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kalininalab / alphafold_non_docker

AlphaFold2 non-docker setup
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Error while running Alphafold without docker #32

Closed skhatri007 closed 2 months ago

skhatri007 commented 2 years ago

Hi all, I am facing the below error while running alphafold. File "/mnt/Alphafold/No_doc/alphafold/run_alphafold.py", line 427, in app.run(main) File "/home/skhatri/anaconda3/envs/alphafold/lib/python3.8/site-packages/absl/app.py", line 312, in run _run_main(main, args) File "/home/skhatri/anaconda3/envs/alphafold/lib/python3.8/site-packages/absl/app.py", line 258, in _run_main sys.exit(main(argv)) File "/mnt/Alphafold/No_doc/alphafold/run_alphafold.py", line 403, in main predict_structure( File "/mnt/Alphafold/No_doc/alphafold/run_alphafold.py", line 166, in predict_structure feature_dict = data_pipeline.process( File "/mnt/Alphafold/No_doc/alphafold/alphafold/data/pipeline_multimer.py", line 266, in process chain_features = self._process_single_chain( File "/mnt/Alphafold/No_doc/alphafold/alphafold/data/pipeline_multimer.py", line 212, in _process_single_chain chain_features = self._monomer_data_pipeline.process( File "/mnt/Alphafold/No_doc/alphafold/alphafold/data/pipeline.py", line 170, in process msa_for_templates = parsers.deduplicate_stockholm_msa( File "/mnt/Alphafold/No_doc/alphafold/alphafold/data/parsers.py", line 350, in deduplicate_stockholm_msa query_align = next(iter(sequence_dict.values())) StopIteration I don't understand where the issue is, as it runs fine with other sequences in alphafold multimer . I use the default input method for multimer . Please help!

Old-Shatterhand commented 1 year ago

Hi @skatri,

could you provide us with the input? Then, we can reproduce the issue. Anyways, it seems to be an issue in the AlphaFold-code.

Best, Roman

Old-Shatterhand commented 2 months ago

I'll close it for now, if it's still a problem, we can reopen it at at a later point.

skhatri007 commented 2 months ago

Hi , Sorry for late reply. The problem has been solved. Thanks for your help.

Regards Shantanu Khatri, PhD Scholar (CSIR-SRF) C/o- Dr.Lipi Thukral Senior Scientist

Computational and Structural Biology Group(CSB) CSIR-IGIB, Mathura road New Delhi-110025

On Fri, 12 Apr 2024 at 8:17 PM, Roman Joeres @.***> wrote:

I'll close it for now, if it's still a problem, we can reopen it at at a later point.

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