[M::bwa_idx_load_from_disk] read 0 ALT contigs
[M::process] read 555558 sequences (80000089 bp)...
[M::process] read 555560 sequences (80000225 bp)...
[M::mem_process_seqs] Processed 555558 reads in 159.006 CPU sec, 19.829 real sec
[M::process] read 555558 sequences (80000076 bp)...
[M::mem_process_seqs] Processed 555560 reads in 164.754 CPU sec, 20.224 real sec
[M::process] read 555560 sequences (80000277 bp)...
[M::mem_process_seqs] Processed 555558 reads in 162.858 CPU sec, 19.963 real sec
[M::process] read 102870 sequences (14813228 bp)...
[M::mem_process_seqs] Processed 555560 reads in 161.375 CPU sec, 19.948 real sec
[M::mem_process_seqs] Processed 102870 reads in 34.567 CPU sec, 4.103 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_Q325\tSM:SewardAK_Q325\tPL:Illumina reference.fasta SewardAK_Q325.R1.fq.gz
[main] Real time: 86.364 sec; CPU: 684.074 sec