[M::bwa_idx_load_from_disk] read 0 ALT contigs
[M::process] read 557446 sequences (80000197 bp)...
[M::process] read 557462 sequences (80000005 bp)...
[M::mem_process_seqs] Processed 557446 reads in 149.007 CPU sec, 18.535 real sec
[M::process] read 552192 sequences (79248735 bp)...
[M::mem_process_seqs] Processed 557462 reads in 152.919 CPU sec, 18.772 real sec
[M::mem_process_seqs] Processed 552192 reads in 150.361 CPU sec, 18.587 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_Q240\tSM:DabobBayWA_Q240\tPL:Illumina reference.fasta DabobBayWA_Q240.R1.fq.gz
[main] Real time: 60.617 sec; CPU: 455.132 sec