[M::bwa_idx_load_from_disk] read 0 ALT contigs
[M::process] read 555884 sequences (80000180 bp)...
[M::process] read 555940 sequences (80000147 bp)...
[M::mem_process_seqs] Processed 555884 reads in 167.097 CPU sec, 20.824 real sec
[M::process] read 555772 sequences (80000040 bp)...
[M::mem_process_seqs] Processed 555940 reads in 169.037 CPU sec, 20.777 real sec
[M::process] read 537054 sequences (77300567 bp)...
[M::mem_process_seqs] Processed 555772 reads in 172.191 CPU sec, 21.171 real sec
[M::mem_process_seqs] Processed 537054 reads in 165.228 CPU sec, 20.437 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_FG216\tSM:DabobBayWA_FG216\tPL:Illumina reference.fasta DabobBayWA_FG216.R1.fq.gz
[main] Real time: 87.884 sec; CPU: 676.475 sec