addMultipleReactions error in mgPipe tutorial

[mmiyasa]

I've been trying to run the tutorial_mgPipe.m, but after the pan-models are created, I get the following error:

Error using addMultipleReactions (line 162) Subscripted assignment dimension mismatch.

Error in addMicrobeCommunityBiomass (line 42) dummy = addMultipleReactions(dummy,rxns,mets,S,'lb',lb,'ub',ub);

Error in createPersonalizedModel (line 73)

I believe all of my cobratoolbox files are up to date. Is there something I might be missing?

Sincerely,

Matt

[almut-heinken]

Hi Matt, may you try also updating the COBRA.papers folder to test if that solves the issue? Best regards, Almut

[yhbae6022]

Hi all,

I think I found a bug in mgPipe tutorial(tutorial_mgPipe.m).

In line 205

[init, netSecretionFluxes, netUptakeFluxes, Y, modelStats, summary] = initMgPipe(modPath, abunFilePath, computeProfiles, 'dietFilePath', dietFilePath, 'infoFilePath', infoFilePath, 'saveConstrModels', saveConstrModels, 'numWorkers', numWorkers);

should be

[init, netSecretionFluxes, netUptakeFluxes, Y, modelStats, summary] = initMgPipe(modPath, abunFilePath, computeProfiles, 'dietFilePath', dietFilePath, 'infoFilePath', infoFilePath, 'numWorkers', numWorkers);

It seems that initMgPipe() module does not support 'saveConstrModels' option anymore.

And I encountered another error in the initMgPipe module like follows

Error using microbiotaModelSimulator>(parfor supply)
An UndefinedFunction error was thrown on the workers for 'Diets'.  This might be because the file
containing 'Diets' is not accessible on the workers.  Use addAttachedFiles(pool, files) to specify
the required files to be attached.  For more information see the documentation for
'parallel.Pool/addAttachedFiles'.

Error in microbiotaModelSimulator (line 179)
        parfor k=s:s+endPnt

Error in mgPipe (line 268)
[exchanges, netProduction, netUptake, presolve, infeasModels] = microbiotaModelSimulator(resPath,
exMets, sampNames, dietFilePath, hostPath, hostBiomassRxn, hostBiomassRxnFlux, numWorkers, rDiet,
pDiet, computeProfiles, lowerBMBound, upperBMBound, includeHumanMets, adaptMedium);

Error in initMgPipe (line 172)
[netSecretionFluxes, netUptakeFluxes, Y, modelStats, summary, statistics, modelsOK] =
mgPipe(modPath, abunFilePath, computeProfiles, resPath, dietFilePath, infoFilePath, hostPath,
hostBiomassRxn, hostBiomassRxnFlux, figForm, numWorkers, rDiet, pDiet, lowerBMBound, upperBMBound,
includeHumanMets, adaptMedium);

Error in tutorial_mgPipe.m (line 205)

Caused by:
    Undefined function or variable 'Diets'.

Could you advise me to solve this problem?

Best regards, Young-Ho

[almut-heinken]

Hi Young-Ho, the input parameter has indeed been removed and models with diet constraints are now always saved. This has already been changed in the tutorial on the develop branch, but not yet in the master branch. Unfortunately, I cannot reproduce the second error. Kind regards, Almut

On Mon, Dec 27, 2021 at 10:26 AM Young-Ho Bae @.***> wrote:

Hi all,

I think I found a bug in mgPipe tutorial(tutorial_mgPipe.m).

In line 205

[init, netSecretionFluxes, netUptakeFluxes, Y, modelStats, summary] = initMgPipe(modPath, abunFilePath, computeProfiles, 'dietFilePath', dietFilePath, 'infoFilePath', infoFilePath, 'saveConstrModels', saveConstrModels, 'numWorkers', numWorkers);

should be

[init, netSecretionFluxes, netUptakeFluxes, Y, modelStats, summary] = initMgPipe(modPath, abunFilePath, computeProfiles, 'dietFilePath', dietFilePath, 'infoFilePath', infoFilePath, 'numWorkers', numWorkers);

It seems that initMgPipe() module does not support 'saveConstrModels' option anymore.

And I encountered another error in the initMgPipe module like follows

Error using microbiotaModelSimulator>(parfor supply) An UndefinedFunction error was thrown on the workers for 'Diets'. This might be because the file containing 'Diets' is not accessible on the workers. Use addAttachedFiles(pool, files) to specify the required files to be attached. For more information see the documentation for 'parallel.Pool/addAttachedFiles'.

Error in microbiotaModelSimulator (line 179) parfor k=s:s+endPnt

Error in mgPipe (line 268) [exchanges, netProduction, netUptake, presolve, infeasModels] = microbiotaModelSimulator(resPath, exMets, sampNames, dietFilePath, hostPath, hostBiomassRxn, hostBiomassRxnFlux, numWorkers, rDiet, pDiet, computeProfiles, lowerBMBound, upperBMBound, includeHumanMets, adaptMedium);

Error in initMgPipe (line 172) [netSecretionFluxes, netUptakeFluxes, Y, modelStats, summary, statistics, modelsOK] = mgPipe(modPath, abunFilePath, computeProfiles, resPath, dietFilePath, infoFilePath, hostPath, hostBiomassRxn, hostBiomassRxnFlux, figForm, numWorkers, rDiet, pDiet, lowerBMBound, upperBMBound, includeHumanMets, adaptMedium);

Error in tutorial_mgPipe.m (line 205)

Caused by: Undefined function or variable 'Diets'.

Could you advise me to solve this problem?

Best regards, Young-Ho

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