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cdanielmachado / carveme

CarveMe: genome-scale metabolic model reconstruction
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Initializing in customized medium composition #76

Closed stellareichling closed 4 years ago

stellareichling commented 4 years ago

Hi Daniel

Thank you for providing and supporting the CarveMe software. I am trying to initialize the carving process in custom medium and tried a similar approach to introducing an own medium composition as with the gapfilling. However I encountered the error "--mediadb can only be used with --gapfill". Is there a possibility to initialize the model in customized medium?

Thank you in advance and kind regards, Stella

cdanielmachado commented 4 years ago

Hi Stella,

I made the initialize option only available in combination with gapfill, because if you don't gapfill the model for the medium you wish to initialize the model with, there is the possibility that it will not grow in that medium.

If you really do not want to gapfill the model for that medium, you can use the gapfill option and then manually remove the reactions that were inserted by gapfill. You can easily find them in the SBML file, these will be the last reactions and will be annotated with GAPFILL.

Best regards, Daniel