[M::bwa_idx_load_from_disk] read 0 ALT contigs
[M::process] read 556638 sequences (80000172 bp)...
[M::process] read 556628 sequences (80000140 bp)...
[M::mem_process_seqs] Processed 556638 reads in 150.923 CPU sec, 18.775 real sec
[M::process] read 556610 sequences (80000249 bp)...
[M::mem_process_seqs] Processed 556628 reads in 154.672 CPU sec, 19.007 real sec
[M::process] read 335436 sequences (48203794 bp)...
[M::mem_process_seqs] Processed 556610 reads in 152.577 CPU sec, 18.795 real sec
[M::mem_process_seqs] Processed 335436 reads in 92.666 CPU sec, 11.378 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_Q236\tSM:DabobBayWA_Q236\tPL:Illumina reference.fasta DabobBayWA_Q236.R1.fq.gz
[main] Real time: 71.115 sec; CPU: 553.035 sec