carveme

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Adding another protein function annotation tool

3

Hello, We have recently published a protein function annotation tool (i.e., [Mantis](https://github.com/PedroMTQ/mantis)) and are now interested in building metabolic networks using the annotations provided from this tool as a seed...

PedroMTQ

containerizing CarveMe

3

Hi, I'm interested in running CarveMe within a Docker or Singularity container. One of the major hurdles is getting CPLEX to work since it requires a license. Switching to Gurobi...

zoey-rw

GPR information is missing in output file

6

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,...

Shakra-A

Permission issues if admin installed carveme

1

There is problem with building the diamond db in the first run (I guess new in 1.4.1;https://github.com/cdanielmachado/carveme/commit/fef1ed29495f3a1e6937c68a9df0b16f8e797890) in cases where carveme was installed system wide with the user of carveme...

phantomas1234

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

1

Hi Everybody, I tried to run CarveMe using DNA data (my_genome.fna: https://www.ncbi.nlm.nih.gov/genome/?term=txid4959[orgn]): ``` carve --dna my_genome.fna ``` I got this message: ``` The input genome did not match sufficient genes/reactions...

AnisMansouri

Hi Everybody, I tried to run CarveMe but I got this error message: Database was built with a different version of Diamond and is incompatible. Failed to run diamond. diamond...

AnisMansouri

hello! I encountered the problem shown in the following picture when installing CarveMe on the Linux platform（Ubuntu 18.04.5 LTS）. Can you please answer it? Thank you！ 

Sail6666

Hello! first, thanks for creating carveMe. It's my favorite metabolic network creator, it's simple to use and the user can easily make the desired modifications (universe, media, experimental data, etc...

NatashaJorge

I meet some errors when I use CarveMe for gap-filling

4

Hi Daniel, After I run the gap-filling command using my defined medium, I meet errors, as below:   please help me, thank you very much, Happy new year!!!

microbial-cookie

Hello The cyanobacteria universe is not working with the latest carve version, is that right? So I found out that I should user carve version 1.4. For the latest carve...

marlaux