Get error in MSA process and find StopIteration error

[233xzl]

Hi, when i`m trying to predict structure of protein sequence YPGKRDEYTR, it stoped after Hmmbuild and i dont know why.

Processing chain A
I0107 10:48:16.433073 140348520649856 pipeline.py:40] Getting protein MSAs for sequence YPGKRDEYTR
I0107 10:48:16.442079 140342601832000 jackhmmer.py:78] Query sequence: YPGKRDEYTR
I0107 10:48:16.442653 140342601832000 subprocess_utils.py:68] Launching subprocess "/hmmer/bin/jackhmmer -o /dev/null -A /tmp/tmpxshlimqm/output.sto --noali --F1 0.0005 --F2 5e-05 --F3 5e-07 --cpu 8 -N 1 -E 0.0001 --incE 0.0001 /tmp/tmpxshlimqm/query.fasta /root/public_databases/uniref90_2022_05.fa"
I0107 10:48:16.443206 140342593439296 jackhmmer.py:78] Query sequence: YPGKRDEYTR
I0107 10:48:16.443528 140342593439296 subprocess_utils.py:68] Launching subprocess "/hmmer/bin/jackhmmer -o /dev/null -A /tmp/tmpomhb2cdy/output.sto --noali --F1 0.0005 --F2 5e-05 --F3 5e-07 --cpu 8 -N 1 -E 0.0001 --incE 0.0001 /tmp/tmpomhb2cdy/query.fasta /root/public_databases/mgy_clusters_2022_05.fa"
I0107 10:48:16.443967 140342585046592 jackhmmer.py:78] Query sequence: YPGKRDEYTR
I0107 10:48:16.444274 140342585046592 subprocess_utils.py:68] Launching subprocess "/hmmer/bin/jackhmmer -o /dev/null -A /tmp/tmpbljt598r/output.sto --noali --F1 0.0005 --F2 5e-05 --F3 5e-07 --cpu 8 -N 1 -E 0.0001 --incE 0.0001 /tmp/tmpbljt598r/query.fasta /root/public_databases/bfd-first_non_consensus_sequences.fasta"
I0107 10:48:16.444640 140342576653888 jackhmmer.py:78] Query sequence: YPGKRDEYTR
I0107 10:48:16.444914 140342576653888 subprocess_utils.py:68] Launching subprocess "/hmmer/bin/jackhmmer -o /dev/null -A /tmp/tmpixho4k20/output.sto --noali --F1 0.0005 --F2 5e-05 --F3 5e-07 --cpu 8 -N 1 -E 0.0001 --incE 0.0001 /tmp/tmpixho4k20/query.fasta /root/public_databases/uniprot_all_2021_04.fa"
I0107 10:49:25.173050 140342585046592 subprocess_utils.py:97] Finished Jackhmmer in 68.729 seconds
I0107 10:53:01.553389 140342601832000 subprocess_utils.py:97] Finished Jackhmmer in 285.111 seconds
I0107 10:55:09.169230 140342576653888 subprocess_utils.py:97] Finished Jackhmmer in 412.724 seconds
I0107 10:55:53.378418 140342593439296 subprocess_utils.py:97] Finished Jackhmmer in 456.935 seconds
I0107 10:55:53.379953 140348520649856 pipeline.py:73] Getting protein MSAs took 456.95 seconds for sequence YPGKRDEYTR
I0107 10:55:53.380220 140348520649856 pipeline.py:79] Deduplicating MSAs and getting protein templates for sequence YPGKRDEYTR
I0107 10:55:53.382555 140342593439296 subprocess_utils.py:68] Launching subprocess "/hmmer/bin/hmmbuild --informat stockholm --hand --amino /tmp/tmp8kivu13d/output.hmm /tmp/tmp8kivu13d/query.msa"
I0107 10:55:53.392291 140342593439296 subprocess_utils.py:97] Finished Hmmbuild in 0.010 seconds
I0107 10:55:53.392671 140342593439296 subprocess_utils.py:68] Launching subprocess "/hmmer/bin/hmmsearch --noali --cpu 8 --F1 0.1 --F2 0.1 --F3 0.1 -E 100 --incE 100 --domE 100 --incdomE 100 -A /tmp/tmphv4lr89t/output.sto /tmp/tmphv4lr89t/query.hmm /root/public_databases/pdb_seqres_2022_09_28.fasta"
I0107 10:55:54.745479 140342593439296 subprocess_utils.py:97] Finished Hmmsearch in 1.353 seconds
Traceback (most recent call last):
  File "/app/alphafold/run_alphafold.py", line 699, in <module>
    app.run(main)
  File "/alphafold3_venv/lib/python3.11/site-packages/absl/app.py", line 308, in run
    _run_main(main, args)
  File "/alphafold3_venv/lib/python3.11/site-packages/absl/app.py", line 254, in _run_main
    sys.exit(main(argv))
             ^^^^^^^^^^
  File "/app/alphafold/run_alphafold.py", line 684, in main
    process_fold_input(
  File "/app/alphafold/run_alphafold.py", line 543, in process_fold_input
    fold_input = pipeline.DataPipeline(data_pipeline_config).process(fold_input)
                 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/alphafold3_venv/lib/python3.11/site-packages/alphafold3/data/pipeline.py", line 462, in process
    processed_chains.append(self.process_protein_chain(chain))
                            ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/alphafold3_venv/lib/python3.11/site-packages/alphafold3/data/pipeline.py", line 411, in process_protein_chain
    unpaired_msa, paired_msa, template_hits = _get_protein_msa_and_templates(
                                              ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/alphafold3_venv/lib/python3.11/site-packages/alphafold3/data/pipeline.py", line 107, in _get_protein_msa_and_templates
    protein_templates = templates_future.result()
                        ^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/usr/lib/python3.11/concurrent/futures/_base.py", line 449, in result
    return self.__get_result()
           ^^^^^^^^^^^^^^^^^^^
  File "/usr/lib/python3.11/concurrent/futures/_base.py", line 401, in __get_result
    raise self._exception
  File "/usr/lib/python3.11/concurrent/futures/thread.py", line 58, in run
    result = self.fn(*self.args, **self.kwargs)
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/alphafold3_venv/lib/python3.11/site-packages/alphafold3/data/templates.py", line 372, in from_seq_and_a3m
    hmmsearch_a3m = run_hmmsearch_with_a3m(
                    ^^^^^^^^^^^^^^^^^^^^^^^
  File "/alphafold3_venv/lib/python3.11/site-packages/alphafold3/data/templates.py", line 888, in run_hmmsearch_with_a3m
    return searcher.query_with_sto(sto, model_construction='hand')
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/alphafold3_venv/lib/python3.11/site-packages/alphafold3/data/tools/hmmsearch.py", line 149, in query_with_sto
    return self.query_with_hmm(hmm)
           ^^^^^^^^^^^^^^^^^^^^^^^^
  File "/alphafold3_venv/lib/python3.11/site-packages/alphafold3/data/tools/hmmsearch.py", line 128, in query_with_hmm
    a3m_out = parsers.convert_stockholm_to_a3m(
              ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/alphafold3_venv/lib/python3.11/site-packages/alphafold3/data/parsers.py", line 154, in convert_stockholm_to_a3m
    query_sequence = next(iter(sequences.values()))
                     ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
StopIteration

[Augustin-Zidek]

Could you post the full input JSON? Could you also update to the latest commit (in particular f22873d should make the log messages a bit more verbose and helpful).

[zhangyumeng1sjtu]

I met a similar problem when running MSA of a short peptide. I guess the variable sequences (File "alphafold3/data/parsers.py" line 154) was an empty dictionary here because no sequence was in the MSA output.