DRAM

DRAM copied to clipboard

KeyError

9

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...

woodoo46

DRAM issue with setting up databases

13

Hi there, I originally ran DRAM-v for annotations and then tried to run the distillation. But I only got outputs in 1/3 of the distillation output files and I couldn't...

yugen-miyahara

dbcan: ++ best hits, subfam ec numbers columns change cutoff to 1e-18

3

This is an attempt at a solution for some problems with CAZY ids from dbCAN. - We will introduce a new column for best hit from the dbCAN database named...

rmFlynn

Hi, I'm wondering if it is possible to get DRAM version from command line? Although we can get it from the release history, a command like `DRAM.py --version` will be...

rujinlong

DRAM error while annotation

11

5 fastas found 2022-07-15 15:49:14.912901: Annotation started 0:00:00.045806: Retrieved database locations and descriptions 0:00:00.045894: Annotating MEGAHIT-group-0.5 0:00:21.937310: Turning genes from prodigal to mmseqs2 db 0:00:23.980066: Getting hits from kofam 0:21:38.160079:...

poddarharsh15

Database preparation error 3

3

Hi there, I am trying to run do database preparation as following: DRAM-setup.py prepare_databases --output_dir ${outdir} --skip_uniref But I had the following error: subprocess.CalledProcessError: Command '['mmseqs', 'msa2profile', 'DRAM_data2/database_files/pfam.mmsmsa', 'DRAM_data2/database_files/pfam.mmspro', '--match-mode',...

woodoo46

Trouble with conda installation for distill function

3

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...

sophienixon

InvalidIndexError: Reindexing only valid with uniquely valued Index objects

10

Hi, I got this error from DRAM-v.py Here the command used `DRAM-v.py annotate -i ENSEMBLE_vRhyme/for-dramv/final-viral-combined-for-dramv_mod.fa -v ENSEMBLE_vRhyme/for-dramv/viral-affi-contigs-for-dramv_mod.tab -o annotation --threads 28 --verbose` Here the log ``` 5:04:00.646081: Getting hits from...

michoug

More modules

9

Hello, we have sucessfully tested DRAM (on 10 MAGs) the output is clear and the HTML is very good to get an overview. I wonder if there aren't more KEGG...

SilasK

How to prepare a single .pep KEGG database for DRAM database setup step

5

Hi, I have a KEGG subscription and want to incorporate it into my DRAM setup. I tried setting up DRAM using a concatenation of the different .pep KEGG files to...

nixon444