DRAM_setup.py stops at processing vog database

[phoebecunningham93]

Description of the bug

Hi there,

I have encountered a problem with preparing the databases, I am running the setup in a conda environment with this command:

DRAM-setup.py prepare_databases --skip_uniref --output_dir DRAM_data

And getting this error:

2025-07-23 17:15:58,202 - Processing vogdb
2025-07-23 17:16:48,952 - The subcommand ['hmmpress', '-f', 'DRAM_data/vog_latest_hmms.txt'] experienced an error:
Error: File format problem in trying to open HMM file DRAM_data/vog_latest_hmms.txt.
File exists, but appears to be empty?

Prior to this the script seemed to be running fine. This error has been reported before and I tried the fix they suggested, but it didn't work.

metagenome-atlas/atlas#718

The vog hmms are definitely there so still looks like a pathway issue in the processing part of the script. Any ideas on why the previous fix is no longer working and what other options there are?

Thanks,
Phoebe

System information

I am using DRAMv1 on an HPC with linux and a conda environment.

Command used and terminal output

DRAM-setup.py prepare_databases --skip_uniref --output_dir DRAM_data

2025-07-23 17:15:58,202 - Processing vogdb
2025-07-23 17:16:48,952 - The subcommand ['hmmpress', '-f', 'DRAM_data/vog_latest_hmms.txt'] experienced an error:
Error: File format problem in trying to open HMM file DRAM_data/vog_latest_hmms.txt.
File exists, but appears to be empty?

Relevant files

No response

[madeline-scyphers]

I am not sure why the fix doesn't work anymore, but we have moved development to DRAM v2 now. Which you can find on dev branch. It is still a work in progress, but it is in a usable state. With DRAM v2, the databases, other than KEGG, we have pre formated and you can just download them and use without a prepare_databases step.