Error in ftINIT (line 283) Failed to find enough good solution within the time frame MIPGap:Inf

[NayeonPark99]

Dear team,
I currently plan to build sample-specific models for the mouse liver bulk RNA-seq data.
( I'm new to genome-scale metabolic modeling)

Following the [Human-GEM guide] (https://sysbiochalmers.github.io/Human-GEM-guide/)
I adapted the code for a mouse GEM as shown below

mouseGEM = importModel('/path/to/GEM_models/Mouse-GEM.xml') % your team's model
liver_tasks = parseTaskList('/path/to/task_file/human_liver_tasks.xlsx')
% Task file was obtained from supplementary information from this paper which made human hepatocyte GEM-model.
% link : https://www.nature.com/articles/ncomms4083

prepLiver = prepINITModel(mouseGEM, liver_tasks)

liver_tpm = readtable('/path/to/liver_data/liver_RNA_tpm.csv')

liver_struct.genes = liver_tpm{:, 2}; % column 2 is mouse gene symbol
liver_struct.tissues = liver_tpm.Properties.VariableNames(3:52); % sample data is started from column 3
liver_struct.levels = liver_tpm{:, 3:52};
liver_struct.threshold = 1

steps = getINITSteps([], '1+1')
testmodel = ftINIT(prepLiver, liver_structure.tissues{1}, [], [], liver_struct, {}, steps, false, true)

However, I encountered the following error:

testmodel = ftINIT(prepLiver, liver_struct.tissues{1}, [], [], liver_struct, {}, steps, false, true)
ftINIT: Running step 1
ftINIT: Running step 2
MipGap too high, trying with a different run. MipGap = Inf New MipGap Limit = 0.0004
MipGap too high, trying with a different run. MipGap = Inf New MipGap Limit = 0.003
Error using dispEM
Failed to find good enough solution within the time frame. MIPGap: Inf

Error in ftINIT (line 283)
dispEM(['Failed to find good enough solution within the time frame. MIPGap: ' num2str(mipGap)]);

There were no issues with parseTaskList() or prepINITModel(),
and the same error occurred across all 50 samples — so it may not be sample-specific.

I feel like I might be missing something, and I would really appreciate any help or guidance.

Thank you!

[johan-gson]

Hi @NayeonPark99,

It is difficult to say why this fails, there are a few things that I would check first:

1. Which version of Gurobi are you using? We have only tested with 9.5 and 10.0.0, and it is pretty sensitive to this - if you have a different version, try to install one of these, preferrably 10.0, and see if it helps.

2. There is a printout of the tasks - do all tasks succeed on the full model? If not, ftINIT will fail.

3. There is a flag called skipScaling in prepINITModel, you could try to set this to true and see if it helps

Try these things first and let me know how it goes.

Best,

Johan