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It sounds like you have Featurecounts configured to look for a feature type that does not exist in your GTF file (3rd column of the reference annotation file is searched with the term set on the tool form). Related Q&A → Problems with the tool featureCounts: Fatal error: Exit code 255 ()
The tutorial data should be consistent with the steps in the tutorial, but if you are using your own reference data instead, you may need to make small adjustments.
For the other problem (an empty file?), it is hard to guess without seeing the data. Are you saying that the upstream Gffcompare step produced an empty result? If you want to generate a share link back to the history and post it into a reply, we can help to troubleshoot what is going wrong.
How to share → How to get faster help with your question
Troubleshooting guide → FAQ: Extended Help for Differential Expression Analysis Tools
Let us know if you solve this or need more help! 