Unrecognized HMM file format

[jackiglar]

Hi,

When I run the MSA creation portion of the AlphaPulldown pipeline (non-Snakemake), I get the following error:

Traceback (most recent call last):
  File "/home/anaconda/24.9.2/envs/AlphaPulldown1/bin/create_individual_features.py", line 449, in <module>
    app.run(main)
  File "/home/anaconda/24.9.2/envs/AlphaPulldown1/lib/python3.11/site-packages/absl/app.py", line 308, in run
    _run_main(main, args)
  File "/home/anaconda/24.9.2/envs/AlphaPulldown1/lib/python3.11/site-packages/absl/app.py", line 254, in _run_main
    sys.exit(main(argv))
             ^^^^^^^^^^
  File "/home/anaconda/24.9.2/envs/AlphaPulldown1/bin/create_individual_features.py", line 440, in main
    process_sequences_individual_mode()
  File "/home/anaconda/24.9.2/envs/AlphaPulldown1/bin/create_individual_features.py", line 369, in process_sequences_individual_mode
    create_and_save_monomer_objects(curr_monomer, pipeline)
  File "/home/anaconda/24.9.2/envs/AlphaPulldown1/bin/create_individual_features.py", line 314, in create_and_save_monomer_objects
    monomer.make_features(
  File "/home/anaconda/24.9.2/envs/AlphaPulldown1/lib/python3.11/site-packages/alphapulldown/objects.py", line 147, in make_features
    self.feature_dict = pipeline.process(
                        ^^^^^^^^^^^^^^^^^
  File "/home/anaconda/24.9.2/envs/AlphaPulldown1/lib/python3.11/site-packages/alphafold/data/pipeline.py", line 215, in process
    hhblits_bfd_uniref_result = run_msa_tool(
                                ^^^^^^^^^^^^^
  File "/home/anaconda/24.9.2/envs/AlphaPulldown1/lib/python3.11/site-packages/alphafold/data/pipeline.py", line 96, in run_msa_tool
    result = msa_runner.query(input_fasta_path)[0]
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/anaconda/24.9.2/envs/AlphaPulldown1/lib/python3.11/site-packages/alphafold/data/tools/hhblits.py", line 143, in query
    raise RuntimeError('HHblits failed\nstdout:\n%s\n\nstderr:\n%s\n' % (
RuntimeError: HHblits failed
stdout:


stderr:
- 18:27:49.295 INFO: Searching 65983866 column state sequences.

- 18:27:51.751 INFO: Searching 36293491 column state sequences.

- 18:27:51.822 INFO: /localhd/16018622/tmpvjyk1frg.fasta is in A2M, A3M or FASTA format

- 18:27:51.823 INFO: Iteration 1

- 18:27:51.913 INFO: Prefiltering database

- 18:29:33.003 INFO: HMMs passed 1st prefilter (gapless profile-profile alignment)  : 1174537

- 18:30:48.434 INFO: HMMs passed 1st prefilter (gapless profile-profile alignment)  : 687814

- 18:30:53.403 INFO: HMMs passed 2nd prefilter (gapped profile-profile alignment)   : 9019

- 18:30:53.403 INFO: HMMs passed 2nd prefilter and not found in previous iterations : 9019

- 18:30:53.403 INFO: Scoring 9019 HMMs using HMM-HMM Viterbi alignment

- 18:30:53.524 INFO: Alternative alignment: 0

- 18:31:01.560 INFO: 2000 alignments done

- 18:31:10.127 INFO: 4000 alignments done

- 18:31:17.516 ERROR: In /opt/conda/conda-bld/hhsuite_1726197675821/work/src/hhdatabase.cpp:443: getTemplateHMM:

- 18:31:17.516 ERROR: 	Unrecognized HMM file format in '106375689'.

- 18:31:17.516 ERROR: 	Context:
'

- 18:31:17.516 ERROR: 

- 18:31:17.516 ERROR: '

Are there any particular steps you would recommend to debug this issue? Thanks for your help!

[DimaMolod]

Hi,
This usually means HHblits ran into a bad database file or a format mismatch (one of the database files is corrupt, incomplete, or was prepared with a different HHsuite version). You can try to re-download or re-de-archive the hhblits databases and make sure all .hhm, .cs219, .ffdata, etc. files are present and not truncated.
If the databases are correct, try running HHblits manually (e.g., hhblits -i test.fasta -d /path/to/db -o out.a3m) to confirm it works outside of the AlphaPulldown pipeline. That should pinpoint whether it’s truly a database issue or a pipeline config error.