[M::bwa_idx_load_from_disk] read 0 ALT contigs
[M::process] read 556410 sequences (80000147 bp)...
[M::process] read 556418 sequences (80000056 bp)...
[M::mem_process_seqs] Processed 556410 reads in 158.294 CPU sec, 19.712 real sec
[M::process] read 556398 sequences (80000089 bp)...
[M::mem_process_seqs] Processed 556418 reads in 161.908 CPU sec, 19.924 real sec
[M::process] read 556422 sequences (80000120 bp)...
[M::mem_process_seqs] Processed 556398 reads in 163.518 CPU sec, 20.089 real sec
[M::process] read 556392 sequences (80000044 bp)...
[M::mem_process_seqs] Processed 556422 reads in 161.110 CPU sec, 19.780 real sec
[M::process] read 102073 sequences (14674927 bp)...
[M::mem_process_seqs] Processed 556392 reads in 160.945 CPU sec, 19.886 real sec
[M::mem_process_seqs] Processed 102073 reads in 33.038 CPU sec, 3.900 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_Q232\tSM:DabobBayWA_Q232\tPL:Illumina reference.fasta DabobBayWA_Q232.R1.fq.gz
[main] Real time: 105.325 sec; CPU: 840.367 sec