Welcome @bioinfokg
Thanks for sharing the parameters! It looks like you are using the default reference index with the most current tool version. And, the topic was tagged as being for UseGalaxy.org, so that is where I am cross testing, but you can clarify if you are working somewhere else?
This is my test using the same configurations, and it ran successfully, so I think the tool and the reference index are working Ok.
My best guess is that there is some problem with your input fasta dataset. Maybe the format? You could run the data through a tool like NormalizeFasta to see if that helps. Other problems could be based on the scientific content – maybe a different reference index would be a better choice?
If that is not enough help to solve this, you are welcome to share more details and we can troubleshoot more. 