Workflow running from CLI, but not being reflected in the GUI

[subCode321]

I have made an "experiment.yaml" as the settings file, and the python file is as follows for running the workflow

import yaml
import os
from alphapept.settings import load_settings
import alphapept.interface

# Define the settings file
YAML_FILE = "experiment.yaml"

def check_required_keys(settings, required_keys):
    """Check if required keys exist in the YAML settings."""
    missing_keys = [key for key in required_keys if key not in settings.get('experiment', {})]
    if missing_keys:
        raise KeyError(f"Missing required keys in 'experiment': {missing_keys}")

def main():
    """Main function to run AlphaPept workflow."""
    if not os.path.exists(YAML_FILE):
        raise FileNotFoundError(f"Settings file '{YAML_FILE}' not found!")

    # Load YAML manually to check required fields
    with open(YAML_FILE, "r") as f:
        settings_dict = yaml.safe_load(f)
    
    # Define required keys
    required_keys = ['sample_group', 'fraction']
    check_required_keys(settings_dict, required_keys)

    # Load settings using AlphaPept's built-in function
    settings = load_settings(YAML_FILE)

    # Run complete workflow
    print("Running AlphaPept workflow...")
    alphapept.interface.run_complete_workflow(settings)
    print("Workflow completed successfully.")

if __name__ == "__main__":
    try:
        main()
    except Exception as e:
        print(f"Error: {e}")

now when I run this, I get workflow completed successfully, but this isn't reflected in the GUI.

2025-03-08 17:08:03> ==== quantification ====
2025-03-08 17:08:03> No results.hdf present.
2025-03-08 17:08:03> No Proteins found.
2025-03-08 17:08:03> ==== export ====
2025-03-08 17:08:03> Settings saved to C:/Users/Soubhagya/Downloads/testalphapept/.yaml
2025-03-08 17:08:03> Analysis complete.
Workflow completed successfully. --> 

this is the output. This happens when the path of the results files is a directory which contains results.hdf

Now I do have a results.hdf file from the previous workflow runs, but that is resulting in an error if I give the absolute path to the results.hdf file

Can anyone help me with this? Thank you!