[M::bwa_idx_load_from_disk] read 0 ALT contigs
[M::process] read 555560 sequences (80000017 bp)...
[M::process] read 555562 sequences (80000250 bp)...
[M::mem_process_seqs] Processed 555560 reads in 169.113 CPU sec, 21.077 real sec
[M::process] read 555562 sequences (80000050 bp)...
[M::mem_process_seqs] Processed 555562 reads in 172.589 CPU sec, 21.233 real sec
[M::process] read 555560 sequences (80000105 bp)...
[M::mem_process_seqs] Processed 555562 reads in 174.612 CPU sec, 21.441 real sec
[M::process] read 555560 sequences (80000173 bp)...
[M::mem_process_seqs] Processed 555560 reads in 173.015 CPU sec, 21.244 real sec
[M::process] read 555560 sequences (80000201 bp)...
[M::mem_process_seqs] Processed 555560 reads in 173.183 CPU sec, 21.276 real sec
[M::process] read 279191 sequences (40203252 bp)...
[M::mem_process_seqs] Processed 555560 reads in 171.916 CPU sec, 21.181 real sec
[M::mem_process_seqs] Processed 279191 reads in 89.716 CPU sec, 11.016 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_FG204\tSM:DabobBayWA_FG204\tPL:Illumina reference.fasta DabobBayWA_FG204.R1.fq.gz
[main] Real time: 141.410 sec; CPU: 1126.229 sec