[M::bwa_idx_load_from_disk] read 0 ALT contigs
[M::process] read 556080 sequences (80000104 bp)...
[M::process] read 556130 sequences (80000013 bp)...
[M::mem_process_seqs] Processed 556080 reads in 167.869 CPU sec, 20.925 real sec
[M::process] read 555968 sequences (80000011 bp)...
[M::mem_process_seqs] Processed 556130 reads in 170.970 CPU sec, 21.037 real sec
[M::process] read 488660 sequences (70308006 bp)...
[M::mem_process_seqs] Processed 555968 reads in 172.408 CPU sec, 21.214 real sec
[M::mem_process_seqs] Processed 488660 reads in 150.061 CPU sec, 18.501 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_FG215\tSM:DabobBayWA_FG215\tPL:Illumina reference.fasta DabobBayWA_FG215.R1.fq.gz
[main] Real time: 86.319 sec; CPU: 664.285 sec