Error creating pan-models from AGORA2 reconstructions

[Ari Ufondu]

Hello Community,

Is it possible to create pan-models such as pan genus models from AGORA2 models? I have created pan genus models from AGORA previously without any issues, but when I try to do it with AGORA2, I run into the following error message:

I already tried deleting the model in the error but it doesn't seem to change anything. I would greatly appreciate any help on this matter!

Best,

Ari Ufondu

[Almut Heinken]

Dear Ari,

it is also possible to create pan-models for AGORA2. Did you change the third input to the file with taxonomic information for AGORA2 (AGORA2_infoFile)?

Best regards,

Almut

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[Almut Heinken]

Sorry, I meant the fifth input (optional)

[Ari Ufondu]

Hi Almut,

Thanks for the reply. I am looking at the AGORA2_infoFile.xlsx found in cobratoolbox > papers > 2021_demeter > input

When you say the fifth input, do you mean the fifth column of the file which is the "species" column or do you mean the fifth row which is the bacterium "Acetanaerobacterium_elongatum_CGMCC_1_5012"?

What should I change it to? Thanks in advance for the clarification!

Best,

Ari

[Almut Heinken]

Dear Ari,

sorry for the confusion. I meant that the (optional) fifth input in the function needs to be set as follows:

createPanModels(agoraPath, panPath, taxonLevel, numWorkers, 'AGORA2_infoFile.xlsx')

I suppose that input could be made mandatory to make the use of the function more clear.

Best regards,

Almut

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[Ari Ufondu]

Dear Almut,

Thanks for the clarification! I tried your suggestion but I am running into the same problem, although the crash happens with a different microbe this time: 

Here are my latest commands for reference:

  solverOK=changeCobraSolver('ibm_cplex','LP');

  agoraPath = [pwd filesep 'AGORA2models']; 

  numWorkers = 4; 

  panPath=[pwd filesep 'panAGORA2GenusModels']; 

  taxonLevel='Genus'; 

  createPanModels(agoraPath,panPath,taxonLevel,numWorkers,'AGORA2_infoFile.xlsx');  

Best,

Ari

[Almut Heinken]

Dear Ariu,

the function requires that all AGORA2 reconstructions are present in the "agoraPath"folder, so you will get an error if it cannot find them.

Best regards,

Almut

To view this discussion on the web visit https://groups.google.com/d/msgid/cobra-toolbox/e89c933e-3407-4ead-8794-7a7d9772451an%40googlegroups.com.