fastgapfill errors

[Nimble]

Hi,

I tried running fastgapfill and got errors.


cmd: [consistModel,

consistMatricesSUX,BlockedRxns]=prepareFastGapFill(model,{'e0','c0'},1e-4,'reaction.lst','KEGG_dictionary.xls')

Errors:

Cell contents indices must be greater than 0

Error in addReactionGEM (line 179)
            rxnCoeff = str2double(parsing{j-1});


Error in createUniversalReactionModel2 (line 144)
[KEGG] = addReactionGEM(KEGG,KEGG.rxns,KEGG.rxns,KEGG.rxnFormulas,KEGG.rev,-10000*ones(length(KEGG.rxns),1),10000*ones(length(KEGG.rxns),1),1);


Error in generateSUXComp (line 48)
KEGG = createUniversalReactionModel2(KEGGFilename, KEGGBlackList);

Error in prepareFastGapFill (line 92)
MatricesSUX = generateSUXComp(consistModel,dictionary, filename,blackList,listCompartments);

I attach my KEGG_dictionary.xls and reacion .lst

Can someone help pls? Thanks

[Will]

Hi Nimble,

I have done some work on the FastGapFill code so am reasonably familiar with it.  Which version of the COBRA Toolbox are you using?  This would help in diagnosing the problem.

Cheers,

Will Bryant.

[Nimble]

Hi Will,

Thanks for your reply.

I have cobratoolbox_2.0.6 installed.

[Nimble]

Hi Will,

I now have my model attached in case this will also be helpful.

Thanks

On Wednesday, 7 December 2016 10:41:09 UTC, Will wrote:

[Nimble]

Apologies!

The latest reaction.lst and KEGG_dictionary.xls also attached now.

On Wednesday, 7 December 2016 10:41:09 UTC, Will wrote:

[Almut Heinken]

Hi Nimble,

maybe it would help to use breakpoints (stop if error) to find out which reaction exactly the program crashes at. You could then inspect if there is a problem with the formulation of this reaction.

Best regards

Almut

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[Nimble]

Hi Almut,

Thanks for your suggestion.

My first error stop is:

addReactionGEM.m
line 179 :             rxnCoeff = str2double(parsing{j-1});


In additon, I have these errors generated while prepareGapFill.m was running:

Flux inconsistent reversible reaction detected:rxn08805_c0
|A|=1407
Flipped 1 reaction.
|A|=1407
Flux inconsistent reversible reaction detected:rxn02391_c0
|A|=1407
Flipped 1 reaction.


So, I went to check my model reactions and found -> and <=> used as ireversibility and reversibility respectively. So, I went to change the addReactionGem.m code accordingly. Changed -->'  to -> and  '<==>'  to '<=>'  to match the format in my model.

Here's is the

addReactionGem.m

line 119:        %if its '-->' or '<==>' then switches IO to 1 which indicates the
line 120:        %next compounds are part of the product
line 121:        elseif strcmp(parsing{j},'<=>') == 1
line 122:            IO = 1;
line 123:            j = j+1;
line 124:        elseif strcmp(parsing{j},'->') == 1

Despite my changes, I still get the same errors. Any ideas what is going on?

Thanks

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[Almut Heinken]

Hi Nimble,

it seems to me there is a problem with the metabolites. Check what this step

rxnCoeff = str2double(parsing{j-1});

was trying to do at the error stop. What variable (it should show up in your workspace if you use break points) was it trying to access?

Best

Almut

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