[M::bwa_idx_load_from_disk] read 0 ALT contigs
[M::process] read 557090 sequences (80000196 bp)...
[M::process] read 557092 sequences (80000116 bp)...
[M::mem_process_seqs] Processed 557090 reads in 147.323 CPU sec, 18.327 real sec
[M::process] read 557042 sequences (80000188 bp)...
[M::mem_process_seqs] Processed 557092 reads in 150.176 CPU sec, 18.435 real sec
[M::process] read 62489 sequences (8971630 bp)...
[M::mem_process_seqs] Processed 557042 reads in 148.581 CPU sec, 18.340 real sec
[M::mem_process_seqs] Processed 62489 reads in 20.041 CPU sec, 2.337 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_Q362\tSM:DabobBayWA_Q362\tPL:Illumina reference.fasta DabobBayWA_Q362.R1.fq.gz
[main] Real time: 60.211 sec; CPU: 468.269 sec