### Author:  [@Mohanchaitanya](https://help.galaxyproject.org/u/Mohanchaitanya)
#### Post date: [June 6, 2025, 4:14pm UTC](https://help.galaxyproject.org/t/dram-distill-error-while-running/15665/1 "2025-06-06T16:14:18Z")
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](http://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: \
---
### Author:  [@jennaj](https://help.galaxyproject.org/u/jennaj)
#### Post date: [June 6, 2025, 9:51pm UTC](https://help.galaxyproject.org/t/dram-distill-error-while-running/15665/2 "2025-06-06T21:51:22Z")
> [@Mohanchaitanya](#):
>
> DRAM
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.
- [https://usegalaxy.eu/u/jenj/h/test-dram-distill](https://usegalaxy.eu/u/jenj/h/test-dram-distill)
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](https://help.galaxyproject.org/t/dram-annotate-gives-empty-files/10422/8)) where a correction was applied.
Thanks for reporting the problem! 🙂
---
### Author:  [@Mohanchaitanya](https://help.galaxyproject.org/u/Mohanchaitanya)
#### Post date: [June 7, 2025, 1:58am UTC](https://help.galaxyproject.org/t/dram-distill-error-while-running/15665/3 "2025-06-07T01:58:11Z")
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](https://usegalaxy.eu/u/mohanchaitanya/w/workflow-constructed-from-history-checkm-for-kp01-1)
Thank you.
---
### Author:  [@jennaj](https://help.galaxyproject.org/u/jennaj)
#### Post date: [July 1, 2025, 5:32pm UTC](https://help.galaxyproject.org/t/dram-distill-error-while-running/15665/4 "2025-07-01T17:32:52Z")
> [@jennaj](#):
>
> [Galaxy](https://usegalaxy.eu/u/jenj/h/test-dram-distill)
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](https://github.com/WrightonLabCSU/DRAM/wiki/3a.-Running-DRAM)
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](https://github.com/usegalaxy-eu/infrastructure-playbook/issues/1562)
Apologies for the delays. Most of the team was involved with our recent release and yearly conference but we are back now. 🙂 Let’s get this working for you!
---
### Author:  [@manokaran\_deva](https://help.galaxyproject.org/u/manokaran_deva)
#### Post date: [September 18, 2025, 7:14pm UTC](https://help.galaxyproject.org/t/dram-distill-error-while-running/15665/5 "2025-09-18T19:14:35Z")
I am also getting similar issues with DRAM annotate tool. My output from DRAM annotate tool does NOT contain functional annotation columns like kegg\_id, uniref\_id, pfam\_id, or gene function in the annotations file. Any solutions for this issue
---
### Author:  [@jennaj](https://help.galaxyproject.org/u/jennaj)
#### Post date: [September 22, 2025, 8:50pm UTC](https://help.galaxyproject.org/t/dram-distill-error-while-running/15665/6 "2025-09-22T20:50:40Z")
Hi @manokaran_deva
Yes, for now you will need to supply your own reference data for the tool to use (from the history, as described in the guide I linked).
For the native index choices, we are still waiting for this request to be processed:
> [@jennaj](#):
>
> 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](https://github.com/usegalaxy-eu/infrastructure-playbook/issues/1562)
Hope this helps to clarify the status! I could get the annotation tool to run correctly (see my original testing history linked above – some test are in the hidden tab) but the data is incomplete with the current limited native indexes. 🙂