Essential metabolic tasks verification

[Flash1593]

For verification of the reference model (Human-GEM) for performing all the essential tasks after performing addBoundaryMets step, it is giving the following error -

checkTasks(ihuman,[],true,false,false,essentialTasks);
PASS: [ER] Aerobic rephosphorylation of ATP from glucose
Index exceeds the number of array elements. Index must not exceed 0.

Error in checkTasks (line 217)
essentialFluxes(:,i) = sol.x(1:numel(model.rxns));

What should I do to troubleshoot the problem? Any help would be really appreciated.

[JonathanRob]

Hi @Flash1593, what version/branch of Human-GEM and RAVEN are you using? And if you could provide the command(s) run prior to this one, as well as their output, that would be helpful.

[Flash1593]

I had cloned both Human-GEM & RAVEN using github
git clone https://github.com/SysBioChalmers/Human-GEM.git
git clone --depth=1 https://github.com/SysBioChalmers/RAVEN.git

These are the commands and their output prior to essential task command

load('Human-GEM.mat')
ihuman=addBoundaryMets(ihuman);

Boundary metabolites were added to 1665 reactions.
New (boundary) versions of 1665 metabolites were added to the model.

essentialTasks=parseTaskList('metabolicTasks_Essential.xlsx')

essentialTasks =

57×1 struct array with fields:

id
description
shouldFail
printFluxes
comments
inputs
LBin
UBin
outputs
LBout
UBout
equations
LBequ
UBequ
changed
LBrxn
UBrxn

checkTasks(ihuman,[],true,false,false,essentialTasks);
PASS: [ER] Aerobic rephosphorylation of ATP from glucose
Index exceeds the number of array elements. Index must
not exceed 0.

Error in checkTasks (line 217)
essentialFluxes(:,i) = sol.x(1:numel(model.rxns));

I tried repeating the last command and it gave this

checkTasks(ihuman,[],true,false,false,essentialTasks);
PASS: [ER] Aerobic rephosphorylation of ATP from glucose
PASS: [ER] Aerobic rephosphorylation of GTP
PASS: [ER] Aerobic rephosphorylation of CTP
Index exceeds the number of array elements. Index must not exceed 0.

Error in checkTasks (line 217)
essentialFluxes(:,i) = sol.x(1:numel(model.rxns));

checkTasks(ihuman,[],true,false,false,essentialTasks);
PASS: [ER] Aerobic rephosphorylation of ATP from glucose
Index exceeds the number of array elements. Index must not exceed 0.

Error in checkTasks (line 217)
essentialFluxes(:,i) = sol.x(1:numel(model.rxns));

Is it a solver problem?

[JonathanRob]

You're correct, it looks like when using glpk, it results in an "Infeasible" solution and failure for many of the tasks. I'm not sure why this is the case, but I think glpk tends to have problems with larger problems/models. Could you try using another solver, such as gurobi?

[Flash1593]

Hi, I had changed the solver to gurobi for RAVEN toolbox but still I'm getting the same error.

[JonathanRob]

We fixed a bug in RAVEN yesterday that prevented users from changing the solver with setRavenSolver unless they restarted Matlab. Can you update to the latest version of RAVEN (released yesterday), restart your Matlab session, and try again with Gurobi?

If you're still getting the same problem after that, then let me know and we can work on a fix.

[Flash1593]

Yeah, I restarted Matlab & changed the solver to gurobi, now the checktask algorithm is working fine. Thanks for the help.

[JonathanRob]

Ok great, glad it's working now.