[M::bwa_idx_load_from_disk] read 0 ALT contigs
[M::process] read 555558 sequences (80000009 bp)...
[M::process] read 555560 sequences (80000275 bp)...
[M::mem_process_seqs] Processed 555558 reads in 157.143 CPU sec, 19.560 real sec
[M::process] read 555558 sequences (80000105 bp)...
[M::mem_process_seqs] Processed 555560 reads in 162.390 CPU sec, 19.911 real sec
[M::process] read 555560 sequences (80000272 bp)...
[M::mem_process_seqs] Processed 555558 reads in 163.654 CPU sec, 20.062 real sec
[M::process] read 266210 sequences (38334102 bp)...
[M::mem_process_seqs] Processed 555560 reads in 163.373 CPU sec, 20.129 real sec
[M::mem_process_seqs] Processed 266210 reads in 81.558 CPU sec, 9.963 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:SewardAK_Q323\tSM:SewardAK_Q323\tPL:Illumina reference.fasta SewardAK_Q323.R1.fq.gz
[main] Real time: 93.635 sec; CPU: 730.456 sec