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Note: This tutorial was made for the purposes of running Cenote-Taker 3 on the Cooper Lab’s beagle server. This is also still a working draft so please reach out if you get stuck or if anything is unclear.

The most recent version of Cenote-Taker as of writing this tutorial is Cenote-Taker 3. The official GitHub document for Cenote-Taker 3 can be found here: https://github.com/mtisza1/Cenote-Taker3.


Install Cenote-Taker 3

We will need to first load miniconda-3 before creating a virtual environment. To learn more on creating virtual environment, refer to my conda virtual environment tutorial.

module load miniconda/miniconda-3
source /opt/miniconda/miniconda3/etc/profile.d/conda.sh


Make sure to change the filepath to your directory when running the following code to create your virtual environment named “ct3_env”:

conda create --prefix /home/nak177/cenote/cenote3/ct3_env -c conda-forge -c bioconda cenote-taker3


When asked, “Proceed ([y]/n)?” for installation of new packages, Type “y” for “yes”.

Now activate your virtual environment:

conda activate ct3_env/


We will need to download the database and name the location “ct3_DBs”. This may take more than an hour depending on the internet speed and stability:

get_ct3_dbs -o ct3_DBs --hmm T --mmseqs_tax T --mmseqs_cdd T --domain_list T --hhCDD T --hhPFAM T --hhPDB T


Then use the following code (making sure to change the filepath to match your path to your ct3_DBs):

conda env config vars set CENOTE_DBS=/home/nak177/cenote/cenote3/ct3_DBs


Run Cenote-Taker 3

To be updated