[M::bwa_idx_load_from_disk] read 0 ALT contigs
[M::process] read 556630 sequences (80000121 bp)...
[M::process] read 556288 sequences (80000011 bp)...
[M::mem_process_seqs] Processed 556630 reads in 157.281 CPU sec, 19.568 real sec
[M::process] read 556076 sequences (80000160 bp)...
[M::mem_process_seqs] Processed 556288 reads in 167.944 CPU sec, 20.664 real sec
[M::process] read 556108 sequences (80000113 bp)...
[M::mem_process_seqs] Processed 556076 reads in 166.408 CPU sec, 20.434 real sec
[M::process] read 556064 sequences (80000105 bp)...
[M::mem_process_seqs] Processed 556108 reads in 166.120 CPU sec, 20.389 real sec
[M::process] read 555950 sequences (80000058 bp)...
[M::mem_process_seqs] Processed 556064 reads in 166.454 CPU sec, 20.446 real sec
[M::process] read 555952 sequences (80000015 bp)...
[M::mem_process_seqs] Processed 555950 reads in 166.124 CPU sec, 20.384 real sec
[M::process] read 123523 sequences (17777416 bp)...
[M::mem_process_seqs] Processed 555952 reads in 167.271 CPU sec, 20.674 real sec
[M::mem_process_seqs] Processed 123523 reads in 41.985 CPU sec, 5.038 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:DabobBayWA_FG200\tSM:DabobBayWA_FG200\tPL:Illumina reference.fasta DabobBayWA_FG200.R1.fq.gz
[main] Real time: 149.836 sec; CPU: 1201.190 sec