[M::bwa_idx_load_from_disk] read 0 ALT contigs
[M::process] read 557524 sequences (80000241 bp)...
[M::process] read 557500 sequences (80000252 bp)...
[M::mem_process_seqs] Processed 557524 reads in 148.465 CPU sec, 18.475 real sec
[M::process] read 557500 sequences (80000050 bp)...
[M::mem_process_seqs] Processed 557500 reads in 151.130 CPU sec, 18.571 real sec
[M::process] read 243249 sequences (34899468 bp)...
[M::mem_process_seqs] Processed 557500 reads in 149.828 CPU sec, 18.494 real sec
[M::mem_process_seqs] Processed 243249 reads in 70.163 CPU sec, 8.533 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_Q364\tSM:DabobBayWA_Q364\tPL:Illumina reference.fasta DabobBayWA_Q364.R1.fq.gz
[main] Real time: 67.314 sec; CPU: 521.869 sec