[M::bwa_idx_load_from_disk] read 0 ALT contigs
[M::process] read 556154 sequences (80000206 bp)...
[M::process] read 556206 sequences (80000008 bp)...
[M::mem_process_seqs] Processed 556154 reads in 165.512 CPU sec, 20.627 real sec
[M::process] read 556106 sequences (80000117 bp)...
[M::mem_process_seqs] Processed 556206 reads in 169.101 CPU sec, 20.800 real sec
[M::process] read 556120 sequences (80000035 bp)...
[M::mem_process_seqs] Processed 556106 reads in 170.289 CPU sec, 20.877 real sec
[M::process] read 125070 sequences (17988666 bp)...
[M::mem_process_seqs] Processed 556120 reads in 169.831 CPU sec, 20.973 real sec
[M::mem_process_seqs] Processed 125070 reads in 42.715 CPU sec, 5.107 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_FG208\tSM:DabobBayWA_FG208\tPL:Illumina reference.fasta DabobBayWA_FG208.R1.fq.gz
[main] Real time: 91.008 sec; CPU: 719.497 sec