[M::bwa_idx_load_from_disk] read 0 ALT contigs
[M::process] read 555560 sequences (80000154 bp)...
[M::process] read 555562 sequences (80000245 bp)...
[M::mem_process_seqs] Processed 555560 reads in 173.394 CPU sec, 21.648 real sec
[M::process] read 555562 sequences (80000051 bp)...
[M::mem_process_seqs] Processed 555562 reads in 176.971 CPU sec, 21.821 real sec
[M::process] read 555562 sequences (80000279 bp)...
[M::mem_process_seqs] Processed 555562 reads in 176.867 CPU sec, 21.736 real sec
[M::process] read 555560 sequences (80000155 bp)...
[M::mem_process_seqs] Processed 555562 reads in 176.543 CPU sec, 21.718 real sec
[M::process] read 555560 sequences (80000007 bp)...
[M::mem_process_seqs] Processed 555560 reads in 176.063 CPU sec, 21.632 real sec
[M::process] read 555560 sequences (80000178 bp)...
[M::mem_process_seqs] Processed 555560 reads in 175.246 CPU sec, 21.564 real sec
[M::process] read 275922 sequences (39732560 bp)...
[M::mem_process_seqs] Processed 555560 reads in 174.002 CPU sec, 21.482 real sec
[M::mem_process_seqs] Processed 275922 reads in 89.425 CPU sec, 10.971 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_FG212\tSM:DabobBayWA_FG212\tPL:Illumina reference.fasta DabobBayWA_FG212.R1.fq.gz
[main] Real time: 165.950 sec; CPU: 1320.795 sec