Recursion Depth Exceeded

[smf2qp09]

Here is the error message that I got.

--- Starting Targeted Test for: 173.12.faa ---
Generating reconstruction....
Reconstruction generating with the following command line:
python -m reconstructor --input_file [/Users/smf2qp/Documents/Leptospirosis/Lepto_Genomes/173.12.faa](https://file+.vscode-resource.vscode-cdn.net/Users/smf2qp/Documents/Leptospirosis/Lepto_Genomes/173.12.faa) --file_type 1 --media 'cpd00001_e','cpd26486_e','cpd04877_e','cpd30726_e','cpd26493_e','cpd26499_e','cpd00100_e','cpd13392_e','cpd01826_e','cpd09464_e','cpd26146_e','cpd19148_e','cpd19118_e','cpd00305_e','cpd00029_e','cpd00211_e','cpd01113_e','cpd03846_e','cpd01107_e','cpd15643_e','cpd01741_e','cpd03847_e','cpd00214_e','cpd24916_e','cpd01080_e','cpd00536_e','cpd01122_e','cpd03850_e' --org default --min_frac 0.01 --max_frac 0.5 --gram negative --out 173.12 --name 173.12 --cpu 6 --gapfill yes --test no

Using Gram negative objective function
Using minimum objective flux fraction of 0.01 and maximum fraction of 0.5
Using 6 processor(s)

Loading GENRE construction databases...
[-----------------------------------------]
Aligning peptide sequences to KEGG database, may take some time...
Blast results will be saved to [/Users/smf2qp/Documents/Leptospirosis/Lepto_Genomes/173.12.KEGGprot.out](https://file+.vscode-resource.vscode-cdn.net/Users/smf2qp/Documents/Leptospirosis/Lepto_Genomes/173.12.KEGGprot.out) 

blasting [/Users/smf2qp/Documents/Leptospirosis/Lepto_Genomes/173.12.faa](https://file+.vscode-resource.vscode-cdn.net/Users/smf2qp/Documents/Leptospirosis/Lepto_Genomes/173.12.faa) vs [/Users/smf2qp/Documents/Leptospirosis/.venv/lib/python3.14/site-packages/reconstructor/resources/screened_kegg_prokaryotes_pep_db.dmnd](https://file+.vscode-resource.vscode-cdn.net/Users/smf2qp/Documents/Leptospirosis/.venv/lib/python3.14/site-packages/reconstructor/resources/screened_kegg_prokaryotes_pep_db.dmnd)
finished blast
Creating draft GENRE from BLAST results...
Traceback (most recent call last):
  File "<frozen runpy>", line 198, in _run_module_as_main
  File "<frozen runpy>", line 88, in _run_code
  File "/Users/smf2qp/Documents/Leptospirosis/.venv/lib/python3.14/site-packages/reconstructor/__main__.py", line 242, in <module>
    draft_genre = create_model(rxns, universal, new_id)
  File "/Users/smf2qp/Documents/Leptospirosis/.venv/lib/python3.14/site-packages/reconstructor/_funcs.py", line 90, in create_model
    new_model.add_reactions([rxn.copy()])
........
File "/Library/Frameworks/Python.framework/Versions/3.14/lib/python3.14/copy.py", line 138, in deepcopy
    y = copier(memo)
  File "/Users/smf2qp/Documents/Leptospirosis/.venv/lib/python3.14/site-packages/cobra/core/reaction.py", line 273, in __deepcopy__
    cop = deepcopy(super(Reaction, self), memo)
  File "/Library/Frameworks/Python.framework/Versions/3.14/lib/python3.14/copy.py", line 157, in deepcopy
    y = _reconstruct(x, memo, *rv)
  File "/Library/Frameworks/Python.framework/Versions/3.14/lib/python3.14/copy.py", line 234, in _reconstruct
    y = func(*args)
  File "/Library/Frameworks/Python.framework/Versions/3.14/lib/python3.14/copy.py", line 233, in <genexpr>
    args = (deepcopy(arg, memo) for arg in args)
            ~~~~~~~~^^^^^^^^^^^
RecursionError: maximum recursion depth exceeded
--- Success! Created model for 173.12 ---
Back in original directory: [/Users/smf2qp/Documents/Leptospirosis](https://file+.vscode-resource.vscode-cdn.net/Users/smf2qp/Documents/Leptospirosis)

Version of reconstructor: 1.2.0
Version of python: 3.14.3
Version of cobra: 0.31.1 and 0.29.1

173.12.faa.zip