sokrypton / sokrypton/ColabFold
Pending. Issue running cell line 331
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Description
Expected Behavior
Colabfold on ChimeraX via Google Colab usually works for me on AF2-Multimer projects. I can download the results easily.
Current Behavior
I am trying to predict the folding of two proteins together. However, currently, I keep getting an output that says that the action in line 331 is pending.
The bottom of the colab window says that it is trying to run cell line 331.
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.
Tried changing the runtime environment on Google Colab and restarting the ChimeraX application
ColabFold Output (for bugs)
Please make sure to also post the complete ColabFold output. You can use gist.github.com for large output.
INFO:main:Starting prediction on 2024-02-28 UTC time
INFO:main:Installing ColabFold on Google Colab virtual machine.
Installing ColabFold
Using Tesla T4 graphics processor
Downloading alphafold2 weights to .: 100%|██████████| 3.82G/3.82G [00:25<00:00, 158MB/s]
2024-02-28 18:02:22,589 Unable to initialize backend 'rocm': NOT_FOUND: Could not find registered platform with name: "rocm". Available platform names are: CUDA
2024-02-28 18:02:22,591 Unable to initialize backend 'tpu': INTERNAL: Failed to open libtpu.so: libtpu.so: cannot open shared object file: No such file or directory
2024-02-28 18:02:26,182 Running on GPU
2024-02-28 18:02:26,391 Found 4 citations for tools or databases
2024-02-28 18:02:26,391 Query 1/1: af510 (length 510)
PENDING: 0%| | 0/300 [elapsed: 00:00 remaining: ?]2024-02-28 18:02:26,940 Sleeping for 7s. Reason: PENDING
PENDING: 0%| | 0/300 [elapsed: 00:08 remaining: ?]2024-02-28 18:02:34,513 Sleeping for 8s. Reason: PENDING
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:
Tried running this on both T4 GPUs and V100 with high RAM
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 reproducing the report in Google Colab after a Factory Reset and inspect the cell at line 331 alongside the supplied ColabFold output. The issue does not name a source file or test, and completion would require identifying why the prediction remains PENDING and documenting or fixing that cause.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- jupyter-notebook
- Domain
- bioinformatics, machine-learning
- Issue type
- Bug
- Difficulty
- 4/5
- Estimated time
- 3-5 days
- Activity status
- Stale
- Clarity
- Needs clarification
- Newbie friendliness
- 25/100