[M::bwa_idx_load_from_disk] read 0 ALT contigs
[M::process] read 555558 sequences (80000071 bp)...
[M::process] read 555560 sequences (80000086 bp)...
[M::mem_process_seqs] Processed 555558 reads in 158.813 CPU sec, 19.750 real sec
[M::process] read 555558 sequences (80000006 bp)...
[M::mem_process_seqs] Processed 555560 reads in 162.868 CPU sec, 20.026 real sec
[M::process] read 555558 sequences (80000121 bp)...
[M::mem_process_seqs] Processed 555558 reads in 162.460 CPU sec, 19.970 real sec
[M::process] read 555560 sequences (80000254 bp)...
[M::mem_process_seqs] Processed 555558 reads in 163.699 CPU sec, 20.088 real sec
[M::process] read 398182 sequences (57337933 bp)...
[M::mem_process_seqs] Processed 555560 reads in 161.316 CPU sec, 19.849 real sec
[M::mem_process_seqs] Processed 398182 reads in 119.539 CPU sec, 14.710 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_Q316\tSM:SewardAK_Q316\tPL:Illumina reference.fasta SewardAK_Q316.R1.fq.gz
[main] Real time: 118.298 sec; CPU: 931.302 sec