DRAM

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Continue the "prepare_database" process

2

Hi developer, I aim to set up the database, but the network connection issue stops the process. Is there a way to continue the "prepare_databases" process without starting everything over?...

chenyj8

hmmpress not found during prepare_databases

1

I have been trying to do a new conda install of DRAM on my server but the prepare_databases step keeps running into an error after downloading all of the raw...

carleton-envbiotech

DRAM 1.5.0 installation issues

6

Hi, I've recently installed DRAM 1.5.0. using `wget https://raw.githubusercontent.com/WrightonLabCSU/DRAM/master/environment.yaml` `conda env create -f environment.yaml -n DRAM` When I started `DRAM-setup.py prepare_databases --output_dir DRAM_data --uniref_loc uniref90.fasta.gz ` I had this error:...

karenhn

Hello, I am having some issues with the database installation process. I was using the following command: DRAM-setup.py prepare_databases --output_dir DRAM_data. The process was going well, but I got this...

apazminov

annotate genes using faa fasta files

3

Hi, I would like to use DRAM to annotate some protein predicted form various genomes, I know that in dram there is a flag ```annotate_genes``` in the pipeline. However, when...

avera1988

Thank you for providing this powerful tool! I am a beginner in DRAM. My DRAM version is 1.5.0. I used DRAM-v.py annotate to discover virus AMGs, and while the log...

fhdbqr

Steps to download all the databases and setup manually in DRAM

3

Dear developers @jrr-microbio @rmFlynn @shafferm For some reason, the database download got interrupted / or not successful in our HPC clusters. So, I am thinking about downloading all the latest...

srisvs33

KeyError: 'amg_database' in DRAM-v

2

I was running DRAM-v to annotate some VirSorter2 results before distillation, but in the error file I got this: /mnt/home/soft/dramv/programs/x86_64/1.4.6/lib/python3.9/site-packages/mag_annotator/database_handler.py:123: UserWarning: Database does not exist at path None warnings.warn("Database does...

nologo68

Dear DRAM team and others, We just got our KEGG subscription - there are a lot of .pep files there. I can see from issues #305 and #182 that concatenation...

caity-s

Hello, I am using DRAM to annotate the metagenome. The genome size is about 3M, and it takes more than 20 minutes to annotate a genome. Is there any way...

qkqk-hub