[M::bwa_idx_load_from_disk] read 0 ALT contigs
[M::process] read 555560 sequences (80000267 bp)...
[M::process] read 555558 sequences (80000026 bp)...
[M::mem_process_seqs] Processed 555560 reads in 169.828 CPU sec, 21.174 real sec
[M::process] read 555560 sequences (80000252 bp)...
[M::mem_process_seqs] Processed 555558 reads in 171.820 CPU sec, 21.171 real sec
[M::process] read 555560 sequences (80000218 bp)...
[M::mem_process_seqs] Processed 555560 reads in 174.859 CPU sec, 21.482 real sec
[M::process] read 555558 sequences (80000056 bp)...
[M::mem_process_seqs] Processed 555560 reads in 174.034 CPU sec, 21.446 real sec
[M::process] read 555558 sequences (80000060 bp)...
[M::mem_process_seqs] Processed 555558 reads in 175.119 CPU sec, 21.536 real sec
[M::process] read 424928 sequences (61189328 bp)...
[M::mem_process_seqs] Processed 555558 reads in 175.158 CPU sec, 21.597 real sec
[M::mem_process_seqs] Processed 424928 reads in 132.847 CPU sec, 16.429 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_FG209\tSM:DabobBayWA_FG209\tPL:Illumina reference.fasta DabobBayWA_FG209.R1.fq.gz
[main] Real time: 149.347 sec; CPU: 1176.476 sec