[M::bwa_idx_load_from_disk] read 0 ALT contigs
[M::process] read 557342 sequences (80000029 bp)...
[M::process] read 557304 sequences (80000147 bp)...
[M::mem_process_seqs] Processed 557342 reads in 147.925 CPU sec, 18.417 real sec
[M::process] read 557306 sequences (80000230 bp)...
[M::mem_process_seqs] Processed 557304 reads in 153.734 CPU sec, 18.866 real sec
[M::process] read 242908 sequences (34862695 bp)...
[M::mem_process_seqs] Processed 557306 reads in 152.865 CPU sec, 18.811 real sec
[M::mem_process_seqs] Processed 242908 reads in 69.385 CPU sec, 8.468 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_Q303\tSM:SewardAK_Q303\tPL:Illumina reference.fasta SewardAK_Q303.R1.fq.gz
[main] Real time: 68.445 sec; CPU: 526.074 sec