sokrypton / sokrypton/ColabFold
Immediate crash upon running ColabFold's AF2 w/ MMseqs2
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Description
Below are the error messages that result, centering on import errors in loading the different parts of the Colab. Perhaps there's updating of AF2 to 2.1.1? Thx, FB
ImportError Traceback (most recent call last)
in ()
5 from colabfold.download import download_alphafold_params, default_data_dir
6 from colabfold.utils import setup_logging
----> 7 from colabfold.batch import get_queries, run, set_model_type
8
9 from colabfold.colabfold import plot_protein
9 frames
/usr/local/lib/python3.7/dist-packages/colabfold/batch.py in ()
41 )
42 from alphafold.data.tools import hhsearch
---> 43 from alphafold.model import model
44
45 from colabfold.alphafold.models import load_models_and_params
/usr/local/lib/python3.7/dist-packages/alphafold/model/model.py in ()
18 from absl import logging
19 from alphafold.common import confidence
---> 20 from alphafold.model import features
21 from alphafold.model import modules
22 from alphafold.model import modules_multimer
/usr/local/lib/python3.7/dist-packages/alphafold/model/features.py in ()
17 from typing import List, Mapping, Tuple
18
---> 19 from alphafold.model.tf import input_pipeline
20 from alphafold.model.tf import proteins_dataset
21
/usr/local/lib/python3.7/dist-packages/alphafold/model/tf/input_pipeline.py in ()
15 """Feature pre-processing input pipeline for AlphaFold."""
16
---> 17 from alphafold.model.tf import data_transforms
18 from alphafold.model.tf import shape_placeholders
19 import tensorflow.compat.v1 as tf
/usr/local/lib/python3.7/dist-packages/alphafold/model/tf/data_transforms.py in ()
16
17 from alphafold.common import residue_constants
---> 18 from alphafold.model.tf import shape_helpers
19 from alphafold.model.tf import shape_placeholders
20 from alphafold.model.tf import utils
/usr/local/lib/python3.7/dist-packages/alphafold/model/tf/shape_helpers.py in ()
14
15 """Utilities for dealing with shapes of TensorFlow tensors."""
---> 16 import tensorflow.compat.v1 as tf
17
18
/usr/local/lib/python3.7/dist-packages/tensorflow/init.py in ()
35 import typing as _typing
36
---> 37 from tensorflow.python.tools import module_util as _module_util
38 from tensorflow.python.util.lazy_loader import LazyLoader as _LazyLoader
39
/usr/local/lib/python3.7/dist-packages/tensorflow/python/init.py in ()
35
36 from tensorflow.python import pywrap_tensorflow as _pywrap_tensorflow
---> 37 from tensorflow.python.eager import context
38
39 # pylint: enable=wildcard-import
/usr/local/lib/python3.7/dist-packages/tensorflow/python/eager/context.py in ()
33 from tensorflow.python import pywrap_tfe
34 from tensorflow.python import tf2
---> 35 from tensorflow.python.client import pywrap_tf_session
36 from tensorflow.python.eager import executor
37 from tensorflow.python.eager import monitoring
/usr/local/lib/python3.7/dist-packages/tensorflow/python/client/pywrap_tf_session.py in ()
17 # pylint: disable=invalid-import-order,g-bad-import-order, wildcard-import, unused-import
18 from tensorflow.python import pywrap_tensorflow
---> 19 from tensorflow.python.client._pywrap_tf_session import *
20 from tensorflow.python.client._pywrap_tf_session import _TF_SetTarget
21 from tensorflow.python.client._pywrap_tf_session import _TF_SetConfig
ImportError: SystemError: <built-in method contains of dict object at 0x7ffa9203aeb0> returned a result with an error set
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 Colab import failure at from colabfold.batch import get_queries, run, set_model_type and follow the traceback through alphafold.model and TensorFlow. Check the installed ColabFold, AlphaFold, and TensorFlow versions in the notebook; done means the notebook imports successfully and can run the AF2 with MMseqs2 workflow.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- jupyter-notebook, python, tensorflow
- 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