[M::bwa_idx_load_from_disk] read 0 ALT contigs
[M::process] read 557274 sequences (80000147 bp)...
[M::process] read 557260 sequences (80000108 bp)...
[M::mem_process_seqs] Processed 557274 reads in 156.750 CPU sec, 19.512 real sec
[M::process] read 557200 sequences (80000239 bp)...
[M::mem_process_seqs] Processed 557260 reads in 161.796 CPU sec, 19.880 real sec
[M::process] read 445794 sequences (63996684 bp)...
[M::mem_process_seqs] Processed 557200 reads in 163.353 CPU sec, 20.106 real sec
[M::mem_process_seqs] Processed 445794 reads in 129.310 CPU sec, 15.933 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_Q245\tSM:DabobBayWA_Q245\tPL:Illumina reference.fasta DabobBayWA_Q245.R1.fq.gz
[main] Real time: 80.085 sec; CPU: 614.416 sec