[M::bwa_idx_load_from_disk] read 0 ALT contigs
[M::process] read 555558 sequences (80000036 bp)...
[M::process] read 555558 sequences (80000014 bp)...
[M::mem_process_seqs] Processed 555558 reads in 165.533 CPU sec, 20.626 real sec
[M::process] read 555560 sequences (80000141 bp)...
[M::mem_process_seqs] Processed 555558 reads in 168.220 CPU sec, 20.707 real sec
[M::process] read 555558 sequences (80000009 bp)...
[M::mem_process_seqs] Processed 555560 reads in 172.892 CPU sec, 21.261 real sec
[M::process] read 555558 sequences (80000013 bp)...
[M::mem_process_seqs] Processed 555558 reads in 170.657 CPU sec, 20.971 real sec
[M::process] read 555558 sequences (80000007 bp)...
[M::mem_process_seqs] Processed 555558 reads in 169.932 CPU sec, 20.896 real sec
[M::process] read 555560 sequences (80000270 bp)...
[M::mem_process_seqs] Processed 555558 reads in 171.921 CPU sec, 21.093 real sec
[M::process] read 316257 sequences (45540828 bp)...
[M::mem_process_seqs] Processed 555560 reads in 170.365 CPU sec, 20.992 real sec
[M::mem_process_seqs] Processed 316257 reads in 99.614 CPU sec, 12.242 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_Q324\tSM:SewardAK_Q324\tPL:Illumina reference.fasta SewardAK_Q324.R1.fq.gz
[main] Real time: 162.590 sec; CPU: 1291.685 sec