[M::bwa_idx_load_from_disk] read 0 ALT contigs
[M::process] read 556066 sequences (80000233 bp)...
[M::process] read 556144 sequences (80000094 bp)...
[M::mem_process_seqs] Processed 556066 reads in 167.144 CPU sec, 20.838 real sec
[M::process] read 556032 sequences (80000250 bp)...
[M::mem_process_seqs] Processed 556144 reads in 171.121 CPU sec, 21.012 real sec
[M::process] read 555982 sequences (80000236 bp)...
[M::mem_process_seqs] Processed 556032 reads in 174.337 CPU sec, 21.395 real sec
[M::process] read 317451 sequences (45669964 bp)...
[M::mem_process_seqs] Processed 555982 reads in 170.193 CPU sec, 20.964 real sec
[M::mem_process_seqs] Processed 317451 reads in 98.962 CPU sec, 12.154 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_306\tSM:SewardAK_306\tPL:Illumina reference.fasta SewardAK_306.R1.fq.gz
[main] Real time: 100.561 sec; CPU: 784.475 sec