caretta needs to be run outside of the input folder

[fjell-dev]

Hi, I'm trying caretta for the first time and I ran into an error AssertionError: Could not understand input caretta_results using the PDB files obtained from ColabFold as well as the ones downloaded from PDB. The command was caretta-cli . -t 8 The whole traceback is:

Traceback (most recent call last):

  File "/home/gsn/mambaforge/envs/caretta/bin/caretta-cli", line 127, in <module>
    app()

  File "/home/gsn/mambaforge/envs/caretta/bin/caretta-cli", line 108, in align
    multiple_alignment.align_from_structure_files(

  File "/home/gsn/mambaforge/envs/caretta/lib/python3.9/site-packages/caretta/multiple_alignment.py", line 476, in align_from_structure_files
    pdb_files = helper.parse_protein_files_and_clean(input_files, output_files.cleaned_pdb_folder)

  File "/home/gsn/mambaforge/envs/caretta/lib/python3.9/site-packages/caretta/helper.py", line 166, in parse_protein_files_and_clean
    protein_files = get_structure_files(input_value)

  File "/home/gsn/mambaforge/envs/caretta/lib/python3.9/site-packages/geometricus/protein_utility.py", line 134, in get_structure_files    assert type(protein_file) == str, f"Could not understand input {protein_file}"

AssertionError: Could not understand input caretta_results

Then I realized that when caretta needs to be run outside of the input folder; otherwise it will take the folder caretta_results as input. Maybe it should be mentioned in the document? Thanks.