[M::bwa_idx_load_from_disk] read 0 ALT contigs
[M::process] read 556662 sequences (80000071 bp)...
[M::process] read 556650 sequences (80000025 bp)...
[M::mem_process_seqs] Processed 556662 reads in 143.634 CPU sec, 17.863 real sec
[M::process] read 556674 sequences (80000077 bp)...
[M::mem_process_seqs] Processed 556650 reads in 145.382 CPU sec, 17.831 real sec
[M::process] read 556630 sequences (80000028 bp)...
[M::mem_process_seqs] Processed 556674 reads in 146.909 CPU sec, 18.025 real sec
[M::process] read 549236 sequences (78927881 bp)...
[M::mem_process_seqs] Processed 556630 reads in 146.699 CPU sec, 17.935 real sec
[M::mem_process_seqs] Processed 549236 reads in 143.966 CPU sec, 17.821 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_FG227\tSM:DabobBayWA_FG227\tPL:Illumina reference.fasta DabobBayWA_FG227.R1.fq.gz
[main] Real time: 93.982 sec; CPU: 729.431 sec