Unbounded Flux In Default Medium-error

[mascencio27]

Hello everyone.

I'm running memote, but the item Unbounded Flux In Default Medium of I get error, just like in the items: Universally Blocked Reactions, Stoichiometrically Balanced Cycles, Metabolite Production In Complete Medium and, Metabolite Consumption In Complete Medium. Does anyone know how to fix it?

[Midnighter]

Hi @mascencio27,

Thanks for the report. It's impossible for me to tell why you get an error without more information. Please run the following command and then copy the error traceback here (there will be a lot of output, but copy only the relevant test output here, please). Also include other options that you might have used for generating the report.

memote run --ignore-git <model file>

[mascencio27]

Thank you for your response. But I do not understand where I should run the command that you indicate me. it is run in anaconda? because I have not been able to do it. If you can tell me, thank you very much!

[Midnighter]

Yes, for example, in an Anaconda shell. Presumably the same way that you generated the above report.

[mascencio27]

Hi @Midnighter , thank you for your answer and your intention to help me. I copy here the parts of the error thrown with the command you shared with me.

I remain attentive. Thank you very much for your help.

   "title": "Stoichiometrically Balanced Cycles"

test_find_reactions_unbounded_flux_default_condition": { "data": null, "duration": 1.3452881000000048, "format_type": "percent", "message": null, "metric": 1.0, "result": "failed", "summary": "A large fraction of model reactions able to carry unlimited flux under\ndefault conditions indicates problems with reaction directionality,\nmissing cofactors, incorrectly defined transport reactions and more.\n\nImplementation:\nWithout changing the default constraints run flux variability analysis.\nFrom the FVA results identify those reactions that carry flux equal to the\nmodel's maximal or minimal flux.", "title": "Unbounded Flux In Default Medium" "test_find_stoichiometrically_balanced_cycles": { "data": null, "duration": 0.6806155999999959, "format_type": "count", "message": null, "metric": 1.0, "result": "failed", "summary": "Stoichiometrically Balanced Cycles are artifacts of insufficiently\nconstrained networks resulting in reactions that can carry flux when\nall the boundaries have been closed.\n\nImplementation:\nClose all model boundary reactions and then use flux variability analysis\n(FVA) to identify reactions that carry flux.",

[Midnighter]

Would you be willing to share your model with me? You can send it to me by email and I promise to keep it confidential. I feel it might be quicker to help you that way.

[mascencio27]

Hi @Midnighter thank you very much. Please share your email with me. Best regards!

[Midnighter]

You can find it in my contact details https://github.com/Midnighter

[mascencio27]

Thank you very much @Midnighter, I have already sent to your email. I remain attentive.

[mascencio27]

Hi @Midnighter I hope you are well and I appreciate your willingness to help me fix the error in the Memote report, but I would like to know if you have been able to analyze it or have not yet had the time. Thank you for your response. Best regards!

[Midnighter]

I have sent you an answer by e-mail. Let's continue the discussion there.