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cdanielmachado / carveme

CarveMe: genome-scale metabolic model reconstruction
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Unusually high growth rates in reconstructed models #133

Closed shreyanshumale closed 3 years ago

shreyanshumale commented 3 years ago

Models reconstructed using v1.5.1 (and earlier versions) still show really high growth rates (values around 15 to 70) in my MAGs. Can you help me identify why this is happening, and is there something I can do to fix this?

P.S: I have tried different gap-filling media, but the problem persists

Please let me know!

cdanielmachado commented 3 years ago

Did you gap-fill and initialize the model with a growth medium? You can do this with -g M9 -i M9

Otherwise the model will come with all uptake reactions unconstrained by default, which could explain the excessive growth rates.

shreyanshumale commented 3 years ago

Ahh, this works! Thanks!