GTDB Forum

How to set up database with symbolic link?

I’ve downloaded my database here:
/usr/local/scratch/METAGENOMICS/jespinoz/db/gtdb-tk_db/release95/

I’ve created a symbolic link here:

    (base) -bash-4.1$ ls -lhS /usr/local/devel/ANNOTATION/jespinoz/anaconda3/envs/gtdbtk_env/share/gtdbtk-1.4.0/db/
    total 1.5K
    lrwxrwxrwx 1 jespinoz tigr 65 Dec 17 15:21 release95 -> /usr/local/scratch/METAGENOMICS/jespinoz/db/gtdb-tk_db/release95/

I keep getting this error:

================================================================================
(gtdbtk_env) -bash-4.1$ gtdbtk check_install -h

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

           The GTDB-Tk reference data does not exist or is corrupted.
GTDBTK_DATA_PATH=/usr/local/devel/ANNOTATION/jespinoz/anaconda3/envs/gtdbtk_env/share/gtdbtk-1.4.0/db/

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

There was a file called .empty in that directory that I had to delete. Then you just symlink everything in the directory:

(gtdbtk_env) -bash-4.1$ rm /usr/local/devel/ANNOTATION/jespinoz/anaconda3/envs/gtdbtk_env/share/gtdbtk-1.4.0/db/.empty
(gtdbtk_env) -bash-4.1$ ln -s /usr/local/scratch/METAGENOMICS/jespinoz/db/gtdb-tk_db/release95/* /usr/local/devel/ANNOTATION/jespinoz/anaconda3/envs/gtdbtk_env/share/gtdbtk-1.4.0/db/

Note, I tried this at first but it didn’t work because of the .empty file which is why I symlinked the entire directory instead.