Problem with Helixer

usegalaxy.org support
,
1

I am trying to run Helixer on a 5 Mb sequence (which corresponds to a specific region from a chromosome I’m interested in). I obtain this error:

            Traceback (most recent call last):
  File "/usr/local/bin/fetch_helixer_models.py", line 35, in <module>
    main(args.lineage, best_only=not args.all, custom_path=args.custom_path)
  File "/usr/local/bin/fetch_helixer_models.py", line 23, in main
    fetch_and_organize_models(models, model_path)
  File "/usr/local/lib/python3.10/dist-packages/helixer/core/data.py", line 29, in fetch_and_organize_models
    os.makedirs(model_path)
  File "/usr/lib/python3.10/os.py", line 215, in makedirs
    makedirs(head, exist_ok=exist_ok)
  File "/usr/lib/python3.10/os.py", line 225, in makedirs
    mkdir(name, mode)
OSError: [Errno 30] Read-only file system: '/cvmfs/main.galaxyproject.org/xdg/data/Helixer'

By reading it, I would assume the error is not on my end, but I could be wrong. Any help is appreciated! I’m trying to run it with default parameters, using “land plant” as the lineage.

2

Welcome @davidjoly

Thanks for reporting the issue here! There is a known issue with Helixer we are tracking here.

We increased the resources but this led to another issue!

For now, the solution is to try at a different public Galaxy server.

Hopefully this helps! :slight_smile:

3

Thanks Jennifer! Indeed, I tried on the EU server and it worked! Cheers!

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