[M::bwa_idx_load_from_disk] read 0 ALT contigs
[M::process] read 555868 sequences (80000085 bp)...
[M::process] read 555888 sequences (80000284 bp)...
[M::mem_process_seqs] Processed 555868 reads in 173.484 CPU sec, 21.633 real sec
[M::process] read 555774 sequences (80000243 bp)...
[M::mem_process_seqs] Processed 555888 reads in 177.991 CPU sec, 21.872 real sec
[M::process] read 288175 sequences (41476555 bp)...
[M::mem_process_seqs] Processed 555774 reads in 177.703 CPU sec, 21.934 real sec
[M::mem_process_seqs] Processed 288175 reads in 97.102 CPU sec, 11.898 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_312\tSM:SewardAK_312\tPL:Illumina reference.fasta SewardAK_312.R1.fq.gz
[main] Real time: 81.348 sec; CPU: 629.009 sec