annotateMyIDs failure

usegalaxy.eu support
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1

Hi, while annotating a count matrix(featureCounts output) the ‘annotateMyIDs’ rises an error:
/data/jwd04/main/056/805/56805599/tool_script.sh: line 9: R: command not found
/data/jwd04/main/056/805/56805599/tool_script.sh: line 10: Rscript: command not found

I saw that it happened also at the .org sever back in Oc’ 22, will it will be fixed in the eu server some time soon? and what other tool can be recommended mean while?(the IDs are by Entrez if it matters)

Thanks!!

Blockquote

2

Hi @g.minor

Please try at least one rerun as that error may have been transient. I couldn’t reproduce a technical problem with a test run just now.

If that still fails for you, there could be a problem with the input or a setting on the AnnotateMyIDs tool form.

Items to check:

  1. Does the input contain any content? (not empty or only a header)
  2. The output from FeatureCounts contains a header by default, and the toggle for a header or not should be set to Yes on the AnnotateMyIDs tool form.
  3. Was the correct Organism and ID Type (geneID) options set to match your data?
  4. Are you using the default set of Output columns or adding in more? What happens if just the defaults are output?
  5. Is there anything special about your data? Meaning, was it manipulated after running FeatureCounts?

Let’s start there :slight_smile:

4

Thanks! checked all this options already, doesn’t work.

5

hi @g.minor

Ok, thanks for checking. Fixing those items is what we can help with here.

Please send in a bug report from the error dataset to the EU server admins. More might be going on and they will be able to check. You can include a link to this topic in the bug report comments as a reference.