Error when running CHRR sampling algorithm

[Gideon Idumah]

Hello all,

I am trying to run the CHRR algorithm in the COBRA toolbox. My code is attached below:

rng(12)

changeCobraSolver('ibm_cplex', 'all');

load('../Gimme_UWB1_289_Mock90.mat')

model = tissueModel_Gimme;

samplerName = 'CHRR';

iters = 100000;

sDens = 10000;

modelname = 'Gimme_UWB1_289_Mock90';

samples = sample_func(model, iters, sDens, modelname, samplerName);

function samples = sample_func(model, iters, sDens, modelname, samplerName)

% model.c = zeros(size(model.c)); % clear objective

options.nStepsPerPoint = sDens; % sampling density

options.nPointsReturned = iters; % number of points returned

options.toRound = 1; % whether or not polytope is rounded

options.optpercentage = 0; %only consider solutions that gives at least a certain percentage of optima solution.

tic

[~, samples] = sampleCbModel(model, [], samplerName, options); % outputs model (polytope) and samples

toc

t_samples = transpose(samples);

filename = [modelname, '_', samplerName, '.csv'];

csvwrite(filename, t_samples)

disp('Finished model')

end

However, I get the following error:

Checking for width 0 facets...
Currently (P.A, P.b) are in 1539 dimensions
Checking for width 0 facets...
Found 76 degenerate reactions, adding them to the equality subspace.
Warning: Rank deficient, rank = 988, tol =  5.817499e-10.
> In preprocess (line 169)
In chrrSampler (line 145)
In sampleCbModel (line 171)
In sampling>sample_func (line 19)
In sampling (line 10)
 
Now in 551 dimensions after restricting
Removed 2914 zero rows
Preconditioning A with gmscale
Rounding...
Error using mve_solver_cobra
x0 not interior

Error in mve_run_cobra (line 32)
    [x,E2,converged] = mve_solver_cobra(A,b,x0,maxiter,tol2,reg); %Ben

Error in preprocess (line 255)
            [T_shift, Tmve,converged] = mve_run_cobra(P.A,P.b, x0,reg);

Error in chrrSampler (line 145)
        [roundedPolytope] = preprocess(P,options);

Error in sampleCbModel (line 171)
        [samples, modelSampling] = chrrSampler(model, nStepsPerPoint, nPointsReturned, toRound, modelSampling, useFastFVA,optPercentage);

Error in sampling>sample_func (line 19)
[~, samples] = sampleCbModel(model, [], samplerName, options); % outputs model (polytope) and samples

Error in sampling (line 10)
samples = sample_func(model, iters, sDens, modelname, samplerName);

I observed that if I take out the bio_mass_reaction objective (first line under the function), the code runs fine.

I will greatly appreciate any comment on why this is happening, and what should be the right approach to take.

Thank you once again

Gideon

[Ronan M.T. Fleming]

Hi Gideon,

please can you confirm that you are using the current master version of the cobra toolbox?

https://github.com/opencobra/cobratoolbox

Regards,

Ronan

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Mr. Ronan MT Fleming B.V.M.S. Dip. Math. Ph.D.
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Associate Professor,
School of Medicine,
University of Galway,

Ireland.

Coordinator of the Horizon Europe project "Reconstruction and Computational Modelling for Inherited Metabolic Diseases" (Recon4IMD)

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[Gideon Idumah]

Thank you Dr Fleming for your reply.

Yes my Cobra is up to date. Here is the output from updateCobraToolbox:

>> updateCobraToolbox
 > Checking for available updates ...
 > remote.origin.url = https://github.com/opencobra/cobratoolbox.git
.
 > currentBranch = master.
 > The COBRA Toolbox is up-to-date.