[M::bwa_idx_load_from_disk] read 0 ALT contigs
[M::process] read 556002 sequences (80000105 bp)...
[M::process] read 556062 sequences (80000259 bp)...
[M::mem_process_seqs] Processed 556002 reads in 170.084 CPU sec, 21.187 real sec
[M::process] read 556132 sequences (80000225 bp)...
[M::mem_process_seqs] Processed 556062 reads in 172.390 CPU sec, 21.145 real sec
[M::process] read 555964 sequences (80000241 bp)...
[M::mem_process_seqs] Processed 556132 reads in 171.150 CPU sec, 21.021 real sec
[M::process] read 555990 sequences (80000152 bp)...
[M::mem_process_seqs] Processed 555964 reads in 174.177 CPU sec, 21.456 real sec
[M::process] read 556058 sequences (80000148 bp)...
[M::mem_process_seqs] Processed 555990 reads in 169.946 CPU sec, 20.894 real sec
[M::process] read 54986 sequences (7910203 bp)...
[M::mem_process_seqs] Processed 556058 reads in 168.715 CPU sec, 20.911 real sec
[M::mem_process_seqs] Processed 54986 reads in 20.985 CPU sec, 2.481 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_300\tSM:SewardAK_300\tPL:Illumina reference.fasta SewardAK_300.R1.fq.gz
[main] Real time: 132.861 sec; CPU: 1049.657 sec