Comments (4)
Hi Rafal,
Sorry this error occurred I suppose you created feature pickles using mmseqs2? Previous version of mmseqs2 could lead to this error in some cases so I recently pushed a fix to the main branch. Could you pull the changes from the main branch and rerun the feature creation jobs using updated mmseqs2? Detailed discussions can be found in this issue: #233
Hope it helps.
Yours
Dingquan
from alphapulldown.
Hi,
Just checking if it works now?
Yours
Dingquan
from alphapulldown.
Dear Dingquan,
I encountered this same issue installing AlphaPulldown from pip:
python3 -m pip install alphapulldown==1.0.4
Has this latest fix been propagated to the pip manager?
Alternatively can I have instructions to build Alphapulldown from the GitHub repo?
Many thanks,
Daniel
from alphapulldown.
Hi @dvbrown
Sorry the fixed version hasn't been released to pip yet but I have published a pre-release version which has this issue fixed on testpypi. Would you mind trying it here:
pip uninstall alphapulldown
pip install --index-url https://test.pypi.org/simple/ --extra-index-url https://pypi.org/simple/ alphapulldown==2.0.0b1
I suppose you generated features via mmseqs2? Then I'm afraid you have to rerun it after installing this pre-released version. An official new release will be published to pypi after testing soon this week.
Yours
Dingquan
from alphapulldown.
Related Issues (20)
- Multiple feature directories HOT 2
- Improve resume predictions HOT 1
- GPU seems not working when run_multimer_jobs.py HOT 5
- Runtime of each prediction HOT 1
- Use DEFINE_list for model_names flag HOT 3
- Clean duplicating functions/ redundant code
- 'ranking_confidence' is not in the result.pkl file after the update HOT 10
- create_indvidual_features.py HOT 3
- Merging individual monomer MSAs for multimer prediction HOT 3
- Problem with MSA for Q6DI86 HOT 2
- rename_colab_search_a3m.py does something unintended HOT 4
- output jupyter notebook is empty HOT 2
- Computing MSA takes long time
- jax error when create_notebook.py is run HOT 4
- create_notebook doesn't work on AlphaPulldown 2.0b? HOT 8
- Remove result pickles HOT 1
- question: correct pipeline for mmseqs alignments in alphapulldown?
- Move Databases download to a common installation step for both snakamake and Python CLI modes? HOT 1
- jax installation version issue HOT 1
- use_mmseqs2=True is no longer possible in 2.0.0b4
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