[M::bwa_idx_load_from_disk] read 0 ALT contigs
[M::process] read 557302 sequences (80000090 bp)...
[M::process] read 557292 sequences (80000282 bp)...
[M::mem_process_seqs] Processed 557302 reads in 148.583 CPU sec, 18.497 real sec
[M::process] read 557312 sequences (80000118 bp)...
[M::mem_process_seqs] Processed 557292 reads in 148.963 CPU sec, 18.311 real sec
[M::process] read 557244 sequences (80000083 bp)...
[M::mem_process_seqs] Processed 557312 reads in 150.501 CPU sec, 18.451 real sec
[M::process] read 518383 sequences (74410913 bp)...
[M::mem_process_seqs] Processed 557244 reads in 150.483 CPU sec, 18.418 real sec
[M::mem_process_seqs] Processed 518383 reads in 137.020 CPU sec, 16.938 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_FG226\tSM:DabobBayWA_FG226\tPL:Illumina reference.fasta DabobBayWA_FG226.R1.fq.gz
[main] Real time: 95.057 sec; CPU: 738.550 sec