I was doing RNA-seq analysis for paired-end data, I used fastp to pre-process paired end data and used HISAT2 and the reference genome of mRatBN7.2 to do alignment and used samtools sort to sort the bam files. Then I uploaded the reference annotation genome of GCF_015227675.2 and used featurecounts to do expression analysis, but this error occurred.
Hi @Xinyang
Are you working at a public Galaxy server? Which one? And can you still reproduce this error now?
Let’s start there. If the error is persistent, you can share back your history for more feedback. How to do this is in the banner of this forum. 
Xref guide → FAQ: Extended Help for Differential Expression Analysis Tools
I had the same error code when I used featureCounts. any suggestion to fix this problem?
Hi @Weibo_Luo and @Xinyang
Please see this FAQ for tips about how to make sure that your reference data is correct, since that is the most common reason for problems.
We also have examples if you want to compare the methods, or are interested in a workflow template. The two introduction tutorials are for discovery+known features, and the end-to-end series is for a deeper dive into known features.
Please give those a review.
If you cannot determine if that is what is going on, it is hard to guess more about what the exact problem may be. You can post an example in a small history for feedback here. Please make sure that the all of the upstream files are there, especially any reference annotation files. How to generate the history share link is in the banner of the forum, also here → How to get faster help with your question. You can post the link back in a reply, and note the problem datasets, then unshare once we are done.
Update:
We have confirmed a problem with one of the versions of Featurecounts at UseGalaxy.org.
If you are working at this server: the solution is to use a different version of the tool to avoid this specific error (only).
Details including how to check and use a different tool version →
Thanks to everyone who reported the problem!
Hi, jennaj. Thanks for the report of the uploading of one of the versions of Featurecounts! Would it be possible for me to ask another issue? I have encountered another problem that said ‘Disk quota exceeded’, and after searching the forum, I noticed that it may be due to the server issues. So I wonder when would it be possible for us to rerun the data or upload the data? Thank you!
Hi @Xinyang
This error is usually from a server problem but it might be expected right now for a few tools (one of our clusters is not available, and some tools only run there). So, first try a rerun. Then if it still fails that way, I would be curious about which tool/version this is. You can share the link to the i-icon view or the history with the error and I’ll confirm.
