No results from simulate the pairwise interactions

[Panji Ilahi Halomoan Banurea]

Hello everyone,

I am Panji, currently learning to use the COBRA Toolbox to study microbe–microbe metabolic interactions.

I have successfully run the steps up to the “Define what counts as significant difference” section in tutorial. However, when I execute the following code:

for i = 1:length(conditions)
    % assign dietary constraints
    [pairwiseInteractions]=simulatePairwiseInteractions(resPath,'inputDiet',dietConstraints{i},'sigD',sigD,'saveSolutionsFlag', false,'numWorkers', numWorkers);
Interactions.(conditions{i})=pairwiseInteractions;
end

the Command Window prints many messages, for example:

Warning: Reaction EX_meoh[u] not in model
> In changeRxnBounds (line 50)
In useDiet (line 54)
Warning: Reaction EX_meoh[u] not in model
> In changeRxnBounds (line 59)
In useDiet (line 54)
Warning: Reaction EX_meoh[u] not in model
> In changeRxnBounds (line 50)
In useDiet (line 62)

However, I do not get any output or saved results.
Could you please advise what could cause the simulation to produce no results?
Thank you very much for your help.

Best regards,  
Panji

[Almut Heinken]

Dear Panji,

did you run the tutorial as is or did you modify it?

The output should be a structure called "Interactions" in the workspace, which contains the predicted pairwise behavior. A figure is also generated. Is this not the case?

The warning messages that appear are not a problem.

Best regards,

Almut

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[Banurea, Panji Ilahi Halomoan]

Dear Almut,

Thank you very much for your response.
I ran the tutorial exactly as written. I meant to say that the interaction results were “Infeasible,” rather than “no result.” However, in the second run, I obtained feasible outcomes such as Commensalism, Amensalism, and Parasitism. Everything is working as expected now.

Best regards,
Panji

2025년 11월 11일 (화) 오전 3:40, Almut Heinken <almut....@gmail.com>님이 작성:

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