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cdanielmachado / carveme

CarveMe: genome-scale metabolic model reconstruction
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carveme archaea models #41

Closed arianccbasile closed 5 years ago

arianccbasile commented 5 years ago

I am trying to generate an archaea model starting from Methanosarcina barkeri genome but it doesn't seem to work as I get this error message.

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

What should I do? I tried these commands:

carve --dna methanosarcina_barkeri.fasta -u archaea --fbc2 -o carve_methanosarcina_barkeri.xml carve --dna methanosarcina_barkeri.fasta -o carve_methanosarcina_barkeri.xml carve --dna methanosarcina_barkeri.fasta -u archaea --fbc2 -o carve_methanosarcina_barkeri.xml

Thank's in advance, Arianna

cdanielmachado commented 5 years ago

Hi Arianna,

Is your genome file already split into individual genes?

arianccbasile commented 5 years ago

Hi Daniel, no it is not yet. Do I need to do annotation first? Which tool would you recommend best? Prokka, Rast or which other?

cdanielmachado commented 5 years ago

Yeah, you need to run something that will identify the ORFs and create a fasta file with the individual genes. I don't have so much experience with that, but I think Prokka should be fine.