sokrypton / sokrypton/ColabFold
Error in specific run
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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
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 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