Trouble with conda installation for distill function

[sophienixon]

Hi there,

I am running DRAM on a number of MAGs and isolate genomes. I am able to annotate ok, but when I try and run the distill function I get the following error:

$DRAM.py distill -i annotations.tsv -o ./Marinobacter_distillate --rrna_path rrnas.tsv --trna_path trnas.tsv /home/mbesssn6/.conda/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/mbesssn6/.conda/envs/DRAM/bin/DRAM.py", line 189, in args.func(**args_dict) File "/home/mbesssn6/.conda/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/mbesssn6/.conda/envs/DRAM/lib/python3.10/site-packages/pandas/util/_decorators.py", line 311, in wrapper return func(*args, **kwargs) File "/home/mbesssn6/.conda/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/mbesssn6/.conda/envs/DRAM/lib/python3.10/site-packages/pandas/io/parsers/readers.py", line 575, in _read parser = TextFileReader(filepath_or_buffer, **kwds) File "/home/mbesssn6/.conda/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/mbesssn6/.conda/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/mbesssn6/.conda/envs/DRAM/lib/python3.10/site-packages/pandas/io/common.py", line 670, in get_handle ioargs = _get_filepath_or_buffer( File "/home/mbesssn6/.conda/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'>

This feels like a conda-config issue to me - any ideas on how to fix?

Cheers, Sophie

[rmFlynn]

Can you post the output of DRAM-setup.py print_config? or just run DRAM-setup.py update_dram_forms and see if it works after that.

[sophienixon]

Hi, so I realised after running that that we didn't have databases configured. After fixing an issue with our server regarding FTP access, I hit a wall with the database setup step:

Can not write to data file /mnt/data/DRAM_data/database_files/uniref90.20220729.mmsdb.idx.0 Traceback (most recent call last): File "/home/mbesssn6/.conda/envs/DRAM/bin/DRAM-setup.py", line 158, in args.func(**args_dict) File "/home/mbesssn6/.conda/envs/DRAM/lib/python3.10/site-packages/mag_annotator/database_processing.py", line 311, in prepare_databases output_dbs['uniref_db_loc'] = download_and_process_uniref(uniref_loc, temporary, uniref_version=uniref_version, File "/home/mbesssn6/.conda/envs/DRAM/lib/python3.10/site-packages/mag_annotator/database_processing.py", line 94, in download_and_process_uniref make_mmseqs_db(uniref_fasta_zipped, uniref_mmseqs_db, create_index=True, threads=threads, verbose=verbose) File "/home/mbesssn6/.conda/envs/DRAM/lib/python3.10/site-packages/mag_annotator/utils.py", line 38, in make_mmseqs_db run_process(['mmseqs', 'createindex', output_loc, tmp_dir, '--threads', str(threads)], verbose=verbose) File "/home/mbesssn6/.conda/envs/DRAM/lib/python3.10/site-packages/mag_annotator/utils.py", line 27, in run_process return subprocess.run(command, check=check, shell=shell, stdout=subprocess.PIPE, File "/home/mbesssn6/.conda/envs/DRAM/lib/python3.10/subprocess.py", line 524, in run raise CalledProcessError(retcode, process.args, subprocess.CalledProcessError: Command '['mmseqs', 'createindex', '/mnt/data/DRAM_data/database_files/uniref90.20220729.mmsdb', '/mnt/data/DRAM_data/database_files/tmp', '--threads', '30']' returned non-zero exit status 1.

Any idea if this is a server or code issue?

[rmFlynn]

Try running mmseqs createindex /mnt/data/DRAM_data/database_files/uniref90.20220729.mmsdb /mnt/data/DRAM_data/database_files/tmp --threads 30 in the same location, I am afraid that dram obviates important command line error messages.