[M::bwa_idx_load_from_disk] read 0 ALT contigs
[M::process] read 555832 sequences (80000102 bp)...
[M::process] read 555746 sequences (80000264 bp)...
[M::mem_process_seqs] Processed 555832 reads in 159.683 CPU sec, 19.901 real sec
[M::process] read 555724 sequences (80000069 bp)...
[M::mem_process_seqs] Processed 555746 reads in 167.827 CPU sec, 20.639 real sec
[M::process] read 555696 sequences (80000032 bp)...
[M::mem_process_seqs] Processed 555724 reads in 165.579 CPU sec, 20.302 real sec
[M::process] read 366144 sequences (52712251 bp)...
[M::mem_process_seqs] Processed 555696 reads in 169.038 CPU sec, 20.857 real sec
[M::mem_process_seqs] Processed 366144 reads in 110.925 CPU sec, 13.659 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_241\tSM:DabobBayWA_241\tPL:Illumina reference.fasta DabobBayWA_241.R1.fq.gz
[main] Real time: 99.327 sec; CPU: 775.529 sec