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cdanielmachado / carveme

CarveMe: genome-scale metabolic model reconstruction
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Gram-positive universe setting produces unknown BiGG identifier #112

Closed mfeierabend closed 3 years ago

mfeierabend commented 3 years ago

Hi, when using a Gram-positive universe in the carving process, the draft contains the reaction: 'R_HSLGTHLK' which is not a known identifer in BiGG. When not explicitely selecting the gram-positive universe with the same input data, the draft contains the reaction 'R-HSK', which represents a valid BiGG identifier. The reaction in question is the homoserine kinase. Is this a potential bug?

Thanks!

cdanielmachado commented 3 years ago

Hi,

That's indeed really strange. Can you upload here the SBML file that contains the reaction called 'R_HSLGTHLK' ?

mfeierabend commented 3 years ago

Sure. I attached the SBML file. SP_fbc1_m_ncbi.xml.zip

cdanielmachado commented 3 years ago

This is indeed quite strange, the identifier should be R_HSK not R_HSLGTHLK, and CarveMe doesn't modify identifier ids at any step.

Is this reproducible? Have you tried running it more than once ?

mfeierabend commented 3 years ago

We are not able to replicate this. I am sorry, I got no idea what happened here. Thanks for your fast response.