[M::bwa_idx_load_from_disk] read 0 ALT contigs
[M::process] read 556704 sequences (80000169 bp)...
[M::process] read 556722 sequences (80000270 bp)...
[M::mem_process_seqs] Processed 556704 reads in 152.784 CPU sec, 19.016 real sec
[M::process] read 556718 sequences (80000181 bp)...
[M::mem_process_seqs] Processed 556722 reads in 157.916 CPU sec, 19.420 real sec
[M::process] read 556732 sequences (80000183 bp)...
[M::mem_process_seqs] Processed 556718 reads in 157.382 CPU sec, 19.302 real sec
[M::process] read 556708 sequences (80000037 bp)...
[M::mem_process_seqs] Processed 556732 reads in 156.083 CPU sec, 19.177 real sec
[M::process] read 127021 sequences (18251054 bp)...
[M::mem_process_seqs] Processed 556708 reads in 157.443 CPU sec, 19.454 real sec
[M::mem_process_seqs] Processed 127021 reads in 39.450 CPU sec, 4.716 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_Q234\tSM:DabobBayWA_Q234\tPL:Illumina reference.fasta DabobBayWA_Q234.R1.fq.gz
[main] Real time: 103.647 sec; CPU: 823.100 sec