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Got an Error in single2IntPopModel function #6

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PratikPathade opened this issue Mar 13, 2023 · 3 comments
Open

Got an Error in single2IntPopModel function #6

PratikPathade opened this issue Mar 13, 2023 · 3 comments

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@PratikPathade
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I am trying to run this command
HMRcore = ScFBAExpSetting(HMRcore, length(BC04.CellType));
got an error like this:-
Error using EditBoundaries
Too many input arguments.

Error in ScFBAExpSetting (line 30)
model = EditBoundaries(model, 'SLC25A5_SLC25A4_SLC25A6', 0,10000, false, false);

I am not sure why I am getting this error.
and in the next step.
BC04 = single2IntPopModel(BC04, HMRcore, IdxExRxns, IdxCoopRxn, 's');

Error:-
Error using parseCobraVarargin
The value of 'osenseStr' is invalid. It must satisfy the function: @(x)strcmp(x,'max')|strcmp(x,'min').

Error in fluxVariability (line 115)
[funParams, cobraParams, solverVarargin] = parseCobraVarargin(varargin, optArgin, defaultValues, validator, problemTypes, 'solverParams', true);

Error in integrateRAS (line 32)
[Fmin,FMax] = fluxVariability(modelPop, 100, '', RxnList); %controllare che 100 vada bene

Error in single2IntPopModel (line 87)
scStruct = integrateRAS(scStruct, 'modelDel');

getting this error I am not able to understand please explain.
Screenshot from 2023-03-13 16-31-22

@kiaradamiani
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We apologize for the inconvenience. We are having compatibility issues with the latest version of Cobra and other dependencies.
We have pushed a new version of the tool that should at least fix the error in fluxVariability (line 115).
Please let us know if you are still having trouble.

@PratikPathade
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Thank you for your reply. it got fixed, I am using cobra version 2.0, and now it's running fine. also, I wanted to ask you I am working on scRNA seq data and if I am using the HUMAN GEM model as a templated model. do I need to make changes to that model, please let me know.

@PratikPathade
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It would be helpful if you help me with this error.
image

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