[M::bwa_idx_load_from_disk] read 0 ALT contigs
[M::process] read 555882 sequences (80000099 bp)...
[M::process] read 555932 sequences (80000233 bp)...
[M::mem_process_seqs] Processed 555882 reads in 176.011 CPU sec, 21.940 real sec
[M::process] read 555788 sequences (80000068 bp)...
[M::mem_process_seqs] Processed 555932 reads in 177.732 CPU sec, 21.871 real sec
[M::process] read 502669 sequences (72351074 bp)...
[M::mem_process_seqs] Processed 555788 reads in 178.671 CPU sec, 21.985 real sec
[M::mem_process_seqs] Processed 502669 reads in 162.598 CPU sec, 20.093 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_308\tSM:SewardAK_308\tPL:Illumina reference.fasta SewardAK_308.R1.fq.gz
[main] Real time: 91.340 sec; CPU: 698.008 sec