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WrightonLabCSU / DRAM

Distilled and Refined Annotation of Metabolism: A tool for the annotation and curation of function for microbial and viral genomes
GNU General Public License v3.0
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KeyError #199

Closed woodoo46 closed 1 year ago

woodoo46 commented 1 year ago

Hi, there,

I ran DRAMv, and got the following error

UserWarning: No descriptions were found for your id's. Does this YP_656630.1 look like an id from viral_description

I am not quite familiar with the viral database, any suggestions?

Thanks.

George

rmFlynn commented 1 year ago

Try DRAM-setup.py --update_description_db this usually solves this problem.

woodoo46 commented 1 year ago

Thanks for your solution. This solves the key error. I am having another issue here:

File "/tools/mylib/python-3.8.0-sqlite/lib/python3.8/site-packages/mag_annotator/annotate_bins.py", line 495, in for i in annotations.columns if i.endswith('_id')} AttributeError: 'int' object has no attribute 'endswith'

woodoo46 commented 1 year ago

By the way, this happens below this line: 0:10:10.725917: Merging ORF annotations

rmFlynn commented 1 year ago

Interesting, I thought we got this solved, what version of dram was it?

woodoo46 commented 1 year ago

I am using 1.3.

rmFlynn commented 1 year ago

What is the output of DRAM-setup.py version ?

woodoo46 commented 1 year ago

Yes. 1.3 is the output of DRAM-setup.py. I did not find options from DRAM-v.py or DRAM.py to print out the version information.

rmFlynn commented 1 year ago

If that is really the version please upgrade to 1.3.6, it should have the correct bug fix. If the problem persists on this version and you can upload the data you ran on please do so and I will find the bug immediately. You may also be able to fix this by manually editing the annotations file in Excel or similar, renaming the column that is 0 if it exists.

woodoo46 commented 1 year ago

To upgrade to 1.3.6, do I need to git clone? I used the "Releases" link and downloaded 1.3. If I want to do the correction myself, namely "renaming the column that is 0 if it exists", where file(s) should change? I mean should change the python code or the annotation files?

Thanks.

rmFlynn commented 1 year ago

Sorry for the delay thing get lost hopfully you got 1.3.6 orherwise things will be fixed in 3.14 wich will hit conda soon.