nanomofit MT-linker install currently broken :: manual fix available

[EricDeveaud]

Hello,

as of today 19 dec 2025, nanomotif MTAse-linker install fails due to mdmparis/defense-finder#91

25-12-19 09:05:40 | INFO     | Running DefenseFinder version 2.0.0
 2025-12-19 09:05:40 | INFO     | Using the following models:


    sys.exit(cli())
    return self.main(*args, **kwargs)
         ^^^^^^^^^^^^^^^^
  File "/home/gensoft/ML_dependencies/ML_envs/eeebb03d1c26a9b40ee78814fcb4a901_/lib/python3.12/site-packages/click/core.py", line 1659, in invoke
    return _process_result(sub_ctx.command.invoke(sub_ctx))
                           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/gensoft/ML_dependencies/ML_envs/eeebb03d1c26a9b40ee78814fcb4a901_/lib/python3.12/site-packages/click/core.py", line 1395, in invoke
    return ctx.invoke(self.callback, **ctx.params)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/gensoft/ML_dependencies/ML_envs/eeebb03d1c26a9b40ee78814fcb4a901_/lib/python3.12/site-packages/click/core.py", line 754, in invoke
    return __callback(*args, **kwargs)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/gensoft/ML_dependencies/ML_envs/eeebb03d1c26a9b40ee78814fcb4a901_/lib/python3.12/site-packages/defense_finder_cli/main.py", line 221, in run
    defense_finder.run(protein_file_name, dbtype, workers, coverage, adf,adf_only, tmp_dir, models_dir, no_cut_ga, loglevel, index_dir, models_main_ver)
  File "/home/gensoft/ML_dependencies/ML_envs/eeebb03d1c26a9b40ee78814fcb4a901_/lib/python3.12/site-packages/defense_finder/__init__.py", line 47, in run
    macsyfinder.main(args=msf_cmd)
  File "/home/gensoft/ML_dependencies/ML_envs/eeebb03d1c26a9b40ee78814fcb4a901_/lib/python3.12/site-packages/macsypy/scripts/macsyfinder.py", line 1218, in main
    all_systems, rejected_candidates = search_systems(config, model_registry, models_def_to_detect, logger)
                                       ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/gensoft/ML_dependencies/ML_envs/eeebb03d1c26a9b40ee78814fcb4a901_/lib/python3.12/site-packages/macsypy/scripts/macsyfinder.py", line 538, in search_systems
    parser.parse(models_def_to_detect)
  File "/home/gensoft/ML_dependencies/ML_envs/eeebb03d1c26a9b40ee78814fcb4a901_/lib/python3.12/site-packages/macsypy/definition_parser.py", line 86, in parse
    model_node = self._get_model_node(def_loc)
                 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/gensoft/ML_dependencies/ML_envs/eeebb03d1c26a9b40ee78814fcb4a901_/lib/python3.12/site-packages/macsypy/definition_parser.py", line 110, in _get_model_node
    raise MacsypyError(msg) from None
macsypy.error.MacsypyError: unable to parse model definition 'CasFinder/CAS_Class1-Type-I' : The model definition CAS_Class1-Type-I.xml has not the right version. version supported is '2.0'. Please update your model.
RuleException:

fix is available trough mdmparis/defense-finder#90 (comment)

regards

Eric

[zevellong]

Hello,

I encountered issues when running nanomotif MTase-linker install. I found that the current defense-finder model update pulls a version of CasFinder (3.1.1) that is incompatible with the current macsyfinder dependencies, causing a version mismatch error (The model definition CAS_Cluster.xml has not the right version). Additionally, the test dataset included in the package had outdated column names.

Here is a summary of the fixes I implemented to successfully install the module. This involves modifying setup.smk, adding git to the conda environment, and updating the test dataset headers.

1. Modify setup.smk to handle CasFinder downgrade

The defense-finder update command fetches the latest models, including the incompatible CasFinder 3.1.1. I modified the defense_finder_update rule in setup.smk to force a downgrade to CasFinder 3.1.0.

File path: nanomotif/mtase_linker/setup.smk

Changes made:

• Added rule all inputs to force the execution of model updates and database creation.
• Updated rule defense_finder_update to clone the specific 3.1.0 tag of CasFinder.

##### Setup rules #####
rule all:
    input:
        "envs/prodigal-2.6.3.yaml",
        "envs/defensefinder-2.0.0.yaml",
        "envs/python_env-3.12.0.yaml",
        "envs/blast-2.14.1.yaml",
        # Added these lines to ensure models and DBs are built
        os.path.join(config["DEPENDENCYDIR"], "df_models", "defense-finder_update.done"),
        os.path.join(config["DEPENDENCYDIR"], "REbase_RecSeq_all", "REbase_RecSeq_all.pdb")

# ... [Keep other rules as is] ...

# Defensefinder to extract MTase genes
rule defense_finder_update:
    conda:
        "envs/defensefinder-2.0.0.yaml"
    output:
        dummy=touch(os.path.join(config["DEPENDENCYDIR"], "df_models", "defense-finder_update.done"))
    params:
        models_dir=os.path.join(config["DEPENDENCYDIR"], "df_models"),
        tmp_dir="/tmp/casfinder_setup"
    shell:
        """
        # Clean up old models
        rm -rf {params.models_dir}
        
        # Update models (fetches incompatible 3.1.1)
        defense-finder update --models-dir {params.models_dir}
        
        # --- FIX: Downgrade CasFinder to 3.1.0 ---
        # 1. Clone CasFinder to temp dir
        rm -rf {params.tmp_dir}
        git clone https://github.com/macsy-models/CasFinder.git {params.tmp_dir}
        
        # 2. Checkout compatible version 3.1.0
        cd {params.tmp_dir} && git checkout 3.1.0
        
        # 3. Remove incompatible 3.1.1
        rm -rf {params.models_dir}/CasFinder
        
        # 4. Copy compatible 3.1.0
        cp -r {params.tmp_dir} {params.models_dir}/CasFinder
        
        # 5. Cleanup
        rm -rf {params.tmp_dir}
        
        # Verify
        echo "CasFinder version check:"
        cat {params.models_dir}/CasFinder/metadata.yml 2>/dev/null || echo "metadata.yml not found"
        """

2. Add git to the Conda environment

Since the fix requires git clone, git must be added to the defensefinder environment yaml.

File path: nanomotif/mtase_linker/envs/defensefinder-2.0.0.yaml

Changes:

channels:
  - conda-forge
  - bioconda
dependencies:
  - python=3.10
  - defense-finder=1.3.0
  - git  # <--- Added this line

3. Fix outdated columns in Test Dataset

The installation check failed with KeyError: 'n_mod' because the included test file (e_coli_bin-motifs.tsv) used old column names (n_mod_bin).

File path: nanomotif/datasets/e_coli_bin-motifs.tsv

Command to fix:

# Rename headers to match current code expectations
sed -i '1s/n_mod_bin/n_mod/' nanomotif/datasets/e_coli_bin-motifs.tsv
sed -i '1s/n_nomod_bin/n_nomod/' nanomotif/datasets/e_coli_bin-motifs.tsv

Note

This CasFinder downgrade (referencing [defense-finder issue #90](mdmparis/defense-finder#90)) serves as a temporary workaround until defense-finder or nanomotif updates to handle the new model definitions natively.

[JSBoejer]

dle the new model definitions natively.

Hi Sorry, for the late reply. I think your proposed workaround will be the best option for now until defense-finder provides updates to handle macsyfinder > V.2.1.6 and the new model definitions.
I will keep an eye out for updates, which might solve this incompatability, and implement it into Nanomotif. Hopefully this will be solved soon, else I might work on a more stable solution for Nanomotif.

Regarding the outdated columns. Which version of Nanomotif are you using? This issue should have been solved from >V1.1.1 (see #141).

[zevellong]

I'm on version 1.0.2 right now. I'll try upgrading to the latest version first and report back if it fixes the problem. Thanks!