[M::bwa_idx_load_from_disk] read 0 ALT contigs
[M::process] read 555558 sequences (80000055 bp)...
[M::process] read 555560 sequences (80000269 bp)...
[M::mem_process_seqs] Processed 555558 reads in 174.567 CPU sec, 21.777 real sec
[M::process] read 555560 sequences (80000203 bp)...
[M::mem_process_seqs] Processed 555560 reads in 179.520 CPU sec, 22.055 real sec
[M::process] read 555558 sequences (80000060 bp)...
[M::mem_process_seqs] Processed 555560 reads in 180.069 CPU sec, 22.137 real sec
[M::process] read 555558 sequences (80000079 bp)...
[M::mem_process_seqs] Processed 555558 reads in 179.797 CPU sec, 22.084 real sec
[M::process] read 555558 sequences (80000051 bp)...
[M::mem_process_seqs] Processed 555558 reads in 181.194 CPU sec, 22.294 real sec
[M::process] read 162762 sequences (23437633 bp)...
[M::mem_process_seqs] Processed 555558 reads in 176.923 CPU sec, 21.864 real sec
[M::mem_process_seqs] Processed 162762 reads in 56.876 CPU sec, 6.876 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_FG203\tSM:DabobBayWA_FG203\tPL:Illumina reference.fasta DabobBayWA_FG203.R1.fq.gz
[main] Real time: 141.924 sec; CPU: 1131.114 sec