Stringtie not running

I am trying to run StringTie on 6 files in batch mode, but upon clicking “Execute,” nothing happens. Trying this one file at a time also isn’t working. No pending jobs show up in my history. I have also tried using different browser to no avail.

Not sure what could be going wrong since there are no jobs to check errors…

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Update: other programs such as HISAT2 are running just fine. My issue seems to be StringTie specific.

Issue resolved. Apparently I had to designate an output transcript prefix name under Advanced Options. I’ve never had to do this before and didn’t think to expand the Advanced Options menu before…

Oh well, hopefully if someone else has the same issue, this will help!


I’m struggling with stringtie output too and after following your method, finally I can run my stringtie. Thank you so much!