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cdanielmachado / carveme

CarveMe: genome-scale metabolic model reconstruction
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GPR information is missing in output file #131

Open Shakra-A opened 3 years ago

Shakra-A commented 3 years ago

Hi. I am new to all this work. I used CarveMe for making a metabolic model from protein fasta file. I used the following code. $ carve genome.faa --output model.xml, from the documentation. The fasta file was consist of locus tags and their protein sequences. The result I got should have locus tags in the column GPR but the column is empty. (I converted the sbml file to excel file for data visualization). Kindly help me to solve this problem.

cdanielmachado commented 3 years ago

Sorry for the late reply. Can you send me the SBML file?

Shakra-A commented 3 years ago

yes I can but here in reply the file format is not supported. Kindly send me your email address so I could send it there.

cdanielmachado commented 3 years ago

cdanielmachado at gmail

cdanielmachado commented 3 years ago

If you run with -v you will see the error message: The input genome did not match sufficient genes/reactions in the database.

There is something strange with your fasta file, most of the proteins have a really short AA sequence. Was this fasta file built from a fully assembled genome? Also, do you know which organism is this?

Shakra-A commented 3 years ago

This organism does not have a GBK file. I used automatic pipe lines for annotation of the whole genome. It is a bacteria. The fasta file is from the automatic annotation proteine seq.

On Thu, Jul 8, 2021 at 4:22 PM Daniel Machado @.***> wrote:

If you run with -v you will see the error message: The input genome did not match sufficient genes/reactions in the database.

There is something strange with your fasta file, most of the proteins have a really short AA sequence. Was this fasta file built from a fully assembled genome? Also, do you know which organism is this?

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/cdanielmachado/carveme/issues/131#issuecomment-876197961, or unsubscribe https://github.com/notifications/unsubscribe-auth/ASUSI6JXMPZMVQU4VZLYUSLTWVG4HANCNFSM46LIBWSA .

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cdanielmachado commented 3 years ago

Maybe you can run it in eggnog-mapper and see how many metabolic enzymes it predicts: http://eggnog-mapper.embl.de/

Or try to run a reconstruction with modelSEED: https://modelseed.org/