Question about

[cherakhan]

Hi

I have run the matTFA for 'GSmodel_Ecoli.mat'. It fails because of infeasibility. I was wondering if the codes works fine on your systems? if not, please let me know what might be the cause of this error?

Thank you

Relaxation of DGo_MECDPS : 28.391 +- 2.256 (sigma) ---> 28.391 +- 72.256
Relaxation of DGo_REPHACCOAI : 16.774 +- 4.121 (sigma) ---> 16.774 +- 24.121
It was not possible to obtain TFA-feasible solutions with the original DGo values calculated by GCM!
We had to relax the following DGo ranges as follows:

ans =

'varName'           'LB-before'    'UB-before'    'LB-relaxed'    'UB-relaxed'
'DGo_MECDPS'        [  26.1357]    [  30.6469]    [   12.6021]    [   44.1805]
'DGo_REPHACCOAI'    [  12.6529]    [  20.8957]    [    8.5316]    [   25.0171]

Error using relaxModelWithDGoSlacks (line 171)
Although we relaxed the DGo variables it was not possible to find a feasible solution!

Error in convToTFA (line 645)
[model, relaxedDGoVarsValues, modelwDGoSlackVars] = relaxModelWithDGoSlacks(model, minObjSolVal,
rxnNameListNoDGoRelax);

Error in tutorial_GEM (line 53)
tmp = convToTFA(prepped_m,ReactionDB,[],'DGo');

[psalvy]

Hi @cherakhan,

I am assuming you are using tutorial_GEM.m ?
Could you please check that the code runs fine if you replace

tmp = convToTFA(prepped_m,ReactionDB,[],'DGo');

by

min_obj = solFBA.f*0.95;
tmp = convToTFA(prepped_m,ReactionDB,[],'DGo', [], min_obj);

Let me know how it goes :)

[psalvy]

Ok. I was able to reproduce your error.
I am pretty sure the issue is that the value of minObjSolVal (1e-6) for validation of the relaxation in convToTFA and relaxModelWithDGoSlacks is below the tolerance of the solver for optimality. I changed its default to 1e-5 and it seems to work.

I will push on the dev branch, and once you have confirmed it works for you too, I will merge to master

[cherakhan]

Hi,

Many thanks for your response. The issue was resolved according to your modification.

BUT, the another error is coming from undefined "solveCobraLP_edited" function from "solveFBAmodelCplex" in "runMinMax". I can not find "solveCobraLP_edited" !

Thank you very much

[psalvy]

Hi,

If I am not mistaken, solveCobraLP_edited is in the same file as solveFBAmodelCplex, L128

Cheers,

Pierre