[M::bwa_idx_load_from_disk] read 0 ALT contigs
[M::process] read 556116 sequences (80000185 bp)...
[M::process] read 556196 sequences (80000239 bp)...
[M::mem_process_seqs] Processed 556116 reads in 165.953 CPU sec, 20.666 real sec
[M::process] read 556136 sequences (80000133 bp)...
[M::mem_process_seqs] Processed 556196 reads in 167.944 CPU sec, 20.675 real sec
[M::process] read 556088 sequences (80000257 bp)...
[M::mem_process_seqs] Processed 556136 reads in 169.515 CPU sec, 20.829 real sec
[M::process] read 367355 sequences (52837217 bp)...
[M::mem_process_seqs] Processed 556088 reads in 169.609 CPU sec, 20.889 real sec
[M::mem_process_seqs] Processed 367355 reads in 112.944 CPU sec, 13.931 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_FG214\tSM:DabobBayWA_FG214\tPL:Illumina reference.fasta DabobBayWA_FG214.R1.fq.gz
[main] Real time: 101.200 sec; CPU: 788.740 sec