Adding exchange reaction ... with default bounds for boundary metabolite: ... & Ignoring reaction ... since it already exists.

[Patrickens]

Hey, for all the models that I carve, when I load them in cobra, I get the following errors.

I run: carve C:\data\differential_bio\fasta\aa\Lrham.faa --universe grampos --fbc2 -o C:\data\differential_bio\gem\Lrham_a7498ba6.xml

and then:

import cobra
gem_path = os.path.join(DATA_DIR, 'gem', STRAINS_INFO['Lrham']['default_gem'])
model = cobra.io.read_sbml_model(gem_path)

And then for every exchange we get:

Adding exchange reaction EX_13ppd_e with default bounds for boundary metabolite: 13ppd_e.
Adding exchange reaction EX_25dkglcn_e with default bounds for boundary metabolite: 25dkglcn_e.
....
Ignoring reaction 'EX_13ppd_e' since it already exists.
Ignoring reaction 'EX_25dkglcn_e' since it already exists.

Something in the storing of the models seems to be off, but i cannot figure out what. For the created model the xml looks as follows:

<reaction metaid="meta_R_EX_13ppd_e" sboTerm="SBO:0000627" id="R_EX_13ppd_e" name="R_EX_13ppd_e" reversible="true" fast="false" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
        <listOfReactants>
          <speciesReference species="M_13ppd_e" stoichiometry="1" constant="true"/>
        </listOfReactants>
      </reaction>
      <reaction metaid="meta_R_EX_25dkglcn_e" sboTerm="SBO:0000627" id="R_EX_25dkglcn_e" name="R_EX_25dkglcn_e" reversible="true" fast="false" fbc:lowerFluxBound="cobra_default_lb" fbc:upperFluxBound="cobra_default_ub">
        <listOfReactants>
          <speciesReference species="M_25dkglcn_e" stoichiometry="1" constant="true"/>
        </listOfReactants>
      </reaction>

For the iJO1366 model, these look as follows:

<reaction id="R_EX_colipa_e" fast="false" reversible="false" name="Core oligosaccharide lipid A exchange" metaid="R_EX_colipa_e" sboTerm="SBO:0000627" fbc:upperFluxBound="cobra_default_ub" fbc:lowerFluxBound="cobra_0_bound">
        <sbml:annotation xmlns:sbml="http://www.sbml.org/sbml/level3/version1/core">
          <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
            <rdf:Description rdf:about="#R_EX_colipa_e">
              <bqbiol:is xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
                <rdf:Bag>
                  <rdf:li rdf:resource="http://identifiers.org/bigg.reaction/EX_colipa_e"/>
                  <rdf:li rdf:resource="http://identifiers.org/metanetx.reaction/MNXR96846"/>
                  <rdf:li rdf:resource="http://identifiers.org/seed.reaction/rxn08244"/>
                </rdf:Bag>
              </bqbiol:is>
            </rdf:Description>
          </rdf:RDF>
        </sbml:annotation>
        <listOfReactants>
          <speciesReference species="M_colipa_e" stoichiometry="1" constant="true"/>
        </listOfReactants>
      </reaction>

I do not see anything that could explain the cobra.io behavior. Do you have any ideas?