Comments (3)
Hi Matt,
may you try also updating the COBRA.papers folder to test if that solves the issue?
Best regards,
Almut
from cobra.tutorials.
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
from cobra.tutorials.
from cobra.tutorials.
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