[M::bwa_idx_load_from_disk] read 0 ALT contigs
[M::process] read 555560 sequences (80000234 bp)...
[M::process] read 555560 sequences (80000199 bp)...
[M::mem_process_seqs] Processed 555560 reads in 159.057 CPU sec, 19.831 real sec
[M::process] read 555562 sequences (80000234 bp)...
[M::mem_process_seqs] Processed 555560 reads in 160.317 CPU sec, 19.710 real sec
[M::process] read 555560 sequences (80000216 bp)...
[M::mem_process_seqs] Processed 555562 reads in 165.441 CPU sec, 20.329 real sec
[M::process] read 555558 sequences (80000107 bp)...
[M::mem_process_seqs] Processed 555560 reads in 162.274 CPU sec, 19.921 real sec
[M::process] read 555560 sequences (80000218 bp)...
[M::mem_process_seqs] Processed 555558 reads in 161.686 CPU sec, 19.874 real sec
[M::process] read 555560 sequences (80000233 bp)...
[M::mem_process_seqs] Processed 555560 reads in 160.788 CPU sec, 19.758 real sec
[M::process] read 254822 sequences (36694263 bp)...
[M::mem_process_seqs] Processed 555560 reads in 161.402 CPU sec, 19.908 real sec
[M::mem_process_seqs] Processed 254822 reads in 78.008 CPU sec, 9.529 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_Q318\tSM:SewardAK_Q318\tPL:Illumina reference.fasta SewardAK_Q318.R1.fq.gz
[main] Real time: 152.282 sec; CPU: 1211.222 sec