Problem with gurobi when running gapfilling function

[Fred C]

Hello there,

I have been trying to gapfill the streptomyces model with universal_cobra model, however, I kept running into these errors, what does it mean?

with model:

model.solver = "gurobi"

model.objective = "BIOMASS_SALB"

solution = gapfill(model, universal, demand_reactions=False)

for reaction in solution[0]:

print(reaction.id)

Bug below:

Read LP format model from file /var/folders/wy/8d18n83n56j78d4j6zkz449m0000gn/T/tmpy1sd08np.lp Reading time = 0.02 seconds : 1874 rows, 4466 columns, 19614 nonzeros Warning: Duplicate section found (read 'St') - Is a variable name equal to an LP file format keyword? Error reading LP format file /var/folders/wy/8d18n83n56j78d4j6zkz449m0000gn/T/tmpdip3ahnp.lp at line 130966 Unexpected symbol Neighboring tokens: " St <= 1000 St_reverse_e3a8b = 0 TAPTPP <= " Unable to read file Warning: Duplicate section found (read 'St') - Is a variable name equal to an LP file format keyword? Error reading LP format file /var/folders/wy/8d18n83n56j78d4j6zkz449m0000gn/T/tmpqcqf7wsv.lp at line 130966 Unexpected symbol Neighboring tokens: " St <= 1000 St_reverse_e3a8b = 0 TAPTPP <= "

Error: Unable to read file

--------------------------------------------------------------------------- GurobiError Traceback (most recent call last) File ~/opt/anaconda3/lib/python3.9/site-packages/cobra/core/model.py:410, in Model.copy(self) 409 try: --> 410 new._solver = deepcopy(self.solver) 411 # Cplex has an issue with deep copies File ~/opt/anaconda3/lib/python3.9/copy.py:172, in deepcopy(x, memo, _nil) 171 else: --> 172 y = _reconstruct(x, memo, *rv) 174 # If is its own copy, don't memoize. File ~/opt/anaconda3/lib/python3.9/copy.py:272, in _reconstruct(x, memo, func, args, state, listiter, dictiter, deepcopy) 271 if hasattr(y, '__setstate__'): --> 272 y.__setstate__(state) 273 else: File ~/opt/anaconda3/lib/python3.9/site-packages/optlang/gurobi_interface.py:619, in Model.__setstate__(self, repr_dict) 618 with TemporaryFilename(suffix=".lp", content=repr_dict["lp"]) as tmp_file_name: --> 619 problem = gurobipy.read(tmp_file_name) 620 self.__init__(problem=problem) File src/gurobipy/gurobi.pxi:3647, in gurobipy.read() File src/gurobipy/gurobi.pxi:86, in gurobipy.gurobi.read()

...

File src/gurobipy/gurobi.pxi:3647, in gurobipy.read() File src/gurobipy/gurobi.pxi:86, in gurobipy.gurobi.read() GurobiError: Unable to read model