Error when giving user universe

[NatashaJorge]

Hi!

i want to start saying that CarveMe is a great tool for metabolical network reconstruction. By far it is the fastest and more user friendly than anything around.

I am trying to reconstruct the metabolic network of a bacteria that I know should not have a periplasm compartment. I've tryed using the -u gramneg/grampos universes, but both generate a network with the periplasm compartment.

I do have a "curated" network of this species which only has two compartments, but it is not on my desired media. So, I've tried using it as a reference/universe. As a reference, everything runs smoothly, but the generated network still has the periplasm compartment. As universe, I get an error and no network file is generated. Please find the error pasted bellow. (I've checked, ATPM is a reaction in BiGG and the model is a valid SBML file).

Please, how could I use my curated model with CarveMe?

Thanks in advance,
Best regards,
Natasha

(base) [natasha@k61 Noras_AGORA2_adamberg]$ carve --refseq GCF_014131675.1 -g CIM8 -i CIM8 --mediadb /scr/k61san/natasha/matomic/trials/CarveMe/cimVIII_noO2.txt -u AcaccaeNB -o acacae_uAGORA.sbml
File exists, skipping.
diamond v2.0.15.153 (C) Max Planck Society for the Advancement of Science
Documentation, support and updates available at http://www.diamondsearch.org
Please cite: http://dx.doi.org/10.1038/s41592-021-01101-x Nature Methods (2021)

#CPU threads: 80
Scoring parameters: (Matrix=BLOSUM62 Lambda=0.267 K=0.041 Penalties=11/1)
Temporary directory:
Percentage range of top alignment score to report hits: 10
Opening the database... [0.032s]
Database: /homes/brauerei/natasha/miniconda3/lib/python3.9/site-packages/carveme/data/generated/bigg_proteins.dmnd (type: Diamond database, sequences: 26727, letters: 11170577)
Block size = 2000000000
Opening the input file... [0.012s]
Opening the output file... [0s]
Loading query sequences... [0.008s]
Masking queries... [0.088s]
Algorithm: Double-indexed
Building query histograms... [0.018s]
Allocating buffers... [0.005s]
Loading reference sequences... [0.028s]
Masking reference... [0.123s]
Initializing temporary storage... [0s]
Building reference histograms... [0.119s]
Allocating buffers... [0.005s]
Processing query block 1, reference block 1/1, shape 1/16, index chunk 1/4.
Building reference seed array... [0.042s]
Building query seed array... [0.02s]
Computing hash join... [0.018s]
Masking low complexity seeds... [0.004s]
Searching alignments... [0.065s]
Processing query block 1, reference block 1/1, shape 1/16, index chunk 2/4.
Building reference seed array... [0.025s]
Building query seed array... [0.016s]
Computing hash join... [0.006s]
Masking low complexity seeds... [0.004s]
Searching alignments... [0.023s]
Processing query block 1, reference block 1/1, shape 1/16, index chunk 3/4.
Building reference seed array... [0.029s]
Building query seed array... [0.02s]
Computing hash join... [0.004s]
Masking low complexity seeds... [0.006s]
Searching alignments... [0.015s]
Processing query block 1, reference block 1/1, shape 1/16, index chunk 4/4.
Building reference seed array... [0.024s]
Building query seed array... [0.018s]
Computing hash join... [0.006s]
Masking low complexity seeds... [0.006s]
Searching alignments... [0.013s]
Processing query block 1, reference block 1/1, shape 2/16, index chunk 1/4.
Building reference seed array... [0.024s]
Building query seed array... [0.017s]
Computing hash join... [0.006s]
Masking low complexity seeds... [0.006s]
Searching alignments... [0.01s]
Processing query block 1, reference block 1/1, shape 2/16, index chunk 2/4.
Building reference seed array... [0.026s]
Building query seed array... [0.015s]
Computing hash join... [0.007s]
Masking low complexity seeds... [0.004s]
Searching alignments... [0.013s]
Processing query block 1, reference block 1/1, shape 2/16, index chunk 3/4.
Building reference seed array... [0.023s]
Building query seed array... [0.017s]
Computing hash join... [0.006s]
Masking low complexity seeds... [0.004s]
Searching alignments... [0.006s]
Processing query block 1, reference block 1/1, shape 2/16, index chunk 4/4.
Building reference seed array... [0.021s]
Building query seed array... [0.014s]
Computing hash join... [0.006s]
Masking low complexity seeds... [0.006s]
Searching alignments... [0.008s]
Processing query block 1, reference block 1/1, shape 3/16, index chunk 1/4.
Building reference seed array... [0.022s]
Building query seed array... [0.019s]
Computing hash join... [0.005s]
Masking low complexity seeds... [0.004s]
Searching alignments... [0.008s]
Processing query block 1, reference block 1/1, shape 3/16, index chunk 2/4.
Building reference seed array... [0.025s]
Building query seed array... [0.017s]
Computing hash join... [0.005s]
Masking low complexity seeds... [0.005s]
Searching alignments... [0.006s]
Processing query block 1, reference block 1/1, shape 3/16, index chunk 3/4.
Building reference seed array... [0.026s]
Building query seed array... [0.019s]
Computing hash join... [0.005s]
Masking low complexity seeds... [0.005s]
Searching alignments... [0.008s]
Processing query block 1, reference block 1/1, shape 3/16, index chunk 4/4.
Building reference seed array... [0.023s]
Building query seed array... [0.015s]
Computing hash join... [0.005s]
Masking low complexity seeds... [0.005s]
Searching alignments... [0.006s]
Processing query block 1, reference block 1/1, shape 4/16, index chunk 1/4.
Building reference seed array... [0.024s]
Building query seed array... [0.015s]
Computing hash join... [0.007s]
Masking low complexity seeds... [0.005s]
Searching alignments... [0.006s]
Processing query block 1, reference block 1/1, shape 4/16, index chunk 2/4.
Building reference seed array... [0.026s]
Building query seed array... [0.015s]
Computing hash join... [0.006s]
Masking low complexity seeds... [0.004s]
Searching alignments... [0.006s]
Processing query block 1, reference block 1/1, shape 4/16, index chunk 3/4.
Building reference seed array... [0.028s]
Building query seed array... [0.017s]
Computing hash join... [0.004s]
Masking low complexity seeds... [0.005s]
Searching alignments... [0.006s]
Processing query block 1, reference block 1/1, shape 4/16, index chunk 4/4.
Building reference seed array... [0.023s]
Building query seed array... [0.015s]
Computing hash join... [0.004s]
Masking low complexity seeds... [0.003s]
Searching alignments... [0.006s]
Processing query block 1, reference block 1/1, shape 5/16, index chunk 1/4.
Building reference seed array... [0.023s]
Building query seed array... [0.014s]
Computing hash join... [0.005s]
Masking low complexity seeds... [0.005s]
Searching alignments... [0.006s]
Processing query block 1, reference block 1/1, shape 5/16, index chunk 2/4.
Building reference seed array... [0.027s]
Building query seed array... [0.018s]
Computing hash join... [0.007s]
Masking low complexity seeds... [0.005s]
Searching alignments... [0.006s]
Processing query block 1, reference block 1/1, shape 5/16, index chunk 3/4.
Building reference seed array... [0.029s]
Building query seed array... [0.018s]
Computing hash join... [0.006s]
Masking low complexity seeds... [0.005s]
Searching alignments... [0.008s]
Processing query block 1, reference block 1/1, shape 5/16, index chunk 4/4.
Building reference seed array... [0.023s]
Building query seed array... [0.015s]
Computing hash join... [0.006s]
Masking low complexity seeds... [0.005s]
Searching alignments... [0.013s]
Processing query block 1, reference block 1/1, shape 6/16, index chunk 1/4.
Building reference seed array... [0.026s]
Building query seed array... [0.018s]
Computing hash join... [0.008s]
Masking low complexity seeds... [0.006s]
Searching alignments... [0.008s]
Processing query block 1, reference block 1/1, shape 6/16, index chunk 2/4.
Building reference seed array... [0.026s]
Building query seed array... [0.015s]
Computing hash join... [0.006s]
Masking low complexity seeds... [0.005s]
Searching alignments... [0.006s]
Processing query block 1, reference block 1/1, shape 6/16, index chunk 3/4.
Building reference seed array... [0.026s]
Building query seed array... [0.017s]
Computing hash join... [0.005s]
Masking low complexity seeds... [0.004s]
Searching alignments... [0.006s]
Processing query block 1, reference block 1/1, shape 6/16, index chunk 4/4.
Building reference seed array... [0.023s]
Building query seed array... [0.017s]
Computing hash join... [0.007s]
Masking low complexity seeds... [0.006s]
Searching alignments... [0.007s]
Processing query block 1, reference block 1/1, shape 7/16, index chunk 1/4.
Building reference seed array... [0.025s]
Building query seed array... [0.019s]
Computing hash join... [0.005s]
Masking low complexity seeds... [0.003s]
Searching alignments... [0.005s]
Processing query block 1, reference block 1/1, shape 7/16, index chunk 2/4.
Building reference seed array... [0.023s]
Building query seed array... [0.018s]
Computing hash join... [0.005s]
Masking low complexity seeds... [0.005s]
Searching alignments... [0.007s]
Processing query block 1, reference block 1/1, shape 7/16, index chunk 3/4.
Building reference seed array... [0.035s]
Building query seed array... [0.019s]
Computing hash join... [0.005s]
Masking low complexity seeds... [0.005s]
Searching alignments... [0.007s]
Processing query block 1, reference block 1/1, shape 7/16, index chunk 4/4.
Building reference seed array... [0.027s]
Building query seed array... [0.016s]
Computing hash join... [0.005s]
Masking low complexity seeds... [0.006s]
Searching alignments... [0.008s]
Processing query block 1, reference block 1/1, shape 8/16, index chunk 1/4.
Building reference seed array... [0.023s]
Building query seed array... [0.019s]
Computing hash join... [0.006s]
Masking low complexity seeds... [0.003s]
Searching alignments... [0.006s]
Processing query block 1, reference block 1/1, shape 8/16, index chunk 2/4.
Building reference seed array... [0.024s]
Building query seed array... [0.017s]
Computing hash join... [0.004s]
Masking low complexity seeds... [0.005s]
Searching alignments... [0.006s]
Processing query block 1, reference block 1/1, shape 8/16, index chunk 3/4.
Building reference seed array... [0.024s]
Building query seed array... [0.017s]
Computing hash join... [0.006s]
Masking low complexity seeds... [0.005s]
Searching alignments... [0.006s]
Processing query block 1, reference block 1/1, shape 8/16, index chunk 4/4.
Building reference seed array... [0.026s]
Building query seed array... [0.018s]
Computing hash join... [0.005s]
Masking low complexity seeds... [0.004s]
Searching alignments... [0.006s]
Processing query block 1, reference block 1/1, shape 9/16, index chunk 1/4.
Building reference seed array... [0.024s]
Building query seed array... [0.017s]
Computing hash join... [0.005s]
Masking low complexity seeds... [0.005s]
Searching alignments... [0.006s]
Processing query block 1, reference block 1/1, shape 9/16, index chunk 2/4.
Building reference seed array... [0.024s]
Building query seed array... [0.015s]
Computing hash join... [0.005s]
Masking low complexity seeds... [0.005s]
Searching alignments... [0.006s]
Processing query block 1, reference block 1/1, shape 9/16, index chunk 3/4.
Building reference seed array... [0.024s]
Building query seed array... [0.017s]
Computing hash join... [0.006s]
Masking low complexity seeds... [0.005s]
Searching alignments... [0.006s]
Processing query block 1, reference block 1/1, shape 9/16, index chunk 4/4.
Building reference seed array... [0.023s]
Building query seed array... [0.02s]
Computing hash join... [0.006s]
Masking low complexity seeds... [0.004s]
Searching alignments... [0.007s]
Processing query block 1, reference block 1/1, shape 10/16, index chunk 1/4.
Building reference seed array... [0.024s]
Building query seed array... [0.015s]
Computing hash join... [0.005s]
Masking low complexity seeds... [0.004s]
Searching alignments... [0.007s]
Processing query block 1, reference block 1/1, shape 10/16, index chunk 2/4.
Building reference seed array... [0.023s]
Building query seed array... [0.017s]
Computing hash join... [0.007s]
Masking low complexity seeds... [0.005s]
Searching alignments... [0.006s]
Processing query block 1, reference block 1/1, shape 10/16, index chunk 3/4.
Building reference seed array... [0.025s]
Building query seed array... [0.017s]
Computing hash join... [0.005s]
Masking low complexity seeds... [0.004s]
Searching alignments... [0.008s]
Processing query block 1, reference block 1/1, shape 10/16, index chunk 4/4.
Building reference seed array... [0.023s]
Building query seed array... [0.02s]
Computing hash join... [0.006s]
Masking low complexity seeds... [0.005s]
Searching alignments... [0.006s]
Processing query block 1, reference block 1/1, shape 11/16, index chunk 1/4.
Building reference seed array... [0.021s]
Building query seed array... [0.015s]
Computing hash join... [0.004s]
Masking low complexity seeds... [0.006s]
Searching alignments... [0.007s]
Processing query block 1, reference block 1/1, shape 11/16, index chunk 2/4.
Building reference seed array... [0.025s]
Building query seed array... [0.016s]
Computing hash join... [0.005s]
Masking low complexity seeds... [0.005s]
Searching alignments... [0.006s]
Processing query block 1, reference block 1/1, shape 11/16, index chunk 3/4.
Building reference seed array... [0.025s]
Building query seed array... [0.017s]
Computing hash join... [0.005s]
Masking low complexity seeds... [0.004s]
Searching alignments... [0.006s]
Processing query block 1, reference block 1/1, shape 11/16, index chunk 4/4.
Building reference seed array... [0.023s]
Building query seed array... [0.017s]
Computing hash join... [0.007s]
Masking low complexity seeds... [0.004s]
Searching alignments... [0.006s]
Processing query block 1, reference block 1/1, shape 12/16, index chunk 1/4.
Building reference seed array... [0.025s]
Building query seed array... [0.018s]
Computing hash join... [0.005s]
Masking low complexity seeds... [0.005s]
Searching alignments... [0.006s]
Processing query block 1, reference block 1/1, shape 12/16, index chunk 2/4.
Building reference seed array... [0.026s]
Building query seed array... [0.018s]
Computing hash join... [0.005s]
Masking low complexity seeds... [0.005s]
Searching alignments... [0.006s]
Processing query block 1, reference block 1/1, shape 12/16, index chunk 3/4.
Building reference seed array... [0.024s]
Building query seed array... [0.015s]
Computing hash join... [0.005s]
Masking low complexity seeds... [0.005s]
Searching alignments... [0.006s]
Processing query block 1, reference block 1/1, shape 12/16, index chunk 4/4.
Building reference seed array... [0.021s]
Building query seed array... [0.014s]
Computing hash join... [0.005s]
Masking low complexity seeds... [0.005s]
Searching alignments... [0.006s]
Processing query block 1, reference block 1/1, shape 13/16, index chunk 1/4.
Building reference seed array... [0.025s]
Building query seed array... [0.017s]
Computing hash join... [0.006s]
Masking low complexity seeds... [0.005s]
Searching alignments... [0.007s]
Processing query block 1, reference block 1/1, shape 13/16, index chunk 2/4.
Building reference seed array... [0.025s]
Building query seed array... [0.016s]
Computing hash join... [0.006s]
Masking low complexity seeds... [0.004s]
Searching alignments... [0.006s]
Processing query block 1, reference block 1/1, shape 13/16, index chunk 3/4.
Building reference seed array... [0.025s]
Building query seed array... [0.016s]
Computing hash join... [0.006s]
Masking low complexity seeds... [0.004s]
Searching alignments... [0.006s]
Processing query block 1, reference block 1/1, shape 13/16, index chunk 4/4.
Building reference seed array... [0.025s]
Building query seed array... [0.015s]
Computing hash join... [0.004s]
Masking low complexity seeds... [0.005s]
Searching alignments... [0.006s]
Processing query block 1, reference block 1/1, shape 14/16, index chunk 1/4.
Building reference seed array... [0.027s]
Building query seed array... [0.017s]
Computing hash join... [0.007s]
Masking low complexity seeds... [0.004s]
Searching alignments... [0.006s]
Processing query block 1, reference block 1/1, shape 14/16, index chunk 2/4.
Building reference seed array... [0.023s]
Building query seed array... [0.016s]
Computing hash join... [0.006s]
Masking low complexity seeds... [0.006s]
Searching alignments... [0.008s]
Processing query block 1, reference block 1/1, shape 14/16, index chunk 3/4.
Building reference seed array... [0.024s]
Building query seed array... [0.018s]
Computing hash join... [0.005s]
Masking low complexity seeds... [0.005s]
Searching alignments... [0.006s]
Processing query block 1, reference block 1/1, shape 14/16, index chunk 4/4.
Building reference seed array... [0.024s]
Building query seed array... [0.015s]
Computing hash join... [0.004s]
Masking low complexity seeds... [0.005s]
Searching alignments... [0.006s]
Processing query block 1, reference block 1/1, shape 15/16, index chunk 1/4.
Building reference seed array... [0.025s]
Building query seed array... [0.018s]
Computing hash join... [0.005s]
Masking low complexity seeds... [0.004s]
Searching alignments... [0.007s]
Processing query block 1, reference block 1/1, shape 15/16, index chunk 2/4.
Building reference seed array... [0.028s]
Building query seed array... [0.019s]
Computing hash join... [0.006s]
Masking low complexity seeds... [0.005s]
Searching alignments... [0.006s]
Processing query block 1, reference block 1/1, shape 15/16, index chunk 3/4.
Building reference seed array... [0.024s]
Building query seed array... [0.017s]
Computing hash join... [0.006s]
Masking low complexity seeds... [0.004s]
Searching alignments... [0.007s]
Processing query block 1, reference block 1/1, shape 15/16, index chunk 4/4.
Building reference seed array... [0.026s]
Building query seed array... [0.018s]
Computing hash join... [0.007s]
Masking low complexity seeds... [0.006s]
Searching alignments... [0.006s]
Processing query block 1, reference block 1/1, shape 16/16, index chunk 1/4.
Building reference seed array... [0.025s]
Building query seed array... [0.016s]
Computing hash join... [0.006s]
Masking low complexity seeds... [0.005s]
Searching alignments... [0.006s]
Processing query block 1, reference block 1/1, shape 16/16, index chunk 2/4.
Building reference seed array... [0.026s]
Building query seed array... [0.014s]
Computing hash join... [0.005s]
Masking low complexity seeds... [0.004s]
Searching alignments... [0.006s]
Processing query block 1, reference block 1/1, shape 16/16, index chunk 3/4.
Building reference seed array... [0.024s]
Building query seed array... [0.014s]
Computing hash join... [0.005s]
Masking low complexity seeds... [0.005s]
Searching alignments... [0.007s]
Processing query block 1, reference block 1/1, shape 16/16, index chunk 4/4.
Building reference seed array... [0.027s]
Building query seed array... [0.017s]
Computing hash join... [0.005s]
Masking low complexity seeds... [0.005s]
Searching alignments... [0.006s]
Deallocating buffers... [0.005s]
Clearing query masking... [0s]
Computing alignments... [0.332s]
Deallocating reference... [0.001s]
Loading reference sequences... [0s]
Deallocating buffers... [0s]
Deallocating queries... [0s]
Loading query sequences... [0s]
Closing the input file... [0s]
Closing the output file... [0.002s]
Cleaning up... [0s]
Total time = 5.097s
Reported 4986 pairwise alignments, 4986 HSPs.
1657 queries aligned.
/homes/brauerei/natasha/miniconda3/lib/python3.9/site-packages/reframed/io/sbml.py:512: UserWarning: Gene association for reaction R_ACLS_a is not DNF
warn(f"Gene association for reaction {reaction_id} is not DNF")
/homes/brauerei/natasha/miniconda3/lib/python3.9/site-packages/reframed/io/sbml.py:512: UserWarning: Gene association for reaction R_GLUSy is not DNF
warn(f"Gene association for reaction {reaction_id} is not DNF")
Traceback (most recent call last):
File "/homes/brauerei/natasha/miniconda3/bin/carve", line 8, in
sys.exit(main())
File "/homes/brauerei/natasha/miniconda3/lib/python3.9/site-packages/carveme/cli/carve.py", line 350, in main
maincall(
File "/homes/brauerei/natasha/miniconda3/lib/python3.9/site-packages/carveme/cli/carve.py", line 202, in maincall
model = carve_model(universe_model, scores, inplace=(not gapfill), default_score=default_score,
File "/homes/brauerei/natasha/miniconda3/lib/python3.9/site-packages/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 "/homes/brauerei/natasha/miniconda3/lib/python3.9/site-packages/carveme/reconstruction/carving.py", line 121, in minmax_reduction
solver.update()
File "/homes/brauerei/natasha/miniconda3/lib/python3.9/site-packages/reframed/solvers/cplex_solver.py", line 217, in update
self.add_constraints(constr_ids, lhs, senses, rhs)
File "/homes/brauerei/natasha/miniconda3/lib/python3.9/site-packages/reframed/solvers/cplex_solver.py", line 142, in add_constraints
self.problem.linear_constraints.add(lin_expr=exprs,
File "/homes/brauerei/natasha/miniconda3/lib/python3.9/site-packages/cplex-22.1.0.0-py3.9.egg/cplex/_internal/_subinterfaces.py", line 1273, in add
return self._add_iter(self.get_num, self._add,
File "/homes/brauerei/natasha/miniconda3/lib/python3.9/site-packages/cplex-22.1.0.0-py3.9.egg/cplex/_internal/_baseinterface.py", line 41, in _add_iter
addfun(*args, **kwargs)
File "/homes/brauerei/natasha/miniconda3/lib/python3.9/site-packages/cplex-22.1.0.0-py3.9.egg/cplex/_internal/_subinterfaces.py", line 1199, in _add
with CPX_PROC.chbmatrix(lin_expr, self._cplex._env_lp_ptr,
File "/homes/brauerei/natasha/miniconda3/lib/python3.9/contextlib.py", line 119, in enter
return next(self.gen)
File "/homes/brauerei/natasha/miniconda3/lib/python3.9/site-packages/cplex-22.1.0.0-py3.9.egg/cplex/_internal/_procedural.py", line 168, in chbmatrix
mat = Pylolmat_to_CHBmat(lolmat, env_lp_ptr, r_c)
File "/homes/brauerei/natasha/miniconda3/lib/python3.9/site-packages/cplex-22.1.0.0-py3.9.egg/cplex/_internal/_procedural.py", line 177, in Pylolmat_to_CHBmat
return CR.Pylolmat_to_CHBmat(lolmat, env_lp_ptr, r_c)
File "/homes/brauerei/natasha/miniconda3/lib/python3.9/site-packages/cplex-22.1.0.0-py3.9.egg/cplex/_internal/_pycplex.py", line 1631, in Pylolmat_to_CHBmat
return _pycplex_platform.Pylolmat_to_CHBmat(lolmat, env_lp_ptr, py_row_col)
ValueError: 1210: Invalid name -- 'R_ATPM'