[M::bwa_idx_load_from_disk] read 0 ALT contigs
[M::process] read 557380 sequences (80000124 bp)...
[M::process] read 557388 sequences (80000245 bp)...
[M::mem_process_seqs] Processed 557380 reads in 145.010 CPU sec, 18.058 real sec
[M::process] read 557386 sequences (80000132 bp)...
[M::mem_process_seqs] Processed 557388 reads in 147.236 CPU sec, 18.106 real sec
[M::process] read 557356 sequences (80000253 bp)...
[M::mem_process_seqs] Processed 557386 reads in 150.929 CPU sec, 18.539 real sec
[M::process] read 557406 sequences (80000276 bp)...
[M::mem_process_seqs] Processed 557356 reads in 147.444 CPU sec, 18.110 real sec
[M::process] read 10812 sequences (1551003 bp)...
[M::mem_process_seqs] Processed 557406 reads in 146.517 CPU sec, 18.086 real sec
[M::mem_process_seqs] Processed 10812 reads in 4.065 CPU sec, 0.480 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_Q235\tSM:DabobBayWA_Q235\tPL:Illumina reference.fasta DabobBayWA_Q235.R1.fq.gz
[main] Real time: 95.713 sec; CPU: 743.984 sec