Issue “No space left on device” error

usegalaxy.eu support
1

Hi, I’m trying to use PPanGGOLiN all and still have 90GB (~34%) storage left but each time i run it with the following outputs selected: “Gene presence absence, Gene families, Matrix, Ushaped plot, PanGenome Graph (Gexf) and (Json)“, it gives me the following error message: “OSError: [Errno 28] No space left on device“. Is my storage somehow not sufficient, or does galaxy not recognize the 90GB I have left ? Is it also possible to get more storage space ?

Here is the link to the history : Galaxy

Greetings and thanks in advance,

Fernando Martin Garcia

2

Hello @Fernando_Martin

This message inside of the stderr specific message is usually referring to the job environment on the cluster node the tool is executing on. This is the runtime working space and is distinct from your own account storage space.

I think we’ll need input from the EU administrators for this one. What do you think @wm75? Can you help? This is the job temp directory running out of space, yes?

Whenever this shows up at the UseGalaxy.org server, it means that a shared storage location has run out of working space. I’m not sure for the EU cluster situation.

For you @Fernando_Martin – if you don’t want to wait, I would suggest these ideas as exploratory items you could try. :slight_smile: You can let us know what happens!

  1. Rerun this exact job to see what happens. Each run hits a different cluster node!
  2. Rerun but leave the identity threshold at 0.8. Can you notice which outputs are growing excessively large? Do you need that output?
  3. If that also fails, try an even stricter identity threshold at 0.9 to see what happens.
  4. Finally, you could also run your tagged groups in different batches. Maybe you can see in the results which genome or group is exploding the final data reporting files to the larger size.

Thanks! :slight_smile:

3

Hi @jennaj ,

For comparison reasons, I cannot change the identity threshold nor the group sizes, but I will try to run the exact job again a few times to see if it hits a different cluster node with sufficient space.

Thanks again for your help!

Best regards,

Fernando Martin

4

Hi @jennaj ,

I ran it several times over the last couple of days, created new histories and ran it there as well, and also submitted two bug reports, but there is still no change. It also doesn’t matter which type of storage I select when running the Ppanggolin tool. Is there anything new on your side ?

Greetings and thanks in advance,

Fernando Martin Garcia