[M::bwa_idx_load_from_disk] read 0 ALT contigs
[M::process] read 555560 sequences (80000257 bp)...
[M::process] read 555560 sequences (80000219 bp)...
[M::mem_process_seqs] Processed 555560 reads in 170.816 CPU sec, 21.290 real sec
[M::process] read 555560 sequences (80000189 bp)...
[M::mem_process_seqs] Processed 555560 reads in 175.749 CPU sec, 21.606 real sec
[M::process] read 555558 sequences (80000055 bp)...
[M::mem_process_seqs] Processed 555560 reads in 173.783 CPU sec, 21.348 real sec
[M::process] read 555558 sequences (80000034 bp)...
[M::mem_process_seqs] Processed 555558 reads in 172.995 CPU sec, 21.270 real sec
[M::process] read 377445 sequences (54351888 bp)...
[M::mem_process_seqs] Processed 555558 reads in 174.170 CPU sec, 21.454 real sec
[M::mem_process_seqs] Processed 377445 reads in 123.459 CPU sec, 15.188 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_FG207\tSM:DabobBayWA_FG207\tPL:Illumina reference.fasta DabobBayWA_FG207.R1.fq.gz
[main] Real time: 126.275 sec; CPU: 993.476 sec