 556180 reads in 180.828 CPU sec, 22.164 real sec
[M::process] read 556094 sequences (80000112 bp)...
[M::mem_process_seqs] Processed 556076 reads in 181.486 CPU sec, 22.286 real sec
[M::process] read 556062 sequences (80000152 bp)...
[M::mem_process_seqs] Processed 556094 reads in 182.789 CPU sec, 22.466 real sec
[M::process] read 333048 sequences (47906324 bp)...
[M::mem_process_seqs] Processed 556062 reads in 179.356 CPU sec, 22.081 real sec
[M::mem_process_seqs] Processed 333048 reads in 110.830 CPU sec, 13.631 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_400\tSM:MontereyBayCA_400\tPL:Illumina reference.fasta MontereyBayCA_400.R1.fq.gz
[main] Real time: 150.842 sec; CPU: 1193.316 sec