Error in Pan-models creation

[pharitporn hianghakun]

Hello, 

 

By following the tutorial instruction both live script and one provided on Creation and simulation of personalized microbiota models through metagenomic data integration — The COBRA Toolbox (opencobra.github.io) , I have problems about creating pan-models from AGORA on different taxonomical levels.  For the solver, I use glpk, LP because some installation problem of IBM. 

Related to adding unmapped species' abundance, the instruction description is not clear since I'm a beginner. Could you give me a step by step for adding the unmapped species?

Kind regards, 

Thiyada

[Almut Heinken]

Hi,

could you make sure that the COBRA.papers folder is up to date and then try again? It seems this is caused by an outdated version of the reaction database. You may need to update COBRA.papers separately in GitHub.

Kind regards,

Almut

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[Almut Heinken]

Hi,

regarding your second question: I have created a function for this purpose, translateMetagenome2AGORA. It takes as input the path to a file with organism abundances with the taxa as rows and the sample names as columns. The tutorial provides an example for such a file. Unfortunately, the function may not work on every possible file since the nomenclature varies. Hence, you need to inspect the output "unmappedRows" to find the taxa that could not be mapped. You could also map the taxa in your file to the corresponding AGORA (pan-)models manually and then normalize the abundances via the function normalizeCoverage.

I hope that helps.

KInd regards,

Almut

[PHARITPORN HIANGHAKUN]

Hello Almut,

I have checked the COBRA.papers folder. It is up to date. After I tried it, there’s the same error.

 

Here is my screen shot in COBRA.papers.

Kind regards,

Pharitporn

 

 

 

From: Almut Heinken
Sent: 22 มิถุนายน 2564 0:32
To: cobra-...@googlegroups.com
Subject: [SOCIAL NETWORK] Re: Error in Pan-models creation

 

Hi,

could you make sure that the COBRA.papers folder is up to date and then try again? It seems this is caused by an outdated version of the reaction database. You may need to update COBRA.papers separately in GitHub.

Kind regards,

Almut

 

On Mon, Jun 21, 2021 at 11:58 AM pharitporn hianghakun <pharitp...@mail.kmutt.ac.th> wrote:

Hello, 

 

 

 

By following the tutorial instruction both live script and one provided on Creation and simulation of personalized microbiota models through metagenomic data integration — The COBRA Toolbox (opencobra.github.io) , I have problems about creating pan-models from AGORA on different taxonomical levels.  For the solver, I use glpk, LP because some installation problem of IBM. 

 

Related to adding unmapped species' abundance, the instruction description is not clear since I'm a beginner. Could you give me a step by step for adding the unmapped species?

 

 

Kind regards, 

 

Thiyada

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[Almut Heinken]

Hi Pharitporn,

may you check that the files cobratoolbox/papers/2021_demeter/input/ReactionDatabase.txt and MetaboliteDatabase.txt are up to date?

The last edit was yesterday. See also https://github.com/opencobra/COBRA.papers/tree/master/2021_demeter/input.

Kind regards,

Almut

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[PHARITPORN HIANGHAKUN]

Hello Almut,

 

It was confirmed that the file is up to date, last modification was on 22^nd of June.

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[Almut Heinken]

Hi Pharitporn,

in that case, I am not what the issue is. Could you run the script with "Stop on errors" active to find out where exactly it crashes and take a screenshot? You probably need to change line 120 from parfor to for.

best,

Almut

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[PHARITPORN HIANGHAKUN]

Hello Almut,

Here is the screenshot.

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[Almut Heinken]

Hi,

could you disable the parfor loop (by changing it to for) so it stops within rebuildModel? Sorry for the trouble.

best,

Almut

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