[M::bwa_idx_load_from_disk] read 0 ALT contigs
[M::process] read 556036 sequences (80000203 bp)...
[M::process] read 555980 sequences (80000050 bp)...
[M::mem_process_seqs] Processed 556036 reads in 166.662 CPU sec, 20.770 real sec
[M::process] read 361839 sequences (52069646 bp)...
[M::mem_process_seqs] Processed 555980 reads in 171.406 CPU sec, 21.145 real sec
[M::mem_process_seqs] Processed 361839 reads in 113.311 CPU sec, 13.956 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_FG218\tSM:DabobBayWA_FG218\tPL:Illumina reference.fasta DabobBayWA_FG218.R1.fq.gz
[main] Real time: 59.991 sec; CPU: 454.080 sec