Open peiyilu168 opened 4 weeks ago
I encountered an issue when running the GIMME algorithm with the example model and expression data. The detail is given below:
--------------------------------------------------------------------------- GurobiError Traceback (most recent call last) Cell In[16], line 12 9 # Run the GIMME algorithm. 10 gimme = GIMME(S=model_wrapper.S, lb=model_wrapper.lb, ub=model_wrapper.ub, properties=properties) ---> 12 gimme_run = gimme.run() File [~/miniconda3/envs/troppo/lib/python3.10/site-packages/troppo/methods/reconstruction/gimme.py:289](http://localhost:8889/lab/tree/miniconda3/envs/troppo/lib/python3.10/site-packages/troppo/methods/reconstruction/gimme.py#line=288), in GIMME.run(self) 280 def run(self): 281 """ 282 Run GIMME algorithm 283 (...) 287 288 """ --> 289 sol = self.gm.optimize_gimme( 290 exp_vector=self.properties['exp_vector'], 291 objectives=self.properties['objectives'], 292 obj_frac=self.properties['obj_frac'], 293 flux_thres=self.properties['flux_threshold'] 294 ) 295 self.sol = sol 296 return sol.get_reaction_activity(self.properties['flux_threshold']) File [~/miniconda3/envs/troppo/lib/python3.10/site-packages/troppo/methods/reconstruction/gimme.py:107](http://localhost:8889/lab/tree/miniconda3/envs/troppo/lib/python3.10/site-packages/troppo/methods/reconstruction/gimme.py#line=106), in GIMMEModel.optimize_gimme(self, exp_vector, objectives, obj_frac, flux_thres) 104 for idx, lb in zip(objective_ids, lbs_id): 105 self.set_reaction_bounds(idx, lb=lb, temporary=True) --> 107 self.set_objective(gimme_model_objective, True) 108 sol = self.optimize() 109 self.revert_to_original_bounds() File [~/miniconda3/envs/troppo/lib/python3.10/site-packages/cobamp/core/models.py:566](http://localhost:8889/lab/tree/miniconda3/envs/troppo/lib/python3.10/site-packages/cobamp/core/models.py#line=565), in ConstraintBasedModel.set_objective(self, coef_dict, minimize) 564 self.model.set_objective(self.c, minimize) 565 elif isinstance(coef_dict, ndarray): --> 566 self.model.set_objective(coef_dict, minimize) 567 else: 568 raise TypeError('`coef_dict` must either be a dict or an ndarray') File [~/miniconda3/envs/troppo/lib/python3.10/site-packages/cobamp/core/linear_systems.py:474](http://localhost:8889/lab/tree/miniconda3/envs/troppo/lib/python3.10/site-packages/cobamp/core/linear_systems.py#line=473), in LinearSystem.set_objective(self, coefficients, minimize, vars) 472 self.model.remove(dummy) 473 self.model.objective.direction = SENSE_MINIMIZE if minimize else SENSE_MAXIMIZE --> 474 self.model.update() File [~/miniconda3/envs/troppo/lib/python3.10/site-packages/optlang/gurobi_interface.py:671](http://localhost:8889/lab/tree/miniconda3/envs/troppo/lib/python3.10/site-packages/optlang/gurobi_interface.py#line=670), in Model.update(self) 670 def update(self): --> 671 super(Model, self).update(callback=self.problem.update) File [~/miniconda3/envs/troppo/lib/python3.10/site-packages/optlang/interface.py:1491](http://localhost:8889/lab/tree/miniconda3/envs/troppo/lib/python3.10/site-packages/optlang/interface.py#line=1490), in Model.update(self, callback) 1489 rm_var = self._pending_modifications.rm_var 1490 if len(rm_var) > 0: -> 1491 self._remove_variables(rm_var) 1492 self._pending_modifications.rm_var = [] 1493 callback() File [~/miniconda3/envs/troppo/lib/python3.10/site-packages/optlang/gurobi_interface.py:707](http://localhost:8889/lab/tree/miniconda3/envs/troppo/lib/python3.10/site-packages/optlang/gurobi_interface.py#line=706), in Model._remove_variables(self, variables) 705 variable.problem = None 706 del self._variables[variable.name] --> 707 self.problem.remove(internal_variable) File src/gurobipy/model.pxi:1096, in gurobipy.Model.remove() File src/gurobipy/model.pxi:1101, in gurobipy.Model._removeone() GurobiError: Item to be removed not a Var, Constr, SOS, QConstr, or GenConstr
I encountered an issue when running the GIMME algorithm with the example model and expression data. The detail is given below: