`optimizeCbModel` returning `NaN` for solution

[nleroy917]

Hello!

I'm having issues running singleGeneDeletion. Speficially, the call to the WT optimizeCbModel returns a solution with NaN, consequently leading to all my growth rate ratios also being NaN. I've believe narrowed it down to line 119 inside singleGeneDeletion.

I've confirmed that changing the line from:

solWT = optimizeCbModel(model,'max','one'); % by default uses the min manhattan distance norm FBA solution.

To:

solWT = optimizeCbModel(model,'max'); % by default uses the min manhattan distance norm FBA solution.

Seems to give something other than NaN, but I don't have the expertise to figure out a.) why this works, and b.) if the solution is still valid.

Any help or insight is appreciated!

I hereby confirm that I have:

• [x] Tried to solve the issue on my own
• [x] Retried to run my code with the latest version of The COBRA Toolbox
• [x] Checked that a similar issue has not already been opened

System specs:

• latest version of cobra
• MATLAB2024a
• macOS Sonoma
• Using the standard core ecoli model