Troubleshooting GTDB-Tk Database Installation and Environment Configuration

[soojunglee98]

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]

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]

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 <#596 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/A6YIDR3Z3QF4XEIZZY62SY3ZNVXBNAVCNFSM6AAAAABK7EFKWGVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDENBTHAYDIMRUGU> . You are receiving this because you authored the thread.Message ID: ***@***.***>

[pchaumeil]

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

[pb-max]

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

I have this problem, the release is 202, And I hadnot this problem relese220,

[pchaumeil]

Hi,
Apologies for the delay,
Do you still have this problem?

[soojunglee98]

Hello, Thank you for the catch up. I still have this error and I was trying to find different taxonomy tools for my MAG identification. Do you have any ideas to figure this out?

…

On Tue, Dec 17, 2024 at 4:19 PM Pierre Chaumeil ***@***.***> wrote: Hi, Apologies for the delay, Do you still have this problem? — Reply to this email directly, view it on GitHub <#596 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/A6YIDR6WQVNIXNR6FNSVCRD2GCIPHAVCNFSM6AAAAABK7EFKWGVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDKNBZGY2TGNJWGM> . You are receiving this because you authored the thread.Message ID: ***@***.***>

[pb-max]

I still have this error

…

---Original--- From: "Soojung ***@***.***&gt; Date: Wed, Dec 18, 2024 05:22 AM To: ***@***.***&gt;; Cc: ***@***.******@***.***&gt;; Subject: Re: [Ecogenomics/GTDBTk] Troubleshooting GTDB-Tk DatabaseInstallation and Environment Configuration (Issue #596) Hello, Thank you for the catch up. I still have this error and I was trying to find different taxonomy tools for my MAG identification. Do you have any ideas to figure this out? On Tue, Dec 17, 2024 at 4:19 PM Pierre Chaumeil ***@***.***&gt; wrote: &gt; Hi, &gt; Apologies for the delay, &gt; Do you still have this problem? &gt; &gt; — &gt; Reply to this email directly, view it on GitHub &gt; <#596 (comment)&gt;, &gt; or unsubscribe &gt; <https://github.com/notifications/unsubscribe-auth/A6YIDR6WQVNIXNR6FNSVCRD2GCIPHAVCNFSM6AAAAABK7EFKWGVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDKNBZGY2TGNJWGM&gt; &gt; . &gt; You are receiving this because you authored the thread.Message ID: &gt; ***@***.***&gt; &gt; — Reply to this email directly, view it on GitHub, or unsubscribe. You are receiving this because you commented.Message ID: ***@***.***&gt;

[pchaumeil]

Does it work if you export GTDBTK_DATA_PATH in the activated conda environment?

export GTDBTK_DATA_PATH=/scratch/raskin_root/raskin0/shared_data/Soojung_Sarah/gtdb_tk/release220