search

qLSLab / integrate

GNU General Public License v3.0
4 stars 0 forks source link

The provided SBML model is not valid #4

Open Xuerlock opened 2 years ago

Xuerlock commented 2 years ago

I'm trying to test the pipeline with provided model ENGRO2.xml, but the getGPRsFromModel.py said that it was not a valid SBML model (The wrong information is attached below). I have validated the model on https://synonym.caltech.edu/validator_servlet/ and the report shows that it passed the validation and is a SBML model (although with some warnings). Is there any problem with the model file?

[integrate]$ python pipeline/getGPRsFromModel.py Set parameter Username Traceback (most recent call last): File "anaconda/lib/python3.8/site-packages/cobra/io/sbml.py", line 244, in read_sbml_model return _sbml_to_model(doc, number=number, f_replace=f_replace, **kwargs) File "anaconda/lib/python3.8/site-packages/cobra/io/sbml.py", line 366, in _sbml_to_model cobra_model = Model(model_id) File "anaconda/lib/python3.8/site-packages/cobra/core/model.py", line 113, in init self._solver = interface.Model() File "anaconda/lib/python3.8/site-packages/optlang/interface.py", line 1191, in init self._initialize_problem() File "anaconda/lib/python3.8/site-packages/optlang/gurobi_interface.py", line 531, in _initialize_problem self.problem = gurobipy.Model() File "src/gurobipy/model.pxi", line 68, in gurobipy.Model.init File "src/gurobipy/gurobi.pxi", line 32, in gurobipy.gurobi._getdefaultenv File "src/gurobipy/env.pxi", line 62, in gurobipy.Env.init gurobipy.GurobiError: HostID mismatch (licensed to 38f6002f, hostid is 38f6002a)

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

Traceback (most recent call last): File "pipeline/getGPRsFromModel.py", line 23, in model = cb.io.read_sbml_model(os.path.join(MODELDIR, modelId + '.xml')) File "anaconda/lib/python3.8/site-packages/cobra/io/sbml.py", line 258, in read_sbml_model raise cobra_error from original_error cobra.io.sbml.CobraSBMLError: Something went wrong reading the SBML model. Most likely the SBML model is not valid. Please check that your model is valid using the cobra.io.sbml.validate_sbml_model function or via the online validator at http://sbml.org/validator . (model, errors) = validate_sbml_model(filename) If the model is valid and cannot be read please open an issue at https://github.com/opencobra/cobrapy/issues .

mdifilippo commented 2 years ago

Hi! Is your gurobi license up to date?