DRAM

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DatabaseHandler - missing database should raise an exception

1

In the DatabaseHandler, if the database is missing, a warning message is printed (https://github.com/WrightonLabCSU/DRAM/blob/master/mag_annotator/database_handler.py#L46-L51) but processing continues and ultimately status code 0 is returned from the caller upon exit, so...

gregvonkuster

Unable to view heatmap

4

Hi there, I'm unable to see the heatmap of the AMGs from the dram-v distill part of the pipeline. Upon opening in my browser the page displays: ``` JavaScript Error:...

MeggyC

Pathway Tools compatible genbank file

2

Just wondering if it's possible to generate a genbank file that contains the product name from the annotations file for integration with Pathway Tools? Or maybe someone knows of a...

kebow

DRAM database installation problem; The subcommand mmseqs createindex DRAM_data/uniref90.20240308.mmsdb DRAM_data/tmp --threads 10 experienced an error

5

Hi, I am having problems installing the DRAM database. I get the same error on two different servers. I installed DRAM following the instructions: git clone https://github.com/WrightonLabCSU/DRAM.git cd DRAM conda...

camillaln

problem about dramv-annotate

4

Hi developer, I met a lot of warmings when running dramv-annotate: it looks like: ``` 2024-03-07 09:45:29,681 - 1 fastas found 2024-03-07 09:45:29,681 - Checking for duplicate names 2024-03-07 09:45:29,817...

xjhzjucas

Receiving a "No descriptions found for your id's" for GT2

6

Hello, I've recently been running DRAM v1.4.6 that was installed manually on a Linux server. It is running smoothly and outputting the desired files, but I am getting a warning...

carleton-envbiotech

error with DRAM-v distill

4

Hi, I have already finished the annotation step and get the annotations.tsv file, now I am doing the distill. step. Here is my command line "DRAM-v.py distill -i annotations.tsv -o...

Qiqi04Tsinghua

dbcan2 url gone ??

3

Hello, dbcan2 url seems to be out of service... since few days. I alway gto. ``` wget http://bcb.unl.edu/dbCAN2/download/Databases/dbCAN-HMMdb-V11.txt --2024-02-19 09:06:12-- http://bcb.unl.edu/dbCAN2/download/Databases/dbCAN-HMMdb-V11.txt Resolving bcb.unl.edu (bcb.unl.edu)... 129.93.162.49 Connecting to bcb.unl.edu (bcb.unl.edu)|129.93.162.49|:80... failed:...

EricDeveaud

key error: K01566 when using DRAM-v.py annotate

1

Hi, Thank you so much for providing this powerful tool,I got an error when using DRAM-v.py annotate. My command line is : DRAM.py annotate -i '/ibex/project/c2252/Chimneys/trim/Metabat/bins/2_bins_dir/2_good_bins/*.fa' -o /ibex/project/c2252/Chimneys/trim/DRAM/2_bis_DRAM_annotation --min_contig_size 1000...

yyyuechen

bug in `v.1.5.0` on the `DRAM-setup.py` help message

1

Hi DRAM community. I just noticed that there is a bug in [DRAM 1.5.0 release](https://github.com/WrightonLabCSU/DRAM/releases/tag/v1.5.0) on the DRUM-setup.py script. Here is the issue: https://github.com/WrightonLabCSU/DRAM/blob/7735a04e58c300d53f9d3611a583b48e507bb843/scripts/DRAM-setup.py#L123C6-L126C66 as you can see there are...

hariszaf