error with DRAM-setup.py prepare_databases

[DrYoungOG]

Thanks for the useful software! I have successfully installed DRAM in a conda environment naned "DRAM". Then I tried to run DRAM-setup.py prepare_databases to download the databases, but an error occured.

The command I run:

!/bin/sh

SBATCH --job-name=DRAM_db

SBATCH --partition=cpuPartition

SBATCH --nodes=1

SBATCH --ntasks-per-node=40

SBATCH --error=/home/yangpc/DRAM_ref_db/download_db_script/DRAM_db.err

SBATCH --output=/home/yangpc/DRAM_ref_db/download_db_script/DRAM_db.out

DRAM-setup.py prepare_databases --output_dir /home/yangpc/DRAM_ref_db --threads 40 --verbose

output of command DRAM-setup.py print_config: 2022-12-18 11:48:12,650 - Logging to console /home/yangpc/anaconda3/envs/DRAM/lib/python3.10/site-packages/mag_annotator/database_handler.py:124: UserWarning: Database does not exist at path None warnings.warn("Database does not exist at path %s" % description_loc) Processed search databases KEGG db: None KOfam db: None KOfam KO list: None UniRef db: None Pfam db: None dbCAN db: None RefSeq Viral db: None

MEROPS peptidase db: None VOGDB db: None Descriptions of search database entries Pfam hmm dat: None dbCAN family activities: None VOG annotations: None

Description db: None

DRAM distillation sheets Genome summary form: None Module step form: None ETC module database: None Function heatmap form: None AMG database: None

DRAM-setup.py version: 1.4.2

The .err file and .log file are attached.

Thank you very much!

DRAM_db_err.txt database_processing.log

[rmFlynn]

Dram 1.4.3 has a key bug fix. However, that may not be your problem, can you visit that url yourself?

[DrYoungOG]

I can download the two urls in the database_processing.log file and the DRAM_db_err.txt file(ftp://ftp.genome.jp/pub/db/kofam/profiles.tar.gz, https://www.genome.jp/ftp/db/kofam/profiles.tar.gz), but what about other databases used in DRAM?

[rmFlynn]

So usually this is a fire wall issue, if you can't download any data bases the you can get the minimalist database from zotaro I will add that to the faq soon and send.

[rmFlynn]

So usually this is a fire wall issue, if you can't download any data bases the you can get the minimalist database from zotaro I will add that to the faq soon and send.

[DrYoungOG]

Please allow me to ask one more question, is there a solution to the fire wall issue?

[rmFlynn]

Sorry, for the delay, but the firewall would need to be fixed by your IT department the only advice I can give you is to use the loc arguments in dram prepare_databases to point to already downloaded data. You can download these by going to the needed website or from zenodo https://zenodo.org/record/7183884