sokrypton / sokrypton/ColabFold
AlphaFold2_advanced.ipynb is resulting error not able to complete run alphafold
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Description
Expected Behavior
Should output a zip file
Current Behavior
Does not output a zip file. Results an error:
AttributeError Traceback (most recent call last)
in <cell line: 67>()
65 # run alphafold
66 ###########################
---> 67 outs, model_rank = cf_af.run_alphafold(feature_dict, opt, runner, num_models, num_samples, subsample_msa,
68 rank_by=rank_by, show_images=show_images)
39 frames
[... skipping hidden 12 frame]
[... skipping hidden 9 frame]
[... skipping hidden 8 frame]
/content/alphafold/alphafold/model/utils.py in mask_mean(mask, value, axis, drop_mask_channel, eps)
54 elif axis is None:
55 axis = list(range(len(mask_shape)))
---> 56 assert isinstance(axis, collections.Iterable), (
57 'axis needs to be either an iterable, integer or "None"')
58
AttributeError: module 'collections' has no attribute 'Iterable'
Steps to Reproduce (for bugs)
Please make sure to reproduce the issue after a "Factory Reset" in Colab.
If running locally ypdate you local installation colabfold_batch to the newest version.
Please provide your input if you can share it.
Use of all default settings hit runtime run all
ColabFold Output (for bugs)
Please make sure to also post the complete ColabFold output. You can use gist.github.com for large output.
Context
Providing context helps us come up with a solution and improve our documentation for the future.
Using online version
Your Environment
Include as many relevant details about the environment you experienced the bug in.
- Git commit used
- If you run it on a local system. Please add the server specifications
- Operating system and version:
Windows 11
Contributor guide
First steps
- Read the whole issue, then the project's contributing guide.
- Comment on the issue to say you are picking it up — it saves two people doing the same work.
- Fork the repository and make your change on a branch.
- Open a pull request that references the issue number.
Research direction
Start by opening AlphaFold2_advanced.ipynb and reproducing the default run in the online Colab environment after a factory reset. Trace the run from the run_alphafold call into alphafold/model/utils.py, especially mask_mean where the collections.Iterable error occurs. Done means the notebook completes and produces the expected zip file.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- jupyter-notebook, python
- Domain
- bioinformatics, machine-learning
- Issue type
- Bug
- Difficulty
- 2/5
- Estimated time
- 1-3 hours
- Activity status
- Stale
- Clarity
- Mostly clear
- Newbie friendliness
- 35/100