Resolved: Fatal error: Exit code 255 () with kraken2?

usegalaxy.org support
1

I having trouble with a workflow that I have used successfully before, but now I get a “Fatal error: Exit code 255 ()” when kraken2 runs. The actual error reads:

FATAL: While checking container encryption: could not open image /cvmfs/singularity.galaxyproject.org/all/kraken2:2.1.3–pl5321hdcf5f25_2: failed to retrieve path for /cvmfs/singularity.galaxyproject.org/all/kraken2:2.1.3–pl5321hdcf5f25_2: lstat /cvmfs/singularity.galaxyproject.org/all/kraken2:2.1.3–pl5321hdcf5f25_2: no such file or directory

I have tried using different databases, but the error persists. I can’t tell if this is something on my end, or a server issue. Any advice would be helpful. History has been shared (I think, first time sharing a history).

2

Hi @DocParker

It looks like a server/connection issue. Ping @jennaj
I hope it will be fixed (after weekend).
You can try it in Europe (it is OK to have accounts on different public Galaxy servers), however, if it is cvmfs issue, some databases might not be available in Europe, as well.

Kind regards,
Igor

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3

Hi @DocParker and thanks @igor !!

I’m reviewing. As a quick fix, please try a rerun @DocParker just to see what happens. Some very small fraction of jobs will fail by chance, so at least one rerun is always a good idea. If a rerun solves the error before I write back, please let us know! :slight_smile:

4

Thanks for the replies, @igor and @jennaj. I tried rerunning, but the error persists, unfortunately.

5

Update

The issue was fixed really quick! Please try a rerun now and let us know if that works for you too (it did with my tests).

Thanks again for reporting the problem! :rocket:

Hi @DocParker

Thanks for checking, it failed for me as well.

There was an updated version of Kraken2 added, and it seems to have a small technical issue server side at UseGalaxy.org. Please switch to using the prior version until we can correct this. Or, you can move your data and run the tool at UseGalaxy.eu or UseGalaxy.org.au as Igor suggests.

The tracking ticket is posted here → Updated version of Kraken2 fails at jetstream2 · Issue #847 · galaxyproject/usegalaxy-tools · GitHub

What to do

Workaround for end users

  1. Switch to use the prior tool version
  2. Use → 2.1.1+galaxy1
  3. How to change tool versions: FAQ: Changing the tool version

Thanks again for posting your shared history in the original question. It made the issue very quick to troubleshoot. Feel free to unshare if you want to now. :hammer_and_wrench:

6

Thanks @jennaj, I appreciate the help. Switching to the previous version worked for me.

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