[M::bwa_idx_load_from_disk] read 0 ALT contigs
[M::process] read 555914 sequences (80000238 bp)...
[M::process] read 555892 sequences (80000091 bp)...
[M::mem_process_seqs] Processed 555914 reads in 172.999 CPU sec, 21.547 real sec
[M::process] read 549731 sequences (79120066 bp)...
[M::mem_process_seqs] Processed 555892 reads in 178.339 CPU sec, 21.956 real sec
[M::mem_process_seqs] Processed 549731 reads in 174.745 CPU sec, 21.636 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_309\tSM:SewardAK_309\tPL:Illumina reference.fasta SewardAK_309.R1.fq.gz
[main] Real time: 71.013 sec; CPU: 529.559 sec