Problem with fastgapfill in Matlab

[Enuh Blaise]

Hello,

Thank you for adding me to the group. I am a new COBRA user presently using the tool to develop a models for Polyhydroxybutyrate production in halophiles.

I have a draft reconstruction from carveme with some blocked reactions and dead end metabolites, tried to do a fastgapfill in cobra but it gives an error after several hours of running.

I used the code

%%Identification of dead-end and Blocked reactions
deadEndMetabolites = detectDeadEnds(model);
[deadEndMetabolites, rootGaps, downstreamGaps] = gapFind(model, 'true');
blockedReactions = findBlockedReaction(model);

%%Gapfinding in the model
%%Metabolites that cannot be produced or consumed by any of the reactions in the network are referred to asrootGaps
 [allGaps, rootGaps, downstreamGaps] = gapFind(model, findNCgaps, verbFlag);

%%Prepare Gapfilling
[consistModel, consistMatricesSUX, blockedRxns] = prepareFastGapFill(model);

Attached is my systems configuration report and a screenshot of the error. I tried re running the code 2 to 3 more times but got the same error. I dont know what happened. Please I need some help. 

Enuh

[Kretaks]

Hey Enuh,

I would suggest you go to the solveCobraLP.m line 943 and put a breakpoint there.

Run the code again and when it stops at that line check what structure LPproblem has. Sense should contain '='. I am guessing your model has wrong values there.

I am guessing there are several ways to fix this. My first try would be deleting model.sense field and test if it works

Hope this helps,

Kristaps

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[Enuh Blaise]

Hello Kristaps,

Thank you for your response, I will implement these suggestions and hopefully it works. 

On a fundamental level, what is the cause of this issue, if I may ask, So i could probably generate other possible fixes and try them.

Enuh 

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[Kretaks]

Hello Enuh,

I would need to see the structure of your model to answer this question.

I suspect sense field is defined incorrectly

Kristaps

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[Enuh Blaise]

Hello Kristaps

I have included the structure. Thats how it looks like when directly read from the CarveMe xml output with readCbModel

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[Kretaks]

Hello Enuh,

Can you show a snippet of model.csense field?

Kristaps

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[Enuh Blaise]

Hello Christaps

Sure, It is an array of only "E"s

Enuh

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[Kretaks]

Hello Enuh,

Seems like none of my initial ideas about causes of your problem turned out to be correct

There are few google results about gurobi errors similar to yours

for example:

https://groups.google.com/g/gurobi/c/Bb2VwVOXLH0

My best guess is that somewhere in prepareFastGapFill.m function model.sense field is created in different length as model.A field and that creates error.

If you could provide your model, I could try to recreate the error you get and try to find a solution

Kristaps

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[Enuh Blaise]

Hello Kristaps,

Sure the model can be accessible from https://drive.google.com/file/d/1E7E8kP038T44JLhKKWWmlzIJ4xWT9SZ9/view?usp=sharing

Thank you for your help

Enuh

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[Ronan M.T. Fleming]

https://github.com/opencobra/cobratoolbox/blob/master/docs/source/notes/COBRAModelFields.md

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[Kretaks]

Hello Enuh,

Sorry that it took so long for me to write this,

Your model contains reactions and metabolites whose names are different from those in the default dictionary file.

For example your model contains met names: "Nicotinamide adenine dinucleotide" while default dictionary file has name NAD

For successful gap fill you should create your own dictionary -> model.metNames to KEGG names

That can be done by parsing your model xml file for met names and their respective KEGG identifiers.

I hope someone who knows this function better can correct me if I am wrong

Best wishes,

Kristaps

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[Enuh Blaise]

Hello Kristaps,

Thank you for your reply. From Dr. Ronan's reply and yours I see there is a problem of file structure. means this could probably be during parsing. I was also thinking maybe there is an incompatibility between gurobi 9.1.1., Matlab 2018b and and cobra v3. I am also trying to vary the versions according to the cobra tutorials to see if it gets solved. While waiting for others response, If i get a fix i will share in the group as well. Thank you once more

Regards

Enuh

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