[M::bwa_idx_load_from_disk] read 0 ALT contigs
[M::process] read 556054 sequences (80000021 bp)...
[M::process] read 555898 sequences (80000255 bp)...
[M::mem_process_seqs] Processed 556054 reads in 153.381 CPU sec, 19.104 real sec
[M::process] read 555916 sequences (80000215 bp)...
[M::mem_process_seqs] Processed 555898 reads in 159.643 CPU sec, 19.644 real sec
[M::process] read 555868 sequences (80000056 bp)...
[M::mem_process_seqs] Processed 555916 reads in 156.658 CPU sec, 19.228 real sec
[M::process] read 258784 sequences (37243882 bp)...
[M::mem_process_seqs] Processed 555868 reads in 158.070 CPU sec, 19.475 real sec
[M::mem_process_seqs] Processed 258784 reads in 76.071 CPU sec, 9.330 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_FG221\tSM:DabobBayWA_FG221\tPL:Illumina reference.fasta DabobBayWA_FG221.R1.fq.gz
[main] Real time: 90.104 sec; CPU: 705.972 sec