[M::bwa_idx_load_from_disk] read 0 ALT contigs
[M::process] read 555560 sequences (80000269 bp)...
[M::process] read 555560 sequences (80000174 bp)...
[M::mem_process_seqs] Processed 555560 reads in 175.936 CPU sec, 21.925 real sec
[M::process] read 555560 sequences (80000001 bp)...
[M::mem_process_seqs] Processed 555560 reads in 179.569 CPU sec, 22.090 real sec
[M::process] read 555560 sequences (80000262 bp)...
[M::mem_process_seqs] Processed 555560 reads in 181.915 CPU sec, 22.394 real sec
[M::process] read 555558 sequences (80000039 bp)...
[M::mem_process_seqs] Processed 555560 reads in 178.419 CPU sec, 21.962 real sec
[M::process] read 555560 sequences (80000244 bp)...
[M::mem_process_seqs] Processed 555558 reads in 181.592 CPU sec, 22.307 real sec
[M::process] read 298608 sequences (42999375 bp)...
[M::mem_process_seqs] Processed 555560 reads in 180.116 CPU sec, 22.217 real sec
[M::mem_process_seqs] Processed 298608 reads in 99.129 CPU sec, 12.168 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_FG206\tSM:DabobBayWA_FG206\tPL:Illumina reference.fasta DabobBayWA_FG206.R1.fq.gz
[main] Real time: 148.878 sec; CPU: 1179.127 sec