Question about sampleCbModel()

[shuyong]

Hi

I got errors when I run 

"[modelSampling, samples] = sampleCbModel(model_GIMME,[], [], options)"

Could anyone tell me what the problem is? 

Thank you.

The errors are:

Checking for width 0 facets...

Currently (P.A, P.b) are in 3898 dimensions

Checking for width 0 facets...

Found 3438 degenerate reactions, adding them to the equality subspace.

Warning: Rank deficient, rank = 3879, tol =  3.298208e-09. 

>In preprocess (line 169)

  In chrrSampler (line 110)

  In sampleCbModel (line 162)

 

Now in 19 dimensions after restricting

Removed 412 zero rows

Preconditioning A with gmscale

Rounding...

Error using mve_chkdata (line 26)

x0 is not interior

Error in mve_run_cobra (line 31)

    mve_chkdata(A,b,x0);

Error in preprocess (line 220)

        [T_shift, Tmve,converged] = mve_run_cobra(P.A,P.b, x0,1e-8);

Error in chrrSampler (line 110)

    [roundedPolytope] = preprocess(P,options);

Error in sampleCbModel (line 162)

        [samples, modelSampling] = chrrSampler(model, nStepsPerPoint, nPointsReturned, toRound,

        modelSampling, useFastFVA,optPercentage);

 

IdleTimeout has been reached.

Parallel pool using the 'local' profile is shutting down.

[Thomas Pfau]

Hi,

Could you provide us with the model you are using for this in order to reproduce the error?

Best

Thomas

On 2018-04-24 20:22, shuyong wrote:

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[shuyong]

Hi Thomas,

Thanks for the reply. I attach the two models in a single matlab file.

Thank you for your help in advance!

Best regards

Shuyong

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[Thomas Pfau]

Hi Shuyong,

One likely reason for your problem is that your model has unbounded reactions (i.e. ub/lb = inf/-inf).

That makes sampling difficult, and often enough impossible, as there is no range in which to place the values.
You could try to set the bounds to some large value (1000/-1000 is often used in FBA, but you can opt for something higher)

Give it a try

Thomas

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[shuyong]

Hi Thomas,

Thanks very much for the help! I will get it a try.

Wish you a good day.

Best regards,

Shuyong