[M::bwa_idx_load_from_disk] read 0 ALT contigs
[M::process] read 556342 sequences (80000279 bp)...
[M::process] read 556352 sequences (80000203 bp)...
[M::mem_process_seqs] Processed 556342 reads in 147.444 CPU sec, 18.299 real sec
[M::process] read 556340 sequences (80000188 bp)...
[M::mem_process_seqs] Processed 556352 reads in 151.027 CPU sec, 18.541 real sec
[M::process] read 556344 sequences (80000080 bp)...
[M::mem_process_seqs] Processed 556340 reads in 149.376 CPU sec, 18.277 real sec
[M::process] read 556310 sequences (80000187 bp)...
[M::mem_process_seqs] Processed 556344 reads in 149.626 CPU sec, 18.364 real sec
[M::process] read 200940 sequences (28893321 bp)...
[M::mem_process_seqs] Processed 556310 reads in 147.778 CPU sec, 18.229 real sec
[M::mem_process_seqs] Processed 200940 reads in 55.301 CPU sec, 6.724 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_FG224\tSM:DabobBayWA_FG224\tPL:Illumina reference.fasta DabobBayWA_FG224.R1.fq.gz
[main] Real time: 101.222 sec; CPU: 802.587 sec