‘prepare_databases’ always tries to download dbCAN fam-activities database even when local file location is provided

[YanjieZhu1997]

Description of the bug

Hi,

Thank you for creating this fantastic tool!

There is a bug that I have been trying to fix over the past month but failed all the time. I have downloaded all the databases required for DRAM. When I try to setup those databases using 'DRAM-setup.py prepare_databases', DRAM always attempts to download CAZyDB.08062022.fam-activities.txt, even though a local file is already provided by the '--dbcan_fam_activities' option. And unfortunetely, the 'https://bcb.unl.edu/' site is under maintenance (for over a month already), so that the file cannot be downloaded.

'Something went wrong with the download of the url: https://bcb.unl.edu/dbCAN2/download/Databases/V9/CAZyDB.08062022.fam-activities.txt 2026-02-12 17:40:48,206 - <urlopen error [SSL: CERTIFICATE_VERIFY_FAILED] certificate verify failed: unable to get local issuer certificate (_ssl.c:1007)>'

This leads to the failure of the entire 'prepare_databases' process.

Could you please advise how to resolve this problem?

Thanks a lot!

System information

-DRAM version: DRAM v1.5.0 (installed via Conda)
-Nextflow version: Not using Nextflow
-Hardware: HPC cluster
-Executor: SLURM
-Container engine: Conda (no Docker/Singularity container)
-OS: Linux (HPC compute node)

Command used and terminal output

Relevant files

No response