[M::bwa_idx_load_from_disk] read 0 ALT contigs
[M::process] read 556920 sequences (80000252 bp)...
[M::process] read 556898 sequences (80000240 bp)...
[M::mem_process_seqs] Processed 556920 reads in 145.056 CPU sec, 18.051 real sec
[M::process] read 556944 sequences (80000088 bp)...
[M::mem_process_seqs] Processed 556898 reads in 146.680 CPU sec, 18.001 real sec
[M::process] read 556864 sequences (80000099 bp)...
[M::mem_process_seqs] Processed 556944 reads in 148.757 CPU sec, 18.222 real sec
[M::process] read 283479 sequences (40716864 bp)...
[M::mem_process_seqs] Processed 556864 reads in 148.291 CPU sec, 18.262 real sec
[M::mem_process_seqs] Processed 283479 reads in 77.287 CPU sec, 9.484 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_FG225\tSM:DabobBayWA_FG225\tPL:Illumina reference.fasta DabobBayWA_FG225.R1.fq.gz
[main] Real time: 85.567 sec; CPU: 668.343 sec