[M::bwa_idx_load_from_disk] read 0 ALT contigs
[M::process] read 556508 sequences (80000177 bp)...
[M::process] read 556496 sequences (80000153 bp)...
[M::mem_process_seqs] Processed 556508 reads in 150.025 CPU sec, 18.669 real sec
[M::process] read 556478 sequences (80000205 bp)...
[M::mem_process_seqs] Processed 556496 reads in 154.854 CPU sec, 19.028 real sec
[M::process] read 367577 sequences (52836656 bp)...
[M::mem_process_seqs] Processed 556478 reads in 154.818 CPU sec, 19.028 real sec
[M::mem_process_seqs] Processed 367577 reads in 103.249 CPU sec, 12.697 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_FG249\tSM:DabobBayWA_FG249\tPL:Illumina reference.fasta DabobBayWA_FG249.R1.fq.gz
[main] Real time: 72.879 sec; CPU: 565.448 sec