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'