[M::bwa_idx_load_from_disk] read 0 ALT contigs
[M::process] read 556418 sequences (80000244 bp)...
[M::process] read 556416 sequences (80000275 bp)...
[M::mem_process_seqs] Processed 556418 reads in 144.943 CPU sec, 18.053 real sec
[M::process] read 556382 sequences (80000075 bp)...
[M::mem_process_seqs] Processed 556416 reads in 150.927 CPU sec, 18.532 real sec
[M::process] read 449058 sequences (64564016 bp)...
[M::mem_process_seqs] Processed 556382 reads in 150.337 CPU sec, 18.481 real sec
[M::mem_process_seqs] Processed 449058 reads in 121.524 CPU sec, 15.006 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_Q248\tSM:DabobBayWA_Q248\tPL:Illumina reference.fasta DabobBayWA_Q248.R1.fq.gz
[main] Real time: 74.293 sec; CPU: 570.402 sec