Closed abarilo closed 1 month ago
Thank you for the hint.
Thanks for this, I also ran into this last week!
It took some time to find the database_processing.py
script in the generated conda env containing mag_annotator, for me it was located in the conda env folder in the atlas db folder:
atlas_db/conda_envs/220fa41099c6afee6550f2ccb565fe10_/lib/python3.11/site-packages/mag_annotator/database_processing.py
The line number you mentioned @abarilo was correct, but the function was called process_vogdb
. I made the change you suggested and just started a new run, I'll report back if it works as intended now.
Hope it works now @boulund. Corrected the function name, thanks!
Folks, can Atlas be linked to a currently existing DRAM db in my environment?
Folks, can Atlas be linked to a currently existing DRAM db in my environment?
Yes.
DRAM-setup.py export_config --output_file
dram_config_file: output_file
https://github.com/metagenome-atlas/atlas/blob/master/workflow/rules/dram.smk
Thanks for the fix! I'm new to this, and I've been trying for a couple days now to figure out why it's not working.
I'm also having the following issue: /data/users/danross/databases/condaenvs/e6506989c58f442efbed441478497d1c/lib/python3.11/site-packages/mag_annotator/database_handler.py:123: UserWarning: Database does not exist at path None warnings.warn("Database does not exist at path %s" % description_loc)
I think it's related to Issue 664, but that was for a previous version of Atlas
Thanks :)
Hi Silas,
I encountered an error during the DRAM download and solved by modifying one of the scripts. Maybe this can be usefull for other users. During the DRAM database download I get the folowing error message that appears both while running ATLAs and DRAM-setup.py:
Here is the relevant log output:
Traceback:
I fixed it by modifying database_processing.py script, line 316 in
process_vogdb
Old script:
New script:
After this fix the download went smoothly.
atlas, version 2.18.1+12.gdc53d3b4
Cheers, Anastasiia