unable to install databases

[peter0k]

Hi,

I installed dammit dev version (pip install git+https://github.com/camillescott/dammit.git).

If I try to install a database ( dammit databases --install --busco-group eukaryota) I'm getting following error:

## submodule: databases Traceback (most recent call last): File "/home/peter/.local/bin/dammit", line 9, in sys.exit(app.DammitApp(arg_src=sys.argv[1:]).run()) File "/home/peter/.local/lib/python3.10/site-packages/dammit/app.py", line 45, in run return self.args.func() File "/home/peter/.local/lib/python3.10/site-packages/dammit/app.py", line 278, in handle_databases handler = databases.get_handler(self.config_d) File "/home/peter/.local/lib/python3.10/site-packages/dammit/databases.py", line 41, in get_handler handler = TaskHandler(config['database_dir'], File "/home/peter/.local/lib/python3.10/site-packages/dammit/handler.py", line 49, in __init__ super(TaskHandler, self).__init__() File "/home/peter/.local/lib/python3.10/site-packages/doit/cmd_base.py", line 289, in __init__ raise NotImplementedError( NotImplementedError: doit.cmd_base.py:TaskLoader was removed on 0.36.0, use TaskLoader2 instead

Yesterday I tried to install dammit via conda and obtained same error.

If somebody has an idea: Thank you!

[Anto007]

@peter0k, I ran into the same issue but fixed it by adding doit=0.35.0 to my conda environment. My .yml file at the time of building the conda dammit environment looked like the below. Hope this helps

name: null

channels: 
    - conda-forge
    - defaults
    - bioconda
 
dependencies:
    - python=3
    - doit=0.35.0
    - dammit

[Anto007]

But subsequently, I ran into the same error as Issue 241 Trying to figure out now a way out of this new error :-(

[Anto007]

Seems like I might need to give up on this. Most required db files were downloaded (my command-line after activating the conda environment- dammit databases --install --database-dir /data/conda_dammit_env/db --full --busco-group eukaryota) excepting the OrthoDB one (as the older version files that dammit requires isn't available on OrthoDB anymore). I got around the OrthoDB download issue by downloading an old version of the db files that was archived at Zenodo by a kind user in this thread. Unzipped this downloaded db and I then replaced busco2db (containing busco fungal lineage) in this dir with the eukaryota lineage containing busco2db that I had downloaded at the initial step. I then set the database path by entering export DAMMIT_DB_DIR=/data/conda_dammit_env/old_db/dbs and ran the command dammit annotate thin2_rnaspades_assembly.fasta --busco-group eukaryota --n_threads 32. I encountered yet another error TypeError: lastal_task() got an unexpected keyword argument 'pbs' which I fixed by commenting out the line starting with pbs in /data/conda_dammit_env/lib/python3.8/site-packages/dammit/annotate.py (as suggested in this thread). I now reran the above damit annotate command-line and I have encountered a new strand error at the hmmscan-gff3:thin2_rnaspades_assembly.fasta.x.pfam-A.gff3 step-

File "pandas/_libs/hashtable_class_helper.pxi", line 4562, in pandas._libs.hashtable.PyObjectHashTable.get_item
KeyError: 'strand'
`

DAMM IT!!!! :-(