I am using MirDeep star tool for RNA sequence alignment. I have tried both GUI version and command line version of this tool. But every time, I am getting empty . result file and .known_mir file. This tool is neither giving any error nor any warning with my data. I have also tried the demo file given with this and this tool is working fine with this (i.e. giving some results in .result and known_mir file).
Can anyone suggest me what could be the possible reason for this. Why I am getting empty file.