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CCThinnes opened this issue May 12, 2025 · 0 comments
Open

Issue with converting .mat into json and sbml #2475

CCThinnes opened this issue May 12, 2025 · 0 comments

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@CCThinnes
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I created a .json from a .mat file (Recon3D):

writeCbModel(humanRecon, 'Recon3DVMH.json', 'format', 'json');

The resulting file does not seem to be compatible with Escher. When doing the conversion from .mat into .json in cobrapy, Escher is happy with the resulting file.

When trying to convert the .mat into sbml, I get an error, after a long list of warnings:

writeCbModel(humanRecon, 'Recon3DVMH.sbml', 'format', 'sbml');
Warning: Colon operands must be real scalars. This warning will become an error in a future release.

In getDefinedFieldProperties (line 90)
In getDatabaseMappings (line 38)
In makeSBMLAnnotationString (line 54)
In writeSBML (line 181)
In writeCbModel (line 231)

Warning: Metabolite M00188[c] has formula C62H89CoN13O14P.C7H8N4O2R2. FBC 2.1 only allows integer values for
coefficients.
Discarding the formula.

In writeSBML (line 191)
In writeCbModel (line 231)
Warning: Metabolite M00189[c] has formula C63H92CoN13O14P.C7H8N4O2R2. FBC 2.1 only allows integer values for
coefficients.
Discarding the formula.
In writeSBML (line 191)
In writeCbModel (line 231)
Warning: Unknown compartment: i.i can be specified in compSymbolList and compNameList.
In writeSBML (line 305)
In writeCbModel (line 231)
Warning: The "rxn2subSystem" field has been generated because it was not in the model.
In findRxnsFromSubSystem (line 31)
In writeSBML (line 460)
In writeCbModel (line 231)
Warning: The "rxn2subSystem" field has been generated because it was not in the model.
In findRxnsFromSubSystem (line 31)
In writeSBML (line 460)
In writeCbModel (line 231)
Warning: The "rxn2subSystem" field has been generated because it was not in the model.
In findRxnsFromSubSystem (line 31)
In writeSBML (line 460)
In writeCbModel (line 231)
Warning: The "rxn2subSystem" field has been generated because it was not in the model.
In findRxnsFromSubSystem (line 31)
In writeSBML (line 460)
In writeCbModel (line 231)
Warning: The "rxn2subSystem" field has been generated because it was not in the model.
In findRxnsFromSubSystem (line 31)
In writeSBML (line 460)
In writeCbModel (line 231)
Warning: The "rxn2subSystem" field has been generated because it was not in the model.
In findRxnsFromSubSystem (line 31)
In writeSBML (line 460)
In writeCbModel (line 231)
Warning: The "rxn2subSystem" field has been generated because it was not in the model.
In findRxnsFromSubSystem (line 31)
In writeSBML (line 460)
In writeCbModel (line 231)
Warning: The "rxn2subSystem" field has been generated because it was not in the model.
In findRxnsFromSubSystem (line 31)
In writeSBML (line 460)
In writeCbModel (line 231)
Warning: The "rxn2subSystem" field has been generated because it was not in the model.
In findRxnsFromSubSystem (line 31)
In writeSBML (line 460)
In writeCbModel (line 231)
Warning: The "rxn2subSystem" field has been generated because it was not in the model.
In findRxnsFromSubSystem (line 31)
In writeSBML (line 460)
In writeCbModel (line 231)
Warning: The "rxn2subSystem" field has been generated because it was not in the model.
In findRxnsFromSubSystem (line 31)
In writeSBML (line 460)
In writeCbModel (line 231)
Warning: The "rxn2subSystem" field has been generated because it was not in the model.
In findRxnsFromSubSystem (line 31)
In writeSBML (line 460)
In writeCbModel (line 231)
Warning: The "rxn2subSystem" field has been generated because it was not in the model.
In findRxnsFromSubSystem (line 31)
In writeSBML (line 460)
In writeCbModel (line 231)
Warning: The "rxn2subSystem" field has been generated because it was not in the model.
In findRxnsFromSubSystem (line 31)
In writeSBML (line 460)
In writeCbModel (line 231)
Warning: The "rxn2subSystem" field has been generated because it was not in the model.
In findRxnsFromSubSystem (line 31)
In writeSBML (line 460)
In writeCbModel (line 231)
Warning: The "rxn2subSystem" field has been generated because it was not in the model.
In findRxnsFromSubSystem (line 31)
In writeSBML (line 460)
In writeCbModel (line 231)
Warning: The "rxn2subSystem" field has been generated because it was not in the model.
In findRxnsFromSubSystem (line 31)
In writeSBML (line 460)
In writeCbModel (line 231)
Warning: The "rxn2subSystem" field has been generated because it was not in the model.
In findRxnsFromSubSystem (line 31)
In writeSBML (line 460)
In writeCbModel (line 231)
Warning: The "rxn2subSystem" field has been generated because it was not in the model.
In findRxnsFromSubSystem (line 31)
In writeSBML (line 460)
In writeCbModel (line 231)
Warning: The "rxn2subSystem" field has been generated because it was not in the model.
In findRxnsFromSubSystem (line 31)
In writeSBML (line 460)
In writeCbModel (line 231)
Warning: The "rxn2subSystem" field has been generated because it was not in the model.
In findRxnsFromSubSystem (line 31)
In writeSBML (line 460)
In writeCbModel (line 231)
Warning: The "rxn2subSystem" field has been generated because it was not in the model.
In findRxnsFromSubSystem (line 31)
In writeSBML (line 460)
In writeCbModel (line 231)
Warning: The "rxn2subSystem" field has been generated because it was not in the model.
In findRxnsFromSubSystem (line 31)
In writeSBML (line 460)
In writeCbModel (line 231)
Warning: The "rxn2subSystem" field has been generated because it was not in the model.
In findRxnsFromSubSystem (line 31)
In writeSBML (line 460)
In writeCbModel (line 231)
Warning: The "rxn2subSystem" field has been generated because it was not in the model.
In findRxnsFromSubSystem (line 31)
In writeSBML (line 460)
In writeCbModel (line 231)
Warning: The "rxn2subSystem" field has been generated because it was not in the model.
In findRxnsFromSubSystem (line 31)
In writeSBML (line 460)
In writeCbModel (line 231)
Warning: The "rxn2subSystem" field has been generated because it was not in the model.
In findRxnsFromSubSystem (line 31)
In writeSBML (line 460)
In writeCbModel (line 231)
Warning: The "rxn2subSystem" field has been generated because it was not in the model.
In findRxnsFromSubSystem (line 31)
In writeSBML (line 460)
In writeCbModel (line 231)
Warning: The "rxn2subSystem" field has been generated because it was not in the model.
In findRxnsFromSubSystem (line 31)
In writeSBML (line 460)
In writeCbModel (line 231)
Warning: The "rxn2subSystem" field has been generated because it was not in the model.
In findRxnsFromSubSystem (line 31)
In writeSBML (line 460)
In writeCbModel (line 231)
Warning: The "rxn2subSystem" field has been generated because it was not in the model.
In findRxnsFromSubSystem (line 31)
In writeSBML (line 460)
In writeCbModel (line 231)
Warning: The "rxn2subSystem" field has been generated because it was not in the model.
In findRxnsFromSubSystem (line 31)
In writeSBML (line 460)
In writeCbModel (line 231)
Warning: The "rxn2subSystem" field has been generated because it was not in the model.
In findRxnsFromSubSystem (line 31)
In writeSBML (line 460)
In writeCbModel (line 231)
Warning: The "rxn2subSystem" field has been generated because it was not in the model.
In findRxnsFromSubSystem (line 31)
In writeSBML (line 460)
In writeCbModel (line 231)
Warning: The "rxn2subSystem" field has been generated because it was not in the model.
In findRxnsFromSubSystem (line 31)
In writeSBML (line 460)
In writeCbModel (line 231)
Warning: The "rxn2subSystem" field has been generated because it was not in the model.
In findRxnsFromSubSystem (line 31)
In writeSBML (line 460)
In writeCbModel (line 231)
Warning: The "rxn2subSystem" field has been generated because it was not in the model.
In findRxnsFromSubSystem (line 31)
In writeSBML (line 460)
In writeCbModel (line 231)
Warning: The "rxn2subSystem" field has been generated because it was not in the model.
In findRxnsFromSubSystem (line 31)
In writeSBML (line 460)
In writeCbModel (line 231)
Warning: The "rxn2subSystem" field has been generated because it was not in the model.
In findRxnsFromSubSystem (line 31)
In writeSBML (line 460)
In writeCbModel (line 231)
Warning: The "rxn2subSystem" field has been generated because it was not in the model.
In findRxnsFromSubSystem (line 31)
In writeSBML (line 460)
In writeCbModel (line 231)
Warning: The "rxn2subSystem" field has been generated because it was not in the model.
In findRxnsFromSubSystem (line 31)
In writeSBML (line 460)
In writeCbModel (line 231)
Warning: The "rxn2subSystem" field has been generated because it was not in the model.
In findRxnsFromSubSystem (line 31)
In writeSBML (line 460)
In writeCbModel (line 231)
Warning: The "rxn2subSystem" field has been generated because it was not in the model.
In findRxnsFromSubSystem (line 31)
In writeSBML (line 460)
In writeCbModel (line 231)
Warning: The "rxn2subSystem" field has been generated because it was not in the model.
In findRxnsFromSubSystem (line 31)
In writeSBML (line 460)
In writeCbModel (line 231)
Warning: The "rxn2subSystem" field has been generated because it was not in the model.
In findRxnsFromSubSystem (line 31)
In writeSBML (line 460)
In writeCbModel (line 231)
Warning: The "rxn2subSystem" field has been generated because it was not in the model.
In findRxnsFromSubSystem (line 31)
In writeSBML (line 460)
In writeCbModel (line 231)
Warning: The "rxn2subSystem" field has been generated because it was not in the model.
In findRxnsFromSubSystem (line 31)
In writeSBML (line 460)
In writeCbModel (line 231)
Warning: The "rxn2subSystem" field has been generated because it was not in the model.
In findRxnsFromSubSystem (line 31)
In writeSBML (line 460)
In writeCbModel (line 231)
Warning: The "rxn2subSystem" field has been generated because it was not in the model.
In findRxnsFromSubSystem (line 31)
In writeSBML (line 460)
In writeCbModel (line 231)
Warning: The "rxn2subSystem" field has been generated because it was not in the model.
In findRxnsFromSubSystem (line 31)
In writeSBML (line 460)
In writeCbModel (line 231)
Warning: The "rxn2subSystem" field has been generated because it was not in the model.
In findRxnsFromSubSystem (line 31)
In writeSBML (line 460)
In writeCbModel (line 231)
Warning: The "rxn2subSystem" field has been generated because it was not in the model.
In findRxnsFromSubSystem (line 31)
In writeSBML (line 460)
In writeCbModel (line 231)
Warning: The "rxn2subSystem" field has been generated because it was not in the model.
In findRxnsFromSubSystem (line 31)
In writeSBML (line 460)
In writeCbModel (line 231)
Warning: The "rxn2subSystem" field has been generated because it was not in the model.
In findRxnsFromSubSystem (line 31)
In writeSBML (line 460)
In writeCbModel (line 231)
Warning: The "rxn2subSystem" field has been generated because it was not in the model.
In findRxnsFromSubSystem (line 31)
In writeSBML (line 460)
In writeCbModel (line 231)
Warning: The "rxn2subSystem" field has been generated because it was not in the model.
In findRxnsFromSubSystem (line 31)
In writeSBML (line 460)
In writeCbModel (line 231)
Warning: The "rxn2subSystem" field has been generated because it was not in the model.
In findRxnsFromSubSystem (line 31)
In writeSBML (line 460)
In writeCbModel (line 231)
Warning: The "rxn2subSystem" field has been generated because it was not in the model.
In findRxnsFromSubSystem (line 31)
In writeSBML (line 460)
In writeCbModel (line 231)
Warning: The "rxn2subSystem" field has been generated because it was not in the model.
In findRxnsFromSubSystem (line 31)
In writeSBML (line 460)
In writeCbModel (line 231)
Warning: The "rxn2subSystem" field has been generated because it was not in the model.
In findRxnsFromSubSystem (line 31)
In writeSBML (line 460)
In writeCbModel (line 231)
Warning: The "rxn2subSystem" field has been generated because it was not in the model.
In findRxnsFromSubSystem (line 31)
In writeSBML (line 460)
In writeCbModel (line 231)
Warning: The "rxn2subSystem" field has been generated because it was not in the model.
In findRxnsFromSubSystem (line 31)
In writeSBML (line 460)
In writeCbModel (line 231)
Warning: The "rxn2subSystem" field has been generated because it was not in the model.
In findRxnsFromSubSystem (line 31)
In writeSBML (line 460)
In writeCbModel (line 231)
Warning: The "rxn2subSystem" field has been generated because it was not in the model.
In findRxnsFromSubSystem (line 31)
In writeSBML (line 460)
In writeCbModel (line 231)
Warning: The "rxn2subSystem" field has been generated because it was not in the model.
In findRxnsFromSubSystem (line 31)
In writeSBML (line 460)
In writeCbModel (line 231)
Warning: The "rxn2subSystem" field has been generated because it was not in the model.
In findRxnsFromSubSystem (line 31)
In writeSBML (line 460)
In writeCbModel (line 231)
Warning: The "rxn2subSystem" field has been generated because it was not in the model.
In findRxnsFromSubSystem (line 31)
In writeSBML (line 460)
In writeCbModel (line 231)
Warning: The "rxn2subSystem" field has been generated because it was not in the model.
In findRxnsFromSubSystem (line 31)
In writeSBML (line 460)
In writeCbModel (line 231)
Warning: The "rxn2subSystem" field has been generated because it was not in the model.
In findRxnsFromSubSystem (line 31)
In writeSBML (line 460)
In writeCbModel (line 231)
Warning: The "rxn2subSystem" field has been generated because it was not in the model.
In findRxnsFromSubSystem (line 31)
In writeSBML (line 460)
In writeCbModel (line 231)
Warning: The "rxn2subSystem" field has been generated because it was not in the model.
In findRxnsFromSubSystem (line 31)
In writeSBML (line 460)
In writeCbModel (line 231)
Warning: The "rxn2subSystem" field has been generated because it was not in the model.
In findRxnsFromSubSystem (line 31)
In writeSBML (line 460)
In writeCbModel (line 231)
Warning: The "rxn2subSystem" field has been generated because it was not in the model.
In findRxnsFromSubSystem (line 31)
In writeSBML (line 460)
In writeCbModel (line 231)
Warning: The "rxn2subSystem" field has been generated because it was not in the model.
In findRxnsFromSubSystem (line 31)
In writeSBML (line 460)
In writeCbModel (line 231)
Warning: The "rxn2subSystem" field has been generated because it was not in the model.
In findRxnsFromSubSystem (line 31)
In writeSBML (line 460)
In writeCbModel (line 231)
Warning: The "rxn2subSystem" field has been generated because it was not in the model.
In findRxnsFromSubSystem (line 31)
In writeSBML (line 460)
In writeCbModel (line 231)
Warning: The "rxn2subSystem" field has been generated because it was not in the model.
In findRxnsFromSubSystem (line 31)
In writeSBML (line 460)
In writeCbModel (line 231)
Warning: The "rxn2subSystem" field has been generated because it was not in the model.
In findRxnsFromSubSystem (line 31)
In writeSBML (line 460)
In writeCbModel (line 231)
Warning: The "rxn2subSystem" field has been generated because it was not in the model.
In findRxnsFromSubSystem (line 31)
In writeSBML (line 460)
In writeCbModel (line 231)
Warning: The "rxn2subSystem" field has been generated because it was not in the model.
In findRxnsFromSubSystem (line 31)
In writeSBML (line 460)
In writeCbModel (line 231)
Warning: The "rxn2subSystem" field has been generated because it was not in the model.
In findRxnsFromSubSystem (line 31)
In writeSBML (line 460)
In writeCbModel (line 231)
Warning: The "rxn2subSystem" field has been generated because it was not in the model.
In findRxnsFromSubSystem (line 31)
In writeSBML (line 460)
In writeCbModel (line 231)
Warning: The "rxn2subSystem" field has been generated because it was not in the model.
In findRxnsFromSubSystem (line 31)
In writeSBML (line 460)
In writeCbModel (line 231)
Warning: The "rxn2subSystem" field has been generated because it was not in the model.
In findRxnsFromSubSystem (line 31)
In writeSBML (line 460)
In writeCbModel (line 231)
Warning: The "rxn2subSystem" field has been generated because it was not in the model.
In findRxnsFromSubSystem (line 31)
In writeSBML (line 460)
In writeCbModel (line 231)
Warning: The "rxn2subSystem" field has been generated because it was not in the model.
In findRxnsFromSubSystem (line 31)
In writeSBML (line 460)
In writeCbModel (line 231)
Warning: The "rxn2subSystem" field has been generated because it was not in the model.
In findRxnsFromSubSystem (line 31)
In writeSBML (line 460)
In writeCbModel (line 231)
Warning: The "rxn2subSystem" field has been generated because it was not in the model.
In findRxnsFromSubSystem (line 31)
In writeSBML (line 460)
In writeCbModel (line 231)
Warning: The "rxn2subSystem" field has been generated because it was not in the model.
In findRxnsFromSubSystem (line 31)
In writeSBML (line 460)
In writeCbModel (line 231)
Warning: The "rxn2subSystem" field has been generated because it was not in the model.
In findRxnsFromSubSystem (line 31)
In writeSBML (line 460)
In writeCbModel (line 231)
Warning: The "rxn2subSystem" field has been generated because it was not in the model.
In findRxnsFromSubSystem (line 31)
In writeSBML (line 460)
In writeCbModel (line 231)
Warning: The "rxn2subSystem" field has been generated because it was not in the model.
In findRxnsFromSubSystem (line 31)
In writeSBML (line 460)
In writeCbModel (line 231)
Warning: The "rxn2subSystem" field has been generated because it was not in the model.
In findRxnsFromSubSystem (line 31)
In writeSBML (line 460)
In writeCbModel (line 231)
Warning: The "rxn2subSystem" field has been generated because it was not in the model.
In findRxnsFromSubSystem (line 31)
In writeSBML (line 460)
In writeCbModel (line 231)
Warning: The "rxn2subSystem" field has been generated because it was not in the model.
In findRxnsFromSubSystem (line 31)
In writeSBML (line 460)
In writeCbModel (line 231)
Warning: The "rxn2subSystem" field has been generated because it was not in the model.
In findRxnsFromSubSystem (line 31)
In writeSBML (line 460)
In writeCbModel (line 231)
Warning: The "rxn2subSystem" field has been generated because it was not in the model.
In findRxnsFromSubSystem (line 31)
In writeSBML (line 460)
In writeCbModel (line 231)
Warning: The "rxn2subSystem" field has been generated because it was not in the model.
In findRxnsFromSubSystem (line 31)
In writeSBML (line 460)
In writeCbModel (line 231)
Warning: The "rxn2subSystem" field has been generated because it was not in the model.
In findRxnsFromSubSystem (line 31)
In writeSBML (line 460)
In writeCbModel (line 231)
Warning: The "rxn2subSystem" field has been generated because it was not in the model.
In findRxnsFromSubSystem (line 31)
In writeSBML (line 460)
In writeCbModel (line 231)
Warning: The "rxn2subSystem" field has been generated because it was not in the model.
In findRxnsFromSubSystem (line 31)
In writeSBML (line 460)
In writeCbModel (line 231)
Warning: The "rxn2subSystem" field has been generated because it was not in the model.
In findRxnsFromSubSystem (line 31)
In writeSBML (line 460)
In writeCbModel (line 231)
Warning: The "rxn2subSystem" field has been generated because it was not in the model.
In findRxnsFromSubSystem (line 31)
In writeSBML (line 460)
In writeCbModel (line 231)
Warning: The "rxn2subSystem" field has been generated because it was not in the model.
In findRxnsFromSubSystem (line 31)
In writeSBML (line 460)
In writeCbModel (line 231)
Warning: The "rxn2subSystem" field has been generated because it was not in the model.
In findRxnsFromSubSystem (line 31)
In writeSBML (line 460)
In writeCbModel (line 231)
Warning: The "rxn2subSystem" field has been generated because it was not in the model.
In findRxnsFromSubSystem (line 31)
In writeSBML (line 460)
In writeCbModel (line 231)
Warning: The "rxn2subSystem" field has been generated because it was not in the model.
In findRxnsFromSubSystem (line 31)
In writeSBML (line 460)
In writeCbModel (line 231)
Warning: The "rxn2subSystem" field has been generated because it was not in the model.
In findRxnsFromSubSystem (line 31)
In writeSBML (line 460)
In writeCbModel (line 231)
Warning: The "rxn2subSystem" field has been generated because it was not in the model.
In findRxnsFromSubSystem (line 31)
In writeSBML (line 460)
In writeCbModel (line 231)
Warning: The "rxn2subSystem" field has been generated because it was not in the model.
In findRxnsFromSubSystem (line 31)
In writeSBML (line 460)
In writeCbModel (line 231)
Warning: The "rxn2subSystem" field has been generated because it was not in the model.
In findRxnsFromSubSystem (line 31)
In writeSBML (line 460)
In writeCbModel (line 231)
Unrecognized function or variable 'OutputSBML'.

Error in writeSBML (line 652)
OutputSBML(sbmlModel,fileName,1,0,[1,0]);
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
Error in writeCbModel (line 231)
outmodel = writeSBML(model, fileName, input.compSymbols, input.compNames);
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
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@CCThinnes