ECM results missing key metabolism or biomass synthesis about ecmtool HOT 3 CLOSED

OK, never mind. I see there is a lower bound constraint on the H2 exchange reaction for iAF692 GEM. Perhaps other GEMs I have looked at also contain poor choices on exchange reactions and explains why they don't produce what I would consider basic/obvious ECMs.

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Hi Joe,
Yes, when running ecmtool it is really important to check the preprocessing. You can make the metabolites and reactions be printed with the arguments "--print_metabolites True" and "--print_reactions True". In the output, you can then see whether the organism is actually able to take up and secrete the correct metabolites. We have tried to infer these input- and output-metabolites as generally as possible, but different model-standards use different conventions, which makes it quite hard. So, please always check this.

Personally, as a sanity check, I like running an FBA that produces biomass, and then check which metabolites are taken up and produced. I then use that information to set the input-, and output-metabolites in ecmtool. Then I am certain that there must be an ECM that produces biomass.

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Thanks for the tip Daan! I have run FBA on the GEMs that don't produce a biomass synthesis ECM, and they do show biomass being produce in the FBA; however, I suspect there is something in the GEMs that are causing the issue. I will continue to sift through them. Thanks for your help!

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