sokrypton / sokrypton/ColabFold

Error in specific run

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Jupyter Notebook
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Description

I tried to run this sequence in the colab: ILKFPSQSITQTLINKYLSTITETNSILPILKPKRLLPIVEQLFPSNTINKPNSKDFETIFQVFSVTNDQLLNLGFITLCLLILFESLNSTVLIPLRDDEHLQLFNVLFNYLPLLKSNLTTLRFEIEKRSMCNIETLRFISLWKYYQFVMDTSSSSSFVIDYDEDMHMACLLSLNHETQNQSHILTWNFIFKNYCWRHLFLGQLPLLMSEPFTNSTPIIDPLLNNDFELIDFEVNLMKYLQSKDQQLSIDKIIQLIKLLKNKNIEVSQGCLTTPSIINNIMDSLIYRNSMLYLNFYLLLQFETLKNYAKFNEILEDFLELSRETLFFVFSNLANIKFAGHEFTFINKSIVVLQTLVLMLLALYQRSFDSSKRTNDANEISEQTDIHSNNDNSKRIKNKNVIHLIINKIAMLLSDYTKNCKKQNKLIENLIIKIKTISKYIKN:YMEVCKVNFPPKAIIIETLNSESLNNLNIEEFLPIFDKTLLLEFVHNSFPNGDTCPSFSTVDLPLSQLTKLGELTVLLLLLNDSMTLFNKQAINNHVSALMNNLRLIRSQITLINLEYYDQETIKFIAITKFYESLYMHDDHKSSLDEDLSCLLSFQIKDFKLFHFLKKMYYSRHSLLGQSSFMVPAAENLSPIPASIDTNDIPLIANDLKLLETQAKLINILQGVPFYLPVNLTKIESLLETLTMGVSNTVDLYFHDNEVRKEWKDTLNFINTIVYTNFFLFVQNESSLSMAVQHSSNNNKTSNSERCAKDLMKIISNMHIFYSITFNFIFPIKSIKSFSSGNNRFHSNGKEFLFANHFIEILQNFIAITFAIFQRCEVILYDEFYKNLSNEEINVQLLLIHDKILEILKKIEIIVSFLRDEMNSNGSFKSIKGFNKVLNLIKYML

and I expected to get structure of a complex.

Current Behavior

Every time I'm getting another error. the latest error is :
Traceback (most recent call last):
File "/usr/local/lib/python3.7/dist-packages/colabfold/batch.py", line 1042, in run
model_type,
File "/usr/local/lib/python3.7/dist-packages/colabfold/batch.py", line 767, in generate_input_feature
input_feature = process_multimer_features(features_for_chain)
File "/usr/local/lib/python3.7/dist-packages/colabfold/batch.py", line 643, in process_multimer_features
chain_features, chain_id
File "/usr/local/lib/python3.7/dist-packages/alphafold/data/pipeline_multimer.py", line 88, in convert_monomer_features
feature = np.argmax(feature, axis=-1).astype(np.int32)
File "<array_function internals>", line 6, in argmax
File "/usr/local/lib/python3.7/dist-packages/numpy/core/fromnumeric.py", line 1188, in argmax
return _wrapfunc(a, 'argmax', axis=axis, out=out)
File "/usr/local/lib/python3.7/dist-packages/numpy/core/fromnumeric.py", line 58, in _wrapfunc
return bound(*args, **kwds)
ValueError: attempt to get argmax of an empty sequence
2021-12-14 10:16:28,729 Done

Context

this is a coplex that we know that work together and we want to see how it's look.

Your Environment

  • Colab version: AlphaFold2.ipynb

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 with AlphaFold2.ipynb and reproduce the supplied sequence and traceback. Trace the input through colabfold/batch.py around generate_input_feature and process_multimer_features, then determine why an empty feature reaches pipeline_multimer.py:88. Done means the cause is identified and the complex run no longer fails at this step.

Written by the indexing model from the issue text.

Assessment

Tech stack
jupyter-notebook, numpy, python
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

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