[M::bwa_idx_load_from_disk] read 0 ALT contigs
[M::process] read 556296 sequences (80000060 bp)...
[M::process] read 556390 sequences (80000275 bp)...
[M::mem_process_seqs] Processed 556296 reads in 165.834 CPU sec, 20.690 real sec
[M::process] read 556390 sequences (80000042 bp)...
[M::mem_process_seqs] Processed 556390 reads in 172.519 CPU sec, 21.208 real sec
[M::process] read 556346 sequences (80000089 bp)...
[M::mem_process_seqs] Processed 556390 reads in 170.391 CPU sec, 20.938 real sec
[M::process] read 503005 sequences (72317870 bp)...
[M::mem_process_seqs] Processed 556346 reads in 172.815 CPU sec, 21.219 real sec
[M::mem_process_seqs] Processed 503005 reads in 152.768 CPU sec, 18.889 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_FG217\tSM:DabobBayWA_FG217\tPL:Illumina reference.fasta DabobBayWA_FG217.R1.fq.gz
[main] Real time: 108.147 sec; CPU: 837.201 sec