Unable to ran model xml in memote

[hites77]

I tried to check the constructed model in memote but it hangs at around testconsistency.

Also when I tried to load draft model in Cobratoolbox it gives error
modelFileName = 'Test1_gapseq_draft.xml';
model = readCbModel(modelFileName);
Output argument "qualifiers" (and maybe others) not assigned during call to "getDataBases".

Error in parseCVTerms (line 27)
[databases,identifiers,relations] = cellfun(@getDataBases, {CVTerms.resources},
{CVTerms.qualifier},'UniformOutput',0);

Error in readSBML (line 121)
[databases,identifiers,qualifiers] = cellfun(@parseCVTerms, cvterms,'UniformOutput',0);

Error in readCbModel (line 211)
model = readSBML(fileName,defaultBound);

Please advice on the compatibility and standard output of the model

[Waschina]

Thank you for reporting this issue. I corrected parts in the SBML model output that caused errors in the SBML validator and in memote. I have tested memote, the SBML validator as well as to read the sbml-file into coprapy for a bacterial example and everything seems to work again just fine. However, I couldn't test it in the cobratoolbox, as I do not have matlab running on my current system. Please let me know if you still experience problems with gapseq's sbml files.

Best
Silvio

[Waschina]

I have tested a couple of further gapseq models with memote, which ran all perfectly. Please re-open this issue if you still experience errors in memote with gapseq models and we will try to resolve it as quickly as possible.
Best
Silvio

[hites77]

Thanks, the sbml file worked with memote, I just skip the blast step as mentioned in the manuscript.