DRAM distill: Error while running

usegalaxy.eu support
, ,
1

DRAM annotate ran successfully, but the output only includes only positional data (start/end coordinates, etc.), gene position, rRNAs, and tRNAs. It does NOT contain functional annotation columns like kegg_id, uniref_id, pfam_id, or gene function in the annotations file.

No product.tsv or genome_summary.tsv was generated either.

Because of this, The error is showing in DRAM distill

Can you please confirm whether the full DRAM databases are enabled on Galaxy.eu, and if functional annotation is supported in this wrapper?

Please let me know if I am going wrong somewhere. I attached the error message below.

Thanks.

2025-06-06 14:24:10,978 - The log file is created at output_dir/distill.log
2025-06-06 14:24:11,056 - Note: the fallowing id fields were not in the annotations file and are not being used: [‘kegg_genes_id’, ‘ko_id’, ‘kegg_id’, ‘kegg_hit’, ‘peptidase_family’, ‘cazy_best_hit’, ‘pfam_hits’, ‘camper_id’, ‘fegenie_id’, ‘sulfur_id’, ‘methyl_id’], but these are
Traceback (most recent call last):
File “/usr/local/tools/_conda/envs/__dram@1.5.0/bin/DRAM.py”, line 211, in
args.func(**args_dict)
File “/usr/local/tools/_conda/envs/__dram@1.5.0/lib/python3.11/site-packages/mag_annotator/summarize_genomes.py”, line 664, in summarize_genomes
genome_summary_form = pd.read_csv(database_handler.config[“dram_sheets”][‘genome_summary_form’], sep=‘\t’)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File “/usr/local/tools/_conda/envs/__dram@1.5.0/lib/python3.11/site-packages/pandas/util/_decorators.py”, line 211, in wrapper
return func(*args, **kwargs)
^^^^^^^^^^^^^^^^^^^^^
File “/usr/local/tools/_conda/envs/__dram@1.5.0/lib/python3.11/site-packages/pandas/util/_decorators.py”, line 331, in wrapper
return func(*args, **kwargs)
^^^^^^^^^^^^^^^^^^^^^
File “/usr/local/tools/_conda/envs/__dram@1.5.0/lib/python3.11/site-packages/pandas/io/parsers/readers.py”, line 950, in read_csv
return _read(filepath_or_buffer, kwds)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File “/usr/local/tools/_conda/envs/__dram@1.5.0/lib/python3.11/site-packages/pandas/io/parsers/readers.py”, line 605, in _read
parser = TextFileReader(filepath_or_buffer, **kwds)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File “/usr/local/tools/_conda/envs/__dram@1.5.0/lib/python3.11/site-packages/pandas/io/parsers/readers.py”, line 1442, in init
self._engine = self._make_engine(f, self.engine)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File “/usr/local/tools/_conda/envs/__dram@1.5.0/lib/python3.11/site-packages/pandas/io/parsers/readers.py”, line 1735, in _make_engine
self.handles = get_handle(
^^^^^^^^^^^
File “/usr/local/tools/_conda/envs/__dram@1.5.0/lib/python3.11/site-packages/pandas/io/common.py”, line 713, in get_handle
ioargs = _get_filepath_or_buffer(
^^^^^^^^^^^^^^^^^^^^^^^^
File “/usr/local/tools/_conda/envs/__dram@1.5.0/lib/python3.11/site-packages/pandas/io/common.py”, line 451, in _get_filepath_or_buffer
raise ValueError(msg)
ValueError: Invalid file path or buffer object type: <class ‘NoneType’>

2

Hi @Mohanchaitanya

I can reproduce the problem with the tiny tool test data and have sent the bug report into the EU team. The tool is only hosted at their server so far, so I don’t have an alternative to suggest yet.

Let’s also ping them here. Hi @wm75 would you be able to let us know if the database should be available or if it has some problem or pending publishing? Apologies is this is noted somewhere already and I missed it. I did find the prior topic about the annotate function from the tool suite (DRAM annotate gives empty files - #8 by wm75) where a correction was applied.

Thanks for reporting the problem! :slight_smile:

3

Hi @jennaj
Thank you for your prompt response.
I could atleast see the columns with ko_id kegg_hit peptidase_id peptidase_family peptidase_hit peptidase_RBH peptidase_identity peptidase_bitScore peptidase_eVal pfam_hits cazy_id cazy_hits, in your annotations table.
I could not find them in mine. Please see this workflow and help me understand where I went wrong.

workflow link

Thank you.

4

Hi @Mohanchaitanya I’m following up about this tool. I reran both tool tests, and had the same result. My run with the gene name option toggle created the same message as your run that also used that option, and I can see the setting in your shared workflow.

Importantly, the test data didn’t include those extra annotation fields. You could also check your output. The upstream tool Dram annotate is what can add those into the tabular annotation output. I not exactly sure which of the three annotation options on the form (UniRef, VOGDB, kofam) adds in those values, or if it is a different toggle, so I started up a test against all three. We can inspect the output to see what happens. These are in the same test history above and I tagged each test.

This is the guide from the tool author I am following → 3a. Running DRAM · WrightonLabCSU/DRAM Wiki · GitHub

Now, while you can supply your own annotation files, it would be nicer to have the native indexes. I’ve requested this at → Request: add native indexes for the DRAM suite of tools · Issue #1562 · usegalaxy-eu/infrastructure-playbook · GitHub

Apologies for the delays. Most of the team was involved with our recent release and yearly conference but we are back now. :slight_smile: Let’s get this working for you!