Problems gapfilling with CPLEX and Gurobi

[Brunokemon]

Hi! Wonderful tool you guys created. Really nice!

I just had this recent problem when I tried gapfilling the AGORA2 sbml models for the medium M9.

I tried running the following command

$ carve  bacteria.faa --gapfill M9 --mediadb media.tsv --universe-file bacteria.xml

Traceback (most recent call last):
File ".local/bin/carve", line 8, in
sys.exit(main())
File ".local/bin/carveme/cli/carve.py", line 357, in main
maincall(
File ".local/bin/carveme/cli/carve.py", line 204, in maincall
model = carve_model(universe_model, scores, inplace=(not gapfill), default_score=default_score,
File ".local/bin/carveme/reconstruction/carving.py", line 231, in carve_model
sol = minmax_reduction(model, scores, default_score=default_score, uptake_score=uptake_score, soft_score=soft_score,
File ".local/bin/carveme/reconstruction/carving.py", line 121, in minmax_reduction
solver.update()
File ".local/bin/reframed/solvers/cplex_solver.py", line 216, in update
self.add_constraints(constr_ids, lhs, senses, rhs)
File ".local/bin/reframed/solvers/cplex_solver.py", line 141, in add_constraints
self.problem.linear_constraints.add(lin_expr=exprs,
File "/CPLEX/cplex/python/3.10/x86-64_linux/cplex/_internal/_subinterfaces.py", line 1273, in add
return self._add_iter(self.get_num, self._add,
File "/CPLEX/cplex/python/3.10/x86-64_linux/cplex/_internal/_baseinterface.py", line 41, in _add_iter
addfun(*args, **kwargs)
File "/CPLEX/cplex/python/3.10/x86-64_linux/cplex/_internal/_subinterfaces.py", line 1199, in _add
with CPX_PROC.chbmatrix(lin_expr, self._cplex._env_lp_ptr,
File "/usr/lib64/python3.10/contextlib.py", line 135, in enter
return next(self.gen)
File "/CPLEX/cplex/python/3.10/x86-64_linux/cplex/_internal/_procedural.py", line 168, in chbmatrix
mat = Pylolmat_to_CHBmat(lolmat, env_lp_ptr, r_c)
File "/CPLEX/cplex/python/3.10/x86-64_linux/cplex/_internal/_procedural.py", line 177, in Pylolmat_to_CHBmat
return CR.Pylolmat_to_CHBmat(lolmat, env_lp_ptr, r_c)
File "/CPLEX/cplex/python/3.10/x86-64_linux/cplex/_internal/_pycplex.py", line 1632, in Pylolmat_to_CHBmat
return _pycplex_platform.Pylolmat_to_CHBmat(lolmat, env_lp_ptr, py_row_col)
ValueError: 1210: Invalid name -- 'R_ATPM'

This error seems to be this one in CPLEX but I'm not sure how to solve it.

So I tried switching from CPLEX to Gurobi adding --solver gurobi to see if works.

$ carve  bacteria.faa --solver gurobi --gapfill M9 --mediadb media.tsv --universe-file bacteria.xml

Traceback (most recent call last):
File ".local/bin/carve", line 8, in
sys.exit(main())
File ".local/bin/carveme/cli/carve.py", line 349, in main
set_default_solver(args.solver)
File ".local/bin/reframed/solvers/init.py", line 82, in set_default_solver
raise RuntimeError(f"Solver {solvername} not available.")
RuntimeError: Solver gurobi not available.

I tried doing as suggested in issue 181 to no avail, then I tried updating the reframed solvers folder from the github repo but to no avail too.
I checked and Gurobi and gurobipy are working fine.

So I'm not sure what to try now, which is the reason for me to be seeking your help now with this.
Thanks in advance.

[cdanielmachado]

Why are you adding this option: --universe-file bacteria.xml ?

[Brunokemon]

That is the AGORA2 sbml model. I thought that would set the model as basis for the gapfilling.
Is it wrong? Should it be done in another way?

[cdanielmachado]

Yep. For gapfilling you should use the gapfill command instead 🙂

[Brunokemon]

Strangely enough the first time I tried using gapfill it didn't work, but now I tried again and it worked. Must've been something I did wrong the first time 😓. Thank you for your help! 😁