[2024-03-13 13:26:05] cli.predict_function INFO: Starting Metagenomic-DeepFRI.
[2024-03-13 13:26:05] pipeline.predict_protein_function INFO: DeepFRI protein sequence limit: 60-1000
[2024-03-13 13:26:05] pipeline.predict_protein_function INFO: EC number prediction is not supported in version 1.1.
[2024-03-13 13:26:05] pipeline.predict_protein_function INFO: Creating PDB100 database. This may take a bit during a first run.
[2024-03-13 13:26:05] pipeline.predict_protein_function INFO: PDB100 database created.
[2024-03-13 13:26:05] database.build_database INFO: Building MMSeqs2 database from /TomaszLab/Lukasz/foldcomp_database/afdb_swissprot_v4
[2024-03-13 13:26:05] database.build_database INFO: Found /TomaszLab/Lukasz/foldcomp_database/afdb_swissprot_v4.fasta.gz in /TomaszLab/Lukasz/foldcomp_database
[2024-03-13 13:26:05] database.build_database INFO: Skipping extraction of FASTA file from FoldComp database.
[2024-03-13 13:26:05] database.build_database INFO: Database created at /TomaszLab/Lukasz/foldcomp_database
[2024-03-13 13:26:05] database.build_database INFO: Found /TomaszLab/Lukasz/foldcomp_database/afdb_swissprot_v4.mmseqsDB in /TomaszLab/Lukasz/foldcomp_database
[2024-03-13 13:26:05] database.build_database INFO: Skipping creation of MMSeqs2 database.
[2024-03-13 13:26:05] pipeline.predict_protein_function INFO: Aligning 2977 sequences against python3
[2024-03-13 13:26:57] mmseqs.filter_mmseqs_results INFO: 2030 pairs after filtering with k=5 best hits.
[2024-03-13 13:26:59] pipeline.predict_protein_function INFO: Aligned 313 sequences.
[2024-03-13 13:26:59] pipeline.predict_protein_function INFO: Aligning 2977 sequences against afdb_swissprot_v4
/TomaszLab/Lukasz/y/envs/deepfri/lib/python3.11/site-packages/numpy/lib/npyio.py:2539: UserWarning: genfromtxt: Empty input file: "/TomaszLab/Lukasz/mDF_output/afdb_swissprot_v4.search_results.tsv"
  output = genfromtxt(fname, **kwargs)
[2024-03-13 13:27:04] pipeline.predict_protein_function INFO: No alignments found for afdb_swissprot_v4
[2024-03-13 13:27:04] pipeline.predict_protein_function INFO: Aligned 0 sequences.
[2024-03-13 13:27:04] pipeline.predict_protein_function INFO: Aligning contact maps for 313 proteins against python3
Skipping entry 2d7d_A which is not in the database.
Skipping entry 2d7d_A.pdb which is not in the database.
Skipping entry 6ovt_A which is not in the database.
Skipping entry 6ovt_A.pdb which is not in the database.
Skipping entry 3zuk_A which is not in the database.
Skipping entry 3zuk_A.pdb which is not in the database.
Skipping entry 4a1o_B which is not in the database.
Skipping entry 4a1o_B.pdb which is not in the database.
multiprocessing.pool.RemoteTraceback: 
"""
Traceback (most recent call last):
  File "/TomaszLab/Lukasz/y/envs/deepfri/lib/python3.11/multiprocessing/pool.py", line 125, in worker
    result = (True, func(*args, **kwds))
                    ^^^^^^^^^^^^^^^^^^^
  File "/TomaszLab/Lukasz/y/envs/deepfri/lib/python3.11/multiprocessing/pool.py", line 48, in mapstar
    return list(map(*args))
           ^^^^^^^^^^^^^^^^
  File "/TomaszLab/Lukasz/y/envs/deepfri/lib/python3.11/site-packages/mDeepFRI/bio_utils.py", line 405, in retrieve_align_contact_map
    coordinates = retrieve_structure_features(idx, database_path=database)[1]
                  ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/TomaszLab/Lukasz/y/envs/deepfri/lib/python3.11/site-packages/mDeepFRI/bio_utils.py", line 266, in retrieve_structure_features
    residues, coords = extract_residues_coordinates(structure, chain=chain)
                                                    ^^^^^^^^^
UnboundLocalError: cannot access local variable 'structure' where it is not associated with a value
"""

The above exception was the direct cause of the following exception:

Traceback (most recent call last):
  File "/TomaszLab/Lukasz/y/envs/deepfri/bin/mDeepFRI", line 8, in <module>
    sys.exit(main())
             ^^^^^^
  File "/TomaszLab/Lukasz/y/envs/deepfri/lib/python3.11/site-packages/click/core.py", line 1157, in __call__
    return self.main(*args, **kwargs)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/TomaszLab/Lukasz/y/envs/deepfri/lib/python3.11/site-packages/click/core.py", line 1078, in main
    rv = self.invoke(ctx)
         ^^^^^^^^^^^^^^^^
  File "/TomaszLab/Lukasz/y/envs/deepfri/lib/python3.11/site-packages/click/core.py", line 1688, in invoke
    return _process_result(sub_ctx.command.invoke(sub_ctx))
                           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/TomaszLab/Lukasz/y/envs/deepfri/lib/python3.11/site-packages/click/core.py", line 1434, in invoke
    return ctx.invoke(self.callback, **ctx.params)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/TomaszLab/Lukasz/y/envs/deepfri/lib/python3.11/site-packages/click/core.py", line 783, in invoke
    return __callback(*args, **kwargs)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/TomaszLab/Lukasz/y/envs/deepfri/lib/python3.11/site-packages/click/decorators.py", line 33, in new_func
    return f(get_current_context(), *args, **kwargs)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/TomaszLab/Lukasz/y/envs/deepfri/lib/python3.11/site-packages/mDeepFRI/cli.py", line 185, in predict_function
    predict_protein_function(
  File "/TomaszLab/Lukasz/y/envs/deepfri/lib/python3.11/site-packages/mDeepFRI/pipeline.py", line 155, in predict_protein_function
    partial_cmaps = p.map(partial_align, db_alignments)
                    ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/TomaszLab/Lukasz/y/envs/deepfri/lib/python3.11/multiprocessing/pool.py", line 367, in map
    return self._map_async(func, iterable, mapstar, chunksize).get()
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/TomaszLab/Lukasz/y/envs/deepfri/lib/python3.11/multiprocessing/pool.py", line 774, in get
    raise self._value
UnboundLocalError: cannot access local variable 'structure' where it is not associated with a value