Hi @natstrong
We can help to troubleshoot.
The warning message can be ignored (is a type or log, and expected), so something else is going on.
The most common issues are with the format of the files, in particular the reference annotation involved. Right now your settings are for a “GTF” formatted annotation given the list of attributes in the log, so start by double checking that your reference annotation is in that format and contains those attributes. Some tools are very strict, and with GTF data that means do not include the header lines some data providers may include from provenance reasons.
This guide has instructions for removing “strict” out-of-specification header lines and other common format/content help tips. Maybe review? → FAQ: Extended Help for Differential Expression Analysis Tools
Please let us know if you solve this or if you need more help. We would need to look at all the inputs and tool form options used to suggest the exact fix. You can generate and post back a share link to your history and note the error dataset to look at. How to share is in the banner of this forum, also here. → How to get faster help with your question
Let’s start there! 