Cannot download Diamond db

[s-junguy]

Hi, I cannot download the DIAMOND db with "checkm2 database --download".
I get the Error:
/home/s-junguy/miniconda3/envs/checkm2/bin/checkm2:4: DeprecationWarning: pkg_resources is deprecated as an API. See https://setuptools.pypa.io/en/latest/pkg_resources.html
import('pkg_resources').run_script('CheckM2==1.0.2', 'checkm2')
[08/29/2023 04:18:05 PM] INFO: Command: Download database. Checking internal path information.
[08/29/2023 04:18:06 PM] INFO: Downloading https://zenodo.org/api/files/fd3bc532-cd84-4907-b078-2e05a1e46803/checkm2_database.tar.gz to /home/s-junguy/databases/checkm2_database.tar.gz.
100%|██████████████████████████████████████████████████████████████████████████████████████| 1.74G/1.74G [04:48<00:00, 6.02MiB/s]
[08/29/2023 04:22:55 PM] INFO: Extracting files from archive...
[08/29/2023 04:23:23 PM] INFO: Verifying version and checksums...
[08/29/2023 04:23:23 PM] INFO: Verification success.
Traceback (most recent call last):
File "/home/s-junguy/miniconda3/envs/checkm2/bin/checkm2", line 4, in
import('pkg_resources').run_script('CheckM2==1.0.2', 'checkm2')
File "/home/s-junguy/miniconda3/envs/checkm2/lib/python3.8/site-packages/pkg_resources/init.py", line 722, in run_script
self.require(requires)[0].run_script(script_name, ns)
File "/home/s-junguy/miniconda3/envs/checkm2/lib/python3.8/site-packages/pkg_resources/init.py", line 1561, in run_script
exec(code, namespace, namespace)
File "/home/s-junguy/miniconda3/envs/checkm2/lib/python3.8/site-packages/CheckM2-1.0.2-py3.8.egg/EGG-INFO/scripts/checkm2", line 282, in
fileManager.DiamondDB().download_database(args.path)
File "/home/s-junguy/miniconda3/envs/checkm2/lib/python3.8/site-packages/CheckM2-1.0.2-py3.8.egg/checkm2/fileManager.py", line 140, in download_database
if versionControl.VersionControl().checksum_version_validate_DIAMOND():
File "/home/s-junguy/miniconda3/envs/checkm2/lib/python3.8/site-packages/CheckM2-1.0.2-py3.8.egg/checkm2/versionControl.py", line 115, in checksum_version_validate_DIAMOND
dbhash = self.__calculate_checksum(database_dir, True)
File "/home/s-junguy/miniconda3/envs/checkm2/lib/python3.8/site-packages/CheckM2-1.0.2-py3.8.egg/checkm2/versionControl.py", line 51, in __calculate_checksum
with open(query_file, "rb") as f:
IsADirectoryError: [Errno 21] Is a directory: '/home/s-junguy/checkm2'

I installed checkm2 with:
git clone --recursive https://github.com/chklovski/checkm2.git && cd checkm2
conda env create -n checkm2 -f checkm2.yml
conda activate checkm2
python setup.py install

[chklovski]

Hi, I would suggest installing CheckM2 through bioconda, as that seems more stable. Alternatively, you can manually download the database from https://zenodo.org/api/files/fd3bc532-cd84-4907-b078-2e05a1e46803/checkm2_database.tar.gz, and point checkm2 to it using 'checkm2 database --setdblocation /path/to/downloaded_database_file'

[chklovski]

Closed due to inactivity, feel free to re-open if issue persists.