Docker error when using Funannotate functional annotation tool

usegalaxy.eu support
1

Hello everyone, I’m trying to use the tool “funannotate functional” to integrate Interpro, AntiSmash and EggNog annotation to the previously structural annotated genome.

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The tool works absolutely fine for some regions in the contigs, however for certain ones I get the following error:

docker: Error response from daemon: error while creating mount source path '/cvmfs/data.galaxyproject.org': mkdir /cvmfs/data.galaxyproject.org: permission denied.

Because of this error, the final output is empty, however I can access the output for the contig regions where the tool threw no errors.

Any ideas on what I can do to fix this issue? Please let me know if you require any additional info. Many thanks!

2

Welcome @gbioinfo

The Docker message is probably something that can be ignored as chatter in the log.

First, try a rerun for these jobs. Maybe the cluster issue was transient.

If these fail again, is there anything special about these contig regions?

We can help to determine that and what else may be going on (including technical issues). We need to see all the job details. You can generate and post back a share link to the history. If the history is large, you can copy the datasets involved into a new history and share that instead (all inputs and outputs please) but this provides less context.

How to share is in the banner of the forum, also here:

Let’s start there, thanks! :slight_smile:

3

Hello @jennaj

Thank you for your response! I went ahead and checked the contigs, but I couldn’t spot anything particularly unusual—except for one contig that strangely has a high number of “TTA” repeats at the beginning. Not sure if this could be affecting the annotation process in some way, as I have soft-masked the contigs before proceeding.

I also tried re-running the job, but I’m still getting the same error at the same contig regions.

I’ve attached the link to my history so you can take a look at all the job details. Let me know if anything stands out or if you need any additional information.

Really appreciate your help! :blush:

4

Hi @gbioinfo

I think we’ll need help from the EU administrators! I sent in a bug report with a link to this topic and you could too. Plus let’s ping them here. @wm75 would you be able to help? Thanks!

5

Hi @gbioinfo

The EU server underwent some upgrades in June. This included job runtime container corrections that impacted all servers but not all jobs! Very confusing.

If you haven’t solved your issues yet, I would try a rerun now. I checked your shared history, and that still has the original errors but maybe you are working in a different history?

In any case, please try again now and anything persistent, we can still follow up about. I think this should work for you and it doesn’t appear to be data related. It seems technical to me. :hammer_and_wrench: