HI @Jane
There was a small cluster issue earlier at UseGalaxy.org, and a rerun might resolve the error you had. So, please try that as well. It seems the tool could not locate the input file.
If the rerun also fails, then start by checking your input fastq file. Does it contain data? Or did the Upload fail?
We can follow up more if you cannot resolve this. A shared history link would be helpful. How to share is in the banner at this forum, and you can post the link back here, then unshare once we are done.
More details about a different way this presented for some people. → mirDeep2 Error - remote job server indicated a problem running - #2 by jennaj
Hope this helps! 