DRAM.py distill : ValueError: Invalid file path or buffer object type: <class 'NoneType'>

[kalonji08]

Hello I'm having issue running the following code: DRAM.py distill -i annotation/annotations.tsv -o distill --trna_path annotation/trnas.tsv --rrna_path annotation/rrnas.tsv

Here is the output:

/home/kalonjilab/miniconda3/envs/DRAM/lib/python3.10/site-packages/mag_annotator/database_handler.py:51: UserWarning: Database does not exist at path None warnings.warn('Database does not exist at path %s' % self.description_loc) Traceback (most recent call last): File "/home/kalonjilab/miniconda3/envs/DRAM/bin/DRAM.py", line 189, in args.func(*args_dict) File "/home/kalonjilab/miniconda3/envs/DRAM/lib/python3.10/site-packages/mag_annotator/summarize_genomes.py", line 582, in summarize_genomes genome_summary_form = pd.read_csv(database_handler.dram_sheet_locs['genome_summary_form'], sep='\t') File "/home/kalonjilab/miniconda3/envs/DRAM/lib/python3.10/site-packages/pandas/util/_decorators.py", line 311, in wrapper return func(args, kwargs) File "/home/kalonjilab/miniconda3/envs/DRAM/lib/python3.10/site-packages/pandas/io/parsers/readers.py", line 680, in read_csv return _read(filepath_or_buffer, kwds) File "/home/kalonjilab/miniconda3/envs/DRAM/lib/python3.10/site-packages/pandas/io/parsers/readers.py", line 575, in _read parser = TextFileReader(filepath_or_buffer, kwds) File "/home/kalonjilab/miniconda3/envs/DRAM/lib/python3.10/site-packages/pandas/io/parsers/readers.py", line 933, in init self._engine = self._make_engine(f, self.engine) File "/home/kalonjilab/miniconda3/envs/DRAM/lib/python3.10/site-packages/pandas/io/parsers/readers.py", line 1217, in _make_engine self.handles = get_handle( # type: ignore[call-overload] File "/home/kalonjilab/miniconda3/envs/DRAM/lib/python3.10/site-packages/pandas/io/common.py", line 670, in get_handle ioargs = _get_filepath_or_buffer( File "/home/kalonjilab/miniconda3/envs/DRAM/lib/python3.10/site-packages/pandas/io/common.py", line 427, in _get_filepath_or_buffer raise ValueError(msg) ValueError: Invalid file path or buffer object type: <class 'NoneType'> (DRAM) kalonjilab@kalonjilab-Precision-T7610:/mnt/db1/dram$

[rmFlynn]

Sorry I thought I got to this but forgot to hit enter. Did you run DRAM-setup.py --update_description_db?

[kalonji08]

@rmFlynn Thank you so much for getting back to me.

Here is the output: DRAM-setup.py update_description_db /home/kalonjilab/miniconda3/envs/DRAM/lib/python3.10/site-packages/mag_annotator/database_handler.py:51: UserWarning: Database does not exist at path None warnings.warn('Database does not exist at path %s' % self.description_loc)

[kalonji08]

@rmFlynn i also run : DRAM-setup.py print_config

And this is what i got: Processed search databases KEGG db: None KOfam db: None KOfam KO list: None UniRef db: None Pfam db: None dbCAN db: None RefSeq Viral db: None MEROPS peptidase db: None VOGDB db: None

Descriptions of search database entries Pfam hmm dat: None dbCAN family activities: None VOG annotations: None

Description db: None

DRAM distillation sheets Genome summary form: None Module step form: None ETC module database: None Function heatmap form: None AMG database: None

Looks like i don't have a DB or i should redo the setup, maybe? How can i do it effectively with 80GB RAM and 32 threads?

[rmFlynn]

Hmm where did you set up the database? If the output files are all there, then you can use DRAM-setup.py set_database_locations, use DRAM-setup.py set_database_locations -h to figure it out. I there is a config file there, it will be named like CONFIG, then you can import it with DRAM-setup.py import_config

[kalonji08]

@rmFlynn the database was set on an second hard drive but it has some superblock issues. I think i will have to replace it and re install evrything follwing the instructions above. Thanks a lot

[rmFlynn]

I hope this worked out but given the problem was likely the drive I am going to close this issue.