Chrr sampler not compatible with windows OS.

[varshit dusad]

Hi,

I am new with Cobra tool box. I attempted to run the function: sampleCbModel on my genome scale model. However, it failed to complete and provided the following error. I have also attached the COBRAconfigReport.log file for your perusal. Please help me troubleshoot it.

Error using nullSpaceOperator (line 97)

Chrr sampler not compatible with windows OS.

Error in getNullSpace (line 32)

nullS = nullSpaceOperator(S,gmscale,printLevel);        % forms a structure nullS.

Error in preprocess (line 32)

N = getNullSpace(P.A_eq,0);

Error in chrrSampler (line 136)

    [roundedPolytope] = preprocess(P, toRound);

Error in sampleCbModel (line 157)

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

        nPointsReturned, toRound, modelSampling, [], [], useFastFVA);

 

IdleTimeout has been reached.

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

Warm regards,

Varshit Dusad

[Laurent Heirendt]

Hi,

As the error message states, the CHRR sampler is not compatible with Windows.

Now, as you are using Windows, you cannot run it on your machine.

Best regards,

Laurent

[varshit dusad]

Hello Laurent,

Thank you for your prompt reply. However, I followed the advice of Thomas (attached below) of updating my Cobra toolbox to the latest version. After the update the previous error was replaced by a new one.

Error using mve_solver_cobra (line 29)

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 250)

            [T_shift, Tmve,converged] = mve_run_cobra(P.A,P.b, x0,reg);

Error in chrrSampler (line 110)

    [roundedPolytope] = preprocess(P,options);

Error in sampleCbModel (line 162)

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

        modelSampling, useFastFVA,optPercentage);

I am thinking if the os was the only issue. Sampler is an important algorithm and I am surprised that it would not work on windows without any substitute. However, I apologize in advance, if my doubts are too naive. I am new to the study of genome scale modelling. Thank you very much for your help!

Warm regards,

Varshit Dusad

--

On Tue, Apr 3, 2018 at 2:35 PM, Thomas Pfau <thoma...@uni.lu> wrote:

Hello Varshit,

You seem to be using a Toolbox version from Last November.
Could you update your toolbox (either by updateCobraToolbox or if that doesn't work be recloning? )

Best

Thomas

 

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[Laurent Heirendt]

Hi,

Good. Yes, the latest version should work.

May you give us more details about how you call the sampler? As the error message suggests, make sure that x0 is interior (i.e., Ax0 < b) as explained here: https://github.com/Bounciness/Volume-and-Sampling/blob/master/external/mve11/mve_cobra/mve_solver_cobra.m#L7

Best,

Laurent