Troubleshooting GTDB-Tk Database Installation and Environment Configuration

soojunglee98 commented 2 months ago

Environment

[ ] Installed via pip (include the output of pip list)
[0] Using a conda environment (include the output of conda list && conda list --revisions)
[ ] Using a Docker container (include the IMAGE ID of the container)

Debugging information

[0 ] gtdbtk.log has been included (drag and drop the file to upload).
[ ] Genomes have been included (if possible, and there are few).

Additional comments

As mentioned on this website, I installed the conda environment and tried to download the database.

When I run download.sh, it says:

"Cannot write to '/home/spotgiet/miniconda3/envs/gtdbtk-2.1.1/share/gtdbtk-2.1.1/db/gtdbtk_r207_v2_data.tar.gz' (No space left on device)."

So, I manually downloaded the database to another directory due to space limitations in my home directory. However, I encountered this error:


================================================================================
                                     ERROR                                      
________________________________________________________________________________

          The 'GTDBTK_DATA_PATH' environment variable is not defined.           

            Please set this variable to your reference data package.            
               https://github.com/Ecogenomics/GTDBTk#installation               
================================================================================

================================================================================
                                     ERROR                                      
________________________________________________________________________________

           The GTDB-Tk reference data does not exist or is corrupted.           
                GTDBTK_DATA_PATH=/path/to/unarchived/gtdbtk/data                

   Please compare the checksum to those provided in the download repository.    
          https://github.com/Ecogenomics/GTDBTk#gtdb-tk-reference-data          
================================================================================

So again, as mentioned on the website, I activated my conda environment and tried to run:

conda env config vars set GTDBTK_DATA_PATH="/scratch/raskin_root/raskin0/shared_data/Soojung_Sarah/gtdb_tk/release220"

But it keeps saying: "To make your changes take effect, please reactivate your environment." even though my conda environment is already activated. Any suggestions? Thank you so much!

pchaumeil commented 2 months ago

you need to deactivate and then reactivate the environment for the changes to be applied properly.

conda deactivate
conda activate your_gtdbtk_environment_name

This step is necessary because of the environment change.

soojunglee98 commented 2 months ago

Yes, I did that several times but it doesn't work. Do you have any more suggestions? Thank you!

On Mon, Jul 22, 2024 at 4:59 PM Pierre Chaumeil @.***> wrote:

you need to deactivate and then reactivate the environment for the changes to be applied properly.

conda deactivate conda activate your_gtdbtk_environment_name

This step is necessary because of the environment change.

— Reply to this email directly, view it on GitHub https://github.com/Ecogenomics/GTDBTk/issues/596#issuecomment-2243804245, or unsubscribe https://github.com/notifications/unsubscribe-auth/A6YIDR3Z3QF4XEIZZY62SY3ZNVXBNAVCNFSM6AAAAABK7EFKWGVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDENBTHAYDIMRUGU . You are receiving this because you authored the thread.Message ID: @.***>

pchaumeil commented 1 month ago

Do you still have the exact same error? or is your error pointing to the new release220 folder now? i.e. is the error similar to

The GTDB-Tk reference data does not exist or is corrupted.           
GTDBTK_DATA_PATH=/path/to/unarchived/gtdbtk/data

or

The GTDB-Tk reference data does not exist or is corrupted.           
GTDBTK_DATA_PATH=/scratch/raskin_root/raskin0/shared_data/Soojung_Sarah/gtdb_tk/release220

Ecogenomics / GTDBTk