crash exit when the custom database finds no hits (bug report)

[cpterfan]

Hi,

I found a little bug when using a custom database for phold.
I was using the following script:

phold run \
  --input $IN_FILE \
  --output $OUT_DIR/${FILENAME::-4} \
  --database $DATABASE \
  --custom_db $RDRP_DB \
  --finetune \
  --foldseek_gpu \
  --threads 4 \
  --force

If there is no hit in the custom database, phold would exit with the following error (complete error log attached):

.
.
.
2026-02-11 09:48:32.947 | INFO     | phold.results.topfunction:get_topcustom_hits:559 - Processing Foldseek output
2026-02-11 09:48:32.949 | WARNING  | phold.results.topfunction:get_topcustom_hits:585 - Foldseek found no custom hits whatsoever - please check your custom database and input.
2026-02-11 09:48:32.949 | WARNING  | phold.results.topfunction:get_topcustom_hits:588 - Phold will continue using only the default databases.
Traceback (most recent call last):
  File "/home/viro/erfan.khamespanah/miniconda3/envs/phold_122/bin/phold", line 10, in <module>
    sys.exit(main())
             ~~~~^^
  File "/home/viro/erfan.khamespanah/miniconda3/envs/phold_122/lib/python3.13/site-packages/phold/__init__.py", line 1714, in main
    main_cli()
    ~~~~~~~~^^
  File "/home/viro/erfan.khamespanah/miniconda3/envs/phold_122/lib/python3.13/site-packages/click/core.py", line 1485, in __call__
    return self.main(*args, **kwargs)
           ~~~~~~~~~^^^^^^^^^^^^^^^^^
  File "/home/viro/erfan.khamespanah/miniconda3/envs/phold_122/lib/python3.13/site-packages/click/core.py", line 1406, in main
    rv = self.invoke(ctx)
  File "/home/viro/erfan.khamespanah/miniconda3/envs/phold_122/lib/python3.13/site-packages/click/core.py", line 1873, in invoke
    return _process_result(sub_ctx.command.invoke(sub_ctx))
                           ~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^
  File "/home/viro/erfan.khamespanah/miniconda3/envs/phold_122/lib/python3.13/site-packages/click/core.py", line 1269, in invoke
    return ctx.invoke(self.callback, **ctx.params)
           ~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/viro/erfan.khamespanah/miniconda3/envs/phold_122/lib/python3.13/site-packages/click/core.py", line 824, in invoke
    return callback(*args, **kwargs)
  File "/home/viro/erfan.khamespanah/miniconda3/envs/phold_122/lib/python3.13/site-packages/click/decorators.py", line 34, in new_func
    return f(get_current_context(), *args, **kwargs)
  File "/home/viro/erfan.khamespanah/miniconda3/envs/phold_122/lib/python3.13/site-packages/phold/__init__.py", line 395, in run
    subcommand_compare(
    ~~~~~~~~~~~~~~~~~~^
        gb_dict,
        ^^^^^^^^
    ...<21 lines>...
        restart=restart
        ^^^^^^^^^^^^^^^
    )
    ^
  File "/home/viro/erfan.khamespanah/miniconda3/envs/phold_122/lib/python3.13/site-packages/phold/subcommands/compare.py", line 575, in subcommand_compare
    tophit_custom_df = get_topcustom_hits(
        result_tsv_custom, structures, proteins_flag
    )
  File "/home/viro/erfan.khamespanah/miniconda3/envs/phold_122/lib/python3.13/site-packages/phold/results/topfunction.py", line 596, in get_topcustom_hits
    foldseek_df[["contig_id", "cds_id"]] = foldseek_df["query"].str.split(
    ~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/viro/erfan.khamespanah/miniconda3/envs/phold_122/lib/python3.13/site-packages/pandas/core/frame.py", line 4660, in __setitem__
    self._setitem_array(key, value)
    ~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^
  File "/home/viro/erfan.khamespanah/miniconda3/envs/phold_122/lib/python3.13/site-packages/pandas/core/frame.py", line 4699, in _setitem_array
    check_key_length(self.columns, key, value)
    ~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/viro/erfan.khamespanah/miniconda3/envs/phold_122/lib/python3.13/site-packages/pandas/core/indexers/utils.py", line 392, in check_key_length
    raise ValueError("Columns must be same length as key")
ValueError: Columns must be same length as key

err_phold_33838186_4.log

Hope this error can be handled more gracefully in the upcoming updates 😃

Thank you so much for this tool.

Best regards,
Erfan