[M::bwa_idx_load_from_disk] read 0 ALT contigs
[M::process] read 556220 sequences (80000080 bp)...
[M::process] read 555982 sequences (80000115 bp)...
[M::mem_process_seqs] Processed 556220 reads in 152.414 CPU sec, 18.955 real sec
[M::process] read 324164 sequences (46653628 bp)...
[M::mem_process_seqs] Processed 555982 reads in 154.335 CPU sec, 19.017 real sec
[M::mem_process_seqs] Processed 324164 reads in 93.341 CPU sec, 11.467 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_FG250\tSM:DabobBayWA_FG250\tPL:Illumina reference.fasta DabobBayWA_FG250.R1.fq.gz
[main] Real time: 52.804 sec; CPU: 402.393 sec