[M::bwa_idx_load_from_disk] read 0 ALT contigs
[M::process] read 555560 sequences (80000098 bp)...
[M::process] read 555560 sequences (80000042 bp)...
[M::mem_process_seqs] Processed 555560 reads in 159.429 CPU sec, 19.873 real sec
[M::process] read 555562 sequences (80000219 bp)...
[M::mem_process_seqs] Processed 555560 reads in 162.311 CPU sec, 19.937 real sec
[M::process] read 555560 sequences (80000244 bp)...
[M::mem_process_seqs] Processed 555562 reads in 163.995 CPU sec, 20.168 real sec
[M::process] read 555560 sequences (80000280 bp)...
[M::mem_process_seqs] Processed 555560 reads in 161.203 CPU sec, 19.796 real sec
[M::process] read 555560 sequences (80000211 bp)...
[M::mem_process_seqs] Processed 555560 reads in 162.291 CPU sec, 19.909 real sec
[M::process] read 465520 sequences (67034532 bp)...
[M::mem_process_seqs] Processed 555560 reads in 162.754 CPU sec, 20.022 real sec
[M::mem_process_seqs] Processed 465520 reads in 137.221 CPU sec, 16.978 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_Q314\tSM:SewardAK_Q314\tPL:Illumina reference.fasta SewardAK_Q314.R1.fq.gz
[main] Real time: 141.731 sec; CPU: 1111.930 sec