'Directory not empty' Error when running demo

[zehanna]

Hi David,

thank you for developing this really nice tool.

After installing it on a new server, I ran into the following error while trying to run the demo:

Command:
python3 prediction_pipeline.py ../data/prediction_demo/regression_models/ genomes_retrieved.txt species_taxonomic.txt

Error:

multiprocessing.pool.RemoteTraceback: 
"""
Traceback (most recent call last):
  File "/cluster/project/umbiol/software/miniconda3/envs/ogt_pred_env/lib/python3.13/multiprocessing/pool.py", line 125, in worker
    result = (True, func(*args, **kwds))
                    ~~~~^^^^^^^^^^^^^^^
  File "/cluster/project/umbiol/software/miniconda3/envs/ogt_pred_env/lib/python3.13/multiprocessing/pool.py", line 48, in mapstar
    return list(map(*args))
  File "/cluster/project/umbiol/software/OGT_prediction/prediction/genome_analysis.py", line 62, in features_per_genome
    external_tools.cleanup((genome_file,species))
    ~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^
  File "/cluster/project/umbiol/software/OGT_prediction/prediction/external_tools.py", line 78, in cleanup
    shutil.rmtree('./output/genomes/'+species+'/'+folder)
    ~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/cluster/project/umbiol/software/miniconda3/envs/ogt_pred_env/lib/python3.13/shutil.py", line 763, in rmtree
    _rmtree_safe_fd(stack, onexc)
    ~~~~~~~~~~~~~~~^^^^^^^^^^^^^^
  File "/cluster/project/umbiol/software/miniconda3/envs/ogt_pred_env/lib/python3.13/shutil.py", line 707, in _rmtree_safe_fd
    onexc(func, path, err)
    ~~~~~^^^^^^^^^^^^^^^^^
  File "/cluster/project/umbiol/software/miniconda3/envs/ogt_pred_env/lib/python3.13/shutil.py", line 658, in _rmtree_safe_fd
    os.rmdir(name, dir_fd=dirfd)
    ~~~~~~~~^^^^^^^^^^^^^^^^^^^^
OSError: [Errno 39] Directory not empty: './output/genomes/thermocrinis_ruber/Thermocrinis_ruber_ASM51273v1_dna_toplevel/barrnap'
"""

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

Traceback (most recent call last):
  File "/cluster/project/umbiol/software/OGT_prediction/prediction/prediction_pipeline.py", line 84, in <module>
    genome_features = genome_analysis.many_genomes(to_analyze)
  File "/cluster/project/umbiol/software/OGT_prediction/prediction/genome_analysis.py", line 83, in many_genomes
    results = p.map(features_per_genome, to_analyze)
  File "/cluster/project/umbiol/software/miniconda3/envs/ogt_pred_env/lib/python3.13/multiprocessing/pool.py", line 367, in map
    return self._map_async(func, iterable, mapstar, chunksize).get()
           ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^
  File "/cluster/project/umbiol/software/miniconda3/envs/ogt_pred_env/lib/python3.13/multiprocessing/pool.py", line 774, in get
    raise self._value
OSError: [Errno 39] Directory not empty: './output/genomes/thermocrinis_ruber/Thermocrinis_ruber_ASM51273v1_dna_toplevel/barrnap'

It seems there is an error in the pool.py script (because the target directory is indeed empty).
Could you maybe look into it?

Thanks a lot in advance,

Hanna