[M::bwa_idx_load_from_disk] read 0 ALT contigs
[M::process] read 555850 sequences (80000178 bp)...
[M::process] read 555908 sequences (80000144 bp)...
[M::mem_process_seqs] Processed 555850 reads in 163.369 CPU sec, 20.320 real sec
[M::process] read 555800 sequences (80000126 bp)...
[M::mem_process_seqs] Processed 555908 reads in 166.204 CPU sec, 20.417 real sec
[M::process] read 555768 sequences (80000177 bp)...
[M::mem_process_seqs] Processed 555800 reads in 167.449 CPU sec, 20.545 real sec
[M::process] read 251870 sequences (36251215 bp)...
[M::mem_process_seqs] Processed 555768 reads in 168.122 CPU sec, 20.754 real sec
[M::mem_process_seqs] Processed 251870 reads in 80.272 CPU sec, 9.828 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_301\tSM:SewardAK_301\tPL:Illumina reference.fasta SewardAK_301.R1.fq.gz
[main] Real time: 95.010 sec; CPU: 747.476 sec