[M::bwa_idx_load_from_disk] read 0 ALT contigs
[M::process] read 557040 sequences (80000027 bp)...
[M::process] read 557006 sequences (80000244 bp)...
[M::mem_process_seqs] Processed 557040 reads in 149.553 CPU sec, 18.620 real sec
[M::process] read 557044 sequences (80000168 bp)...
[M::mem_process_seqs] Processed 557006 reads in 152.165 CPU sec, 18.664 real sec
[M::process] read 556962 sequences (80000208 bp)...
[M::mem_process_seqs] Processed 557044 reads in 152.904 CPU sec, 18.743 real sec
[M::process] read 279393 sequences (40125371 bp)...
[M::mem_process_seqs] Processed 556962 reads in 152.326 CPU sec, 18.735 real sec
[M::mem_process_seqs] Processed 279393 reads in 77.038 CPU sec, 9.439 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_FG230\tSM:DabobBayWA_FG230\tPL:Illumina reference.fasta DabobBayWA_FG230.R1.fq.gz
[main] Real time: 87.047 sec; CPU: 686.072 sec