I am trying to create a GEM model for my transcriptomic data using Cobra toolbox and gurobi solver in Matlab. The code I am running uses the ftINIT algorithm and is the same I have used before for creating other models. Now it's showing me some error due to high MipGap and I feel it is because of the solver.
Below is the general representation of my code:
model1 = ftINIT(prepData, data_struct.tissues{1}, [], [], data_struct, {}, getHumanGEMINITSteps('1+0'), false, true);
The prepData is a reference model data from Human-GEM repository. data_struct.tissues is the name for the sample(1st row in column 2). data_struct is the transcriptomic data having genes in column 1 and counts in the column 2.
This is the main command for creating a model (https://sysbiochalmers.github.io/Human-GEM-guide/gem_extraction/).
The error shown after running this is:
ftINIT: Running step 1
MILP detected.
MipGap too high, trying with a different run. MipGap = Inf New MipGap Limit = 0.003
MILP detected.
Error using dispEM
Failed to find good enough solution within the time frame. MIPGap: Inf
Error in ftINIT (line 281)
dispEM(['Failed to find good enough solution within the time frame. MIPGap: ' num2str(mipGap)]);
Any help would be appreciated. Thank you.