Hello!
I am trying to use the ‘Annotate DESeq2/DEXSeq output table’ tool on usegalaxy.org, however I keep getting the same error. I have attached below a screenshot of the error page and job information details.
I was wondering if I would be able to get some help with resolving this issue. Thanks!!
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! 
Hi @jennaj,
I ended up transferring the files I needed to usegalaxy.eu and the annotate DESeq2/DEXSeq tool ended up working over there, so it doesn’t seem to be an issue with my files, inputs or settings.
I just tried rerunning the command on usegalaxy.org this morning to see if I got the same error as I was receiving previously and still doesn’t seem to be working.
I have the files I need now through the eu galaxy, but just wanted to let you know incase people run into the same issue.
Thanks!
Ok, thanks @natstrong and glad you have this going!
I see a bug report with the same error today, and I’ll review to figure out what might be going on then update back here in case anyone else runs into this. Thanks for reporting the issue, testing, and following up! Maybe a cluster node is bad. We’ll figure it out.
Update
The issue has to do with a small change we made with how compressed GFT.gz data is handled. We will be addressing this.
For now, please try the work-around below for issues with gtf.gz data.
gtf file and use the fileor
gtf.gz file, run gffread with the gtf output option selected, and use the file. This must be done as the first step when using the file in Galaxy. If other steps were done first, you may need to load the data again to start over.We will update back here when this is completed. Thanks again for alerting us to the issue! 