Error importing KBase SBML model in COBRA Toolbox

[Panji Ilahi Halomoan Banurea]

Hello everyone,

I am new to MATLAB and COBRA Toolbox, and I am trying to load an SBML model

exported from KBase into COBRA.

Here is the code I used:

>>initCobraToolbox(false);

changeCobraSolver('gurobi','LP',1);

 

>>fileName = 'D:\Shared\Lab\Methylocystis_NC52PC_rumen.gbk_genome.mdl.xml';

modelOri = readCbModel(fileName)

 

But I am getting the following error message:
Error using  :
Colon operands must be real scalars.

Error in getDefinedFieldProperties (line 90)
        for i = 1:size(relarray)
                 ^
Error in getDatabaseMappings (line 38)
mappings = getDefinedFieldProperties('Database',true);
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
Error in mapAnnotationsToFields (line 46)
knownMappings = getDatabaseMappings(field);
                ^^^^^^^^^^^^^^^^^^^^^^^^^^
Error in readSBML (line 122)
        model = mapAnnotationsToFields(model,databases,identifiers,qualifiers,'met');
                ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
Error in readCbModel (line 211)
        model = readSBML(fileName,defaultBound);
                ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

My setup:

- MATLAB R2025b

- COBRA Toolbox 0.30.0

- Windows 11

 

I’m not sure what I did wrong. I would really appreciate any guidance or suggestions.

Best regards,
Banurea

[Farid Zare]

Dear Panji,
Please send me the SBML model that you are working on so that I can reproduce the error and see what the problem is.
Regards,
Farid

--

Farid Zare MSc

-----------------------------------------------------

Ph.D. Student at the University of Galway, Ireland

Digital Metabolic Twin Centre

Member of Recon4IMD & COBRA toolbox

Mobile: +353 87 490 1738

LinkedIn: farid-zare

GitHub: farid-zare

GitLab: farid-zare

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