DRAM

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1. We are able to launch this command and get all the database set up and files. DRAM-setup.py prepare_databases --output_dir dramv --skip_uniref 2. This is the content of the configuration...

hgingras

GH families are annotated in the genome based on the information in metabolism_summary.xlsx, but they are missing in the cazy summary heatmap inside prouduct.html. Upon hovering, the respective GH families,...

Aiswarya-prasad

Hello, I'm having difficulty setting up the databases for DRAM on the server I'm using. The command I'm running is `DRAM-setup.py prepare_databases --output_dir DRAM_data --uniref_loc /global/cfs/cdirs/m3264/databases/dram_database_files/uniref90.fasta.gz --vogdb_loc /global/cfs/cdirs/m3264/databases/dram_database_files/vog.hmm.tar.gz --pfam_loc /global/cfs/cdirs/m3264/databases/dram_database_files/Pfam-A.full.gz...

ileleiwi

I got this error when trying to specify the location of dbcan_fam_activities: usage: DRAM-setup.py [-h] {version,prepare_databases,set_database_locations,mv_db_folder,update_description_db,update_dram_forms,print_config,print_settings,import_config,export_config} ... DRAM-setup.py: error: unrecognized arguments: --dbcan_fam_activities_loc /storage/jufengLab/jinlingrong/Database/dbCAN2/CAZyDB.08062022.fam-activities.txt Here is the code I used for...

lingrongjin

Problem during prepare the database

16

Hi, I'm trying the tools, but have a problem. I download the files needed and then run the commands, but it always stuck at the "populating the description db" step....

Gu2uMo

download database step is extremely slow

2

Hello Dram team, It seems running the DRAM-steup.py is very very slow, more than several days. Downloading uniref90.fasta.gz takes more than 12 hours? wget is very slow, no idea why....

jianshu93

description_db.sqlite is taking extremely long to write

1

Hello, I have been running the setup with 29 cores for 5 days and 15 hours at this point. My server only allows a wall time of up to 7...

BurchamLab

DRAM-v databases

1

We are interested in mostly using the DRAM-v part of DRAM. In running the `DRAM-setup.py prepare_databases` command with no special options (no KEGG), we see that the database is quite...

pooranis

dbCAN

10

Hello, I could set up DRAM and I am running it without KEGG database. I found this warning happening every time. Is there anything going wrong here or just a...

JoseLopezArcondo

Hello, dear DRAM core team, thank you for developing such a perfect tool and helping me a lot, but when I use your tool to identify the AMG of my...

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