 /opt/chipster/tools/bwa/bwa aln -t 2 -o 1 -e -1 -d 16 -i 5 -l 32 -k 2 -O 11 -E 4 -q 0 -B 0 -M 3 -n 0.04  /opt/chipster/tools/bwa_indexes/hg19.fa reads.txt 
[bwa_aln] 17bp reads: max_diff = 2
[bwa_aln] 38bp reads: max_diff = 3
[bwa_aln] 64bp reads: max_diff = 4
[bwa_aln] 93bp reads: max_diff = 5
[bwa_aln] 124bp reads: max_diff = 6
[bwa_aln] 157bp reads: max_diff = 7
[bwa_aln] 190bp reads: max_diff = 8
[bwa_aln] 225bp reads: max_diff = 9
[bwa_aln_core] calculate SA coordinate... 30.15 sec
[bwa_aln_core] write to the disk... 0.01 sec
[bwa_aln_core] 51570 sequences have been processed.
[main] Version: 0.6.1-r104
[main] CMD: /opt/chipster/tools/bwa/bwa aln -t 2 -o 1 -e -1 -d 16 -i 5 -l 32 -k 2 -O 11 -E 4 -q 0 -B 0 -M 3 -n 0.04 /opt/chipster/tools/bwa_indexes/hg19.fa reads.txt
[main] Real time: 18.822 sec; CPU: 32.530 sec
[bwa_aln_core] convert to sequence coordinate... 3.38 sec
[bwa_aln_core] refine gapped alignments... 0.61 sec
[bwa_aln_core] print alignments... 0.14 sec
[bwa_aln_core] 51570 sequences have been processed.
[main] Version: 0.6.1-r104
[main] CMD: /opt/chipster/tools/bwa/bwa samse -n 3 /opt/chipster/tools/bwa_indexes/hg19.fa alignment.sai reads.txt
[main] Real time: 4.246 sec; CPU: 4.244 sec
