No such option: --use_mmseqs_gpu

[baifan-wang]

Hi,

I have installed lightning-boltz using the Bare Metal Setup, as detailed at https://github.com/RomeroLab/lightning-boltz#bare-metal-setup. Owing to a slow network connection, I manually downloaded the database and processed it in accordance with the instructions provided in setup_boltz_mmseqs_dbs.sh. I then attempted to run a test example located in ./example with the following command:

boltz predict affinity.yaml --mmseqs_db_dir /mnt/sda/Database/boltz_db

However, the command yielded the following error:

Error: No such option: --use_mmseqs_gpu (Possible options: --mmseqs_gpu_device, --mmseqs_temp_dir)

Could you kindly advise what might be incorrect?

Thank you very much,
Baifan

[jasonkim8652]

Hi Baifan,

Thanks for the detailed report — and apologies, this one is on us. It's a documentation gap, not a problem with your setup.

We recently switched the local MSA backend to a ColabFold-based search, which renamed the --use_mmseqs_gpu flag to --use_colabfold_search. The code already used the new flag, but the README still referenced the old one — so following it produced the No such option: --use_mmseqs_gpu error you saw. We've now updated the README (and the run_multigpu.sh helper) on main, so the Bare Metal Setup instructions are current.

Please use the new flag. Note that you also need to pass it explicitly to enable local MSA generation (the command needs an MSA backend flag, otherwise it errors out asking for one):

boltz predict affinity.yaml \
      --use_colabfold_search \
      --mmseqs_db_dir /mnt/sda/Database/boltz_db

Your manually downloaded/processed database is fine for this — --use_colabfold_search expects exactly the ColabFold databases (uniref30_2302_db + colabfold_envdb_202108_db) that setup_boltz_mmseqs_dbs.sh produces in its default mode.

Could you pull the latest main (or just re-read the updated README) and try the command above? If it still doesn't work, please send the full output and we'll dig in further.

Thanks again for catching this,
Jeonghyeon