[M::bwa_idx_load_from_disk] read 0 ALT contigs
[M::process] read 555560 sequences (80000163 bp)...
[M::process] read 555560 sequences (80000181 bp)...
[M::mem_process_seqs] Processed 555560 reads in 176.911 CPU sec, 22.060 real sec
[M::process] read 555560 sequences (80000105 bp)...
[M::mem_process_seqs] Processed 555560 reads in 179.649 CPU sec, 22.095 real sec
[M::process] read 555560 sequences (80000165 bp)...
[M::mem_process_seqs] Processed 555560 reads in 180.307 CPU sec, 22.189 real sec
[M::process] read 555560 sequences (80000248 bp)...
[M::mem_process_seqs] Processed 555560 reads in 179.910 CPU sec, 22.138 real sec
[M::process] read 555558 sequences (80000023 bp)...
[M::mem_process_seqs] Processed 555560 reads in 179.476 CPU sec, 22.084 real sec
[M::process] read 555558 sequences (80000026 bp)...
[M::mem_process_seqs] Processed 555558 reads in 179.676 CPU sec, 22.134 real sec
[M::process] read 555560 sequences (80000267 bp)...
[M::mem_process_seqs] Processed 555558 reads in 178.826 CPU sec, 21.958 real sec
[M::process] read 555560 sequences (80000241 bp)...
[M::mem_process_seqs] Processed 555560 reads in 179.404 CPU sec, 22.050 real sec
[M::process] read 143147 sequences (20613083 bp)...
[M::mem_process_seqs] Processed 555560 reads in 179.036 CPU sec, 22.128 real sec
[M::mem_process_seqs] Processed 143147 reads in 49.722 CPU sec, 5.964 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_FG210\tSM:DabobBayWA_FG210\tPL:Illumina reference.fasta DabobBayWA_FG210.R1.fq.gz
[main] Real time: 206.962 sec; CPU: 1664.423 sec