fastGapFill example problem

[Betul Baz]

Hi everyone,

I want to use 'fastGapFill' function and I try to understand first from their 'runGapFill_example' tutorial but even in tutorial, I got some errors. 

These are the model in the tutorial:

Filename={'iTZ479_v2.mat'; % Thermotoga maritima as published in Nogales et al., Int J Hydrogen Energ, 37(17), 12205–12218 (2012)

    'iJN678_Published.mat'; % Synechocystis sp. PCC6803 as published in Nogales et al., PNAS, 109(7):2678-83 (2012)

    'iAF1260.mat'; % E. coli as published in Feist et al., Mol Syst Biol (2007)

    'IEC1907.mat'; % small intestinal entercyte as published in Sahoo et al., Human Mol Genet, 22(13):2705-2722 (2012)

    '121114_Recon2betaRecon.mat'; % Human metabolic reconstruction as published in Thiele et al., Nat. Biotech., 31(5):419-25 (2013)

    };

and for the first 3 three model I got this error:

___________________________________________________________________

The following problems have been encountered in the model structure

inconsistentFields:

csense: mets: Size of csense does not match elements in mets

Error using buildLPproblemFromModel (line 62)

The input model does have inconsistent fields! Use verifyModel(model) for further information.

Error in fastcc (line 53)

LPproblem = buildLPproblemFromModel(model);

Error in prepareFastGapFill (line 151)

A = fastcc(MatricesSUX, epsilon);

For the green one( 'IEC1907.mat'; ), 'prepareFastGapFill' could run but it stucked with 'fastGapFill' for several hours and when I terminate it, I got:

________________________________________________________________________

|J|=629  

Interrupt request received

Error using isfinite

Requested 265948x217278 (53.8GB) array exceeds maximum

array size preference. Creation of arrays greater than

this limit may take a long time and cause MATLAB to become

unresponsive. See array size limit or preference panel for

more information.

Error in solveCobraLP (line 1450)

    if any(any(~isfinite(A)))

Error in LP9weighted (line 45)

solution = solveCobraLP(LP9problem);

Error in findSparseModeWeighted (line 44)

V = LP9weighted( weights, K, P, model, LPproblem, epsilon

);

Error in fastCoreWeighted (line 43)

Supp = findSparseModeWeighted( J, P, singleton, model,

LPproblem, weights, epsilon );

Error in fastGapFill (line 54)

A2 = fastCoreWeighted(consistMatricesSUX.C1,

consistMatricesSUX,consistMatricesSUX.weights, epsilon);

For the last model( '121114_Recon2betaRecon.mat';),

__________________________________________________________________________

multiple matchesC16217

Combining Genes in Progress ...

25%     [..........                              ]Error using subsasgn

Conversion to cell from double is not possible.

Error in extendIndicesInDimenion (line 28)

added = subsasgn(input,S,value);

Error in extendModelFieldsForType (line 139)

            model.(cfield) =

            extendIndicesInDimenion(model.(cfield),cdim,defaultValue,

            targetSize-originalSize);

Error in mergeTwoModels>mergeFields (line 223)

modelNew =

extendModelFieldsForType(modelNew,type,'originalSize',nType1,'targetSize',nType1+nType2);

Error in mergeTwoModels (line 107)

modelNew =

mergeFields(modelNew,model1,model2,'rxns');

Error in generateSUXComp (line 68)

    [modelExpanded] =

    mergeTwoModels(modelExpanded,KEGGComp,1);

Error in prepareFastGapFill (line 81)

MatricesSUX =

generateSUXComp(consistModel,dictionary,

filename,blackList,listCompartments);

________________________________________________________________________

Can anyone kindly help me on this regard? 

Thank you,

Betül

[Betul Baz]

Hi everyone,

Is there anyone also got these errors or is it because of another occassion? Also in this error;

'The following problems have been encountered in the model structure

inconsistentFields:

csense: mets: Size of csense does not match elements in mets'

it actually generated required field for model in the function('buildLPproblemFromModel') but when I run verifyModel(model) it says: Field does not match the required properties.

What are the required properties??

Thank you in advance,

Betül

1 Nisan 2019 Pazartesi 10:10:18 UTC+3 tarihinde Betul Baz yazdı:

[Xiaokang Zhang]

We have got exactly the same error as you (an open issue on GitHub: https://github.com/opencobra/cobratoolbox/issues/1486)

Have you solved this problem? Thanks!

[Thomas Pfau]

Hi,

This is likely due to the runGapFill_example.m file using load instead of readCbModel, and the models having inconsistent fields in the .mat file.

if you replace the line:

model = content.(F{1}) by model = readCbModel(Filename{i}), that error should not happen.

Best

Thomas

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