DRAM

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KeyError vogdb categories

3

Hello, I was running dram_v for seven genomes, all passed but one failed, with this error message: ``` /fs02/ie79/Zarul/prophage_detection/.snakemake/conda/a41f0976fb8154f5853379be34959793/lib/python3.10/site-packages/mag_annotator/annotate_bins.py:603: UserWarning: No rRNAs were detected, no rrnas.tsv file will be created....

ZarulHanifah

No descriptions were found for your IDs error

25

Hi, I am running a recent version of DRAM, and get the following error (after some MAGs were annotated without a problem). I tried updating the description db, but the...

MaxRubinBlum

A question about viral hallmark gene and viral-like gene

2

Hi， I have some confusion when analyzing AMG, so I hope I can get some help. 1.In the published papter of DRAM, the figure 6(a) display the definition of auxiliary...

fanlu-f

FileExistsError: [Errno 17] File exists: './dramv-annotate' when specifying output dir

8

An error is being thrown when I specify the output dir when the folder exists. `DRAM-v.py annotate -i /backup/user_data/linda/f_dynamics/vs2-pass2/final-viral-combined-for-dramv.fa -v /backup/user_data/linda/f_dynamics/vs2-pass2/for-dramv/viral-affi-contigs-for-dramv.tab -o ./dramv-annotate --skip_trnascan --threads 10 --min_contig_size 1000` ``` File...

flannsmith

DRAM-setup.py prepare_databases --skip_uniref produces error

1

I run `DRAM-setup.py prepare_databases --skip_uniref --output_dir DRAM_data`, trying to skip UNIRef DB step, but it fails twice. Maybe it's related to previous CONFIG file (envs/dram/lib/python3.10/site-packages/mag_annotator/CONFIG)? ```/home/ipetrushin/miniconda3/envs/dram/lib/python3.10/site-packages/mag_annotator/database_handler.py:51: UserWarning: Database does not...

ipetrushin

Is there a way to predict if a genome is anaerobic / (factultative) aerobic?

1

Is there a way to predict if a genome is anaerobic / (factultative) aerobic? e.g. Based on the complex 1-5 output? Kind regards Sila

SilasK

Database does not exist at path %s' % self.description_loc

18

Hello, I have installed DRAM on my cluster home account and have attempted to use the script for the last few weeks. However, every time I try to run the...

pulidofabs

Issues while updating databases using DRAM-setup.py set_database_locations

13

Hi, Thank you for this wonderful tool. I am facing an issue while updating description db using `DRAM-setup.py set_database_locations --update_description_db.` After installing DRAM, everything was working fine except for a...

avishekdutta14

How to understand the butyrate pathways

5

Hallo @shafferm, I was a bit disappointed that there are no SCFA modules in Kegg, but then someone told me that you made some extra modules for them. Thank you....

SilasK

database does not exist at path none

5

Thanks first. this is the database setup. So, uniref, pfam and dbcan is ok for use? DRAM-setup.py prepare_databases --output_dir DRAM_data --threads 28 2021-04-27 21:32:56.852851: Database preparation started 9:55:06.911831: UniRef database...

yulong0827