[M::bwa_idx_load_from_disk] read 0 ALT contigs
[M::process] read 555846 sequences (80000253 bp)...
[M::process] read 555906 sequences (80000277 bp)...
[M::mem_process_seqs] Processed 555846 reads in 167.566 CPU sec, 20.897 real sec
[M::process] read 555806 sequences (80000087 bp)...
[M::mem_process_seqs] Processed 555906 reads in 171.924 CPU sec, 21.123 real sec
[M::process] read 555772 sequences (80000217 bp)...
[M::mem_process_seqs] Processed 555806 reads in 174.734 CPU sec, 21.492 real sec
[M::process] read 290855 sequences (41862230 bp)...
[M::mem_process_seqs] Processed 555772 reads in 172.643 CPU sec, 21.314 real sec
[M::mem_process_seqs] Processed 290855 reads in 90.670 CPU sec, 11.154 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_FG213\tSM:DabobBayWA_FG213\tPL:Illumina reference.fasta DabobBayWA_FG213.R1.fq.gz
[main] Real time: 99.181 sec; CPU: 779.750 sec