sokrypton / sokrypton/ColabFold

AlphaFold2_batch hangs at 'Install dependencies'

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Jupyter Notebook
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Description

Expected Behavior

I expect to see that ColabFold and other dependencies are being installed.

Current Behavior

No change after several minutes. Just a spinning wheel. I am connected to a V100 high-RAM machine. No progress, but still consuming my resources.

Steps to Reproduce (for bugs)

Please make sure to reproduce the issue after a "Factory Reset" in Colab.
If running locally update your local installation colabfold_batch to the newest version.
Please provide your input if you can share it.

I reproduced this issue on two different days. I tried restarting the runtime more than once. Google Drive was successfully mounted, so that is not the issue.

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.

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:

I tried both Chrome and Safari browsers. Both gave the same behavior.

Contributor guide

Open the contributing guide

First steps

  1. Read the whole issue, then the project's contributing guide.
  2. Comment on the issue to say you are picking it up — it saves two people doing the same work.
  3. Fork the repository and make your change on a branch.
  4. Open a pull request that references the issue number.

Research direction

Start by reproducing the notebook's "Install dependencies" step after a Colab factory reset, using the newest local colabfold_batch if applicable. Collect the complete ColabFold output and environment details; done means the dependency installation progresses and completes instead of hanging while consuming resources.

Written by the indexing model from the issue text.

Assessment

Tech stack
jupyter-notebook
Domain
bioinformatics
Issue type
Bug
Difficulty
4/5
Estimated time
3-5 days
Activity status
Stale
Clarity
Needs clarification
Newbie friendliness
25/100

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