I am using the MapMi miRNA prediction software developed by the Enright Group of EBI. I downloaded MapMi, got all the dependencies sorted and tried running the software with a custom genome I have. I edited the configuration file and tried matching all the miRNAs in miRBase (~28,000) to find any matches in my genome. However, I get no alignments whatsoever which I find highly unlikely. Please suggest as to what I could be doing wrong. I will upload my files via dropbox.

My custom genome: https://www.dropbox.com/s/58ti793289qpofv/allresult.fa?dl=0

My configuration file: https://www.dropbox.com/s/838bt7p29j4nwu0/PipelineConfig.conf?dl=0