Hello, I'm having some issues with running ftINIT on the Mouse-GEM in order to generate some models. I tried to follow steps in fix/ftINITScaling but am still getting the same solver error. I'm also attaching some of the files I've used to generate this error.
prepData_mouse = prepGEMForftINIT(mouseGEM, false, 'Reference_Models\Human1_metabolicTasks\metabolicTasks_Essential.txt', fullfile('..\Mouse-GEM-1.8.0\Mouse-GEM-1.8.0\','model','reactions.tsv'));
transcriptomic_file = 'TPM_Data/Amaya_Project/Brain1_3_TPM_Clusters.csv';
load('Reference_Models/prepData_mouse.mat')
build_models(transcriptomic_file,prepData_mouse,modelpath)
Model: 1 of 14
ftINIT: Running step 1
WARNING: Exchange metabolites are still present in the model. Use simplifyModel if this is not intended
MILP detected.
Set parameter Username
Set parameter TimeLimit to value 120
Set parameter FeasibilityTol to value 1e-09
Set parameter IntFeasTol to value 1e-09
Set parameter MIPGap to value 0.0004
Set parameter OptimalityTol to value 1e-09
Set parameter DisplayInterval to value 1
Set parameter Presolve to value 2
Set parameter Seed to value 1
Academic license - for non-commercial use only - expires 2026-09-29
Gurobi Optimizer version 10.0.1 build v10.0.1rc0 (win64)
CPU model: AMD Ryzen Threadripper PRO 3955WX 16-Cores, instruction set [SSE2|AVX|AVX2]
Thread count: 16 physical cores, 32 logical processors, using up to 32 threads
Optimize a model with 12341 rows, 23095 columns and 61818 nonzeros
Model fingerprint: 0xa54da16b
Variable types: 19753 continuous, 3342 integer (3342 binary)
Coefficient statistics:
Matrix range [1e-04, 8e+04]
Objective range [1e-02, 3e+02]
Bounds range [1e-01, 1e+03]
RHS range [0e+00, 0e+00]
Presolve removed 0 rows and 7168 columns
Presolve time: 0.00s
Explored 0 nodes (0 simplex iterations) in 0.03 seconds (0.01 work units)
Thread count was 1 (of 32 available processors)
Solution count 0
Model is infeasible
Best objective -, best bound -, gap -
MipGap too high, trying with a different run. MipGap = Inf New MipGap Limit = 0.003
WARNING: Exchange metabolites are still present in the model. Use simplifyModel if this is not intended
MILP detected.
Set parameter Username
Set parameter TimeLimit to value 5000
Set parameter FeasibilityTol to value 1e-09
Set parameter IntFeasTol to value 1e-09
Set parameter MIPGap to value 0.003
Set parameter OptimalityTol to value 1e-09
Set parameter DisplayInterval to value 1
Set parameter Presolve to value 2
Set parameter Seed to value 1234
Academic license - for non-commercial use only - expires 2026-09-29
Gurobi Optimizer version 10.0.1 build v10.0.1rc0 (win64)
CPU model: AMD Ryzen Threadripper PRO 3955WX 16-Cores, instruction set [SSE2|AVX|AVX2]
Thread count: 16 physical cores, 32 logical processors, using up to 32 threads
Optimize a model with 12341 rows, 23095 columns and 61818 nonzeros
Model fingerprint: 0xa54da16b
Variable types: 19753 continuous, 3342 integer (3342 binary)
Coefficient statistics:
Matrix range [1e-04, 8e+04]
Objective range [1e-02, 3e+02]
Bounds range [1e-01, 1e+03]
RHS range [0e+00, 0e+00]
Presolve removed 0 rows and 7168 columns
Presolve time: 0.00s
Explored 0 nodes (0 simplex iterations) in 0.03 seconds (0.01 work units)
Thread count was 1 (of 32 available processors)
Solution count 0
Model is infeasible
Best objective -, best bound -, gap -
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)]);
Error in build_models (line 15)
built_model = ftINIT(prepData, tissue, [], [], data_struct, {}, getHumanGEMINITSteps('1+0'), false, true);
Hello, I'm having some issues with running ftINIT on the Mouse-GEM in order to generate some models. I tried to follow steps in fix/ftINITScaling but am still getting the same solver error. I'm also attaching some of the files I've used to generate this error.
ftINIT_files_mouse.zip