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cdanielmachado / carveme

CarveMe: genome-scale metabolic model reconstruction
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Carveme EggNog mapper error #144

Closed fcastillo1993 closed 3 years ago

fcastillo1993 commented 3 years ago

Hi I am trying to build a metabolic model from an EggNog Mapper annotation using the following command:

$ carve --egg EggNog_HybridAssembly.tsv

When I run the above command it throws me the following error:

The input genome did not match sufficient genes / reactions in the database.

Thank's in advance,

Freddy

cdanielmachado commented 3 years ago

Hi, sorry for the late reply. Can you share the that tsv file ?

fcastillo1993 commented 3 years ago

Don't worry, I appreciate your response. I am attaching the tsv file, thank you very much

fichero.tsv.zip

cdanielmachado commented 3 years ago

It seems that the problem was that the last version of eggnog-mapper added more columns to the annotations file and the file was not being parsed correctly.

I have now fixed that and if you install the latest version directly from github it should work now.

But I have noticed that eggnog only matches around 100 genes from your file with genes from the BiGG database, and they are all yeast genes. This results in a very poor reconstruction, since CarveMe does not build eukaryote models at the moment.

qikongwanli commented 1 year ago

It seems that the problem was that the last version of eggnog-mapper added more columns to the annotations file and the file was not being parsed correctly.

I have now fixed that and if you install the latest version directly from github it should work now.

But I have noticed that eggnog only matches around 100 genes from your file with genes from the BiGG database, and they are all yeast genes. This results in a very poor reconstruction, since CarveMe does not build eukaryote models at the moment.

Hi, The result of new version of eggnog-mapper did not contain BIGG_gene column.