AlphaFold: HHblits failed


I had a problem using AlphaFold-Multimer with the full_dbs flag. The error message was the following:

E0207 18:12:26.269619 46988191018688] HHblits failed. HHblits stderr begin:
E0207 18:12:26.269661 46988191018688] - 18:12:26.220 ERROR: Could find neither hhm_db nor a3m_db!
E0207 18:12:26.269691 46988191018688] HHblits stderr end

By using the reduced_dbs flag, I manage to finalize the run.

Apparently, this is could be due to either to a memory issue (not really sure, given the error message) or a permission issue in the bfd/ directory:

chmod 755 or chmod 444 should both work. Could you please check this? @team.alphafold

Thank you.

Hello, which bank are you using ? if it is the 2022-02-02 one, please see answer here: Update/download of pdb_mmcif in alphafold2/2022-02-02 - #2 par Francois

I do not think that the issue is related to the bank version (i.e. current vs 2022/02/02), but rather to file permission privileges (file size are comparable, so no problems related to failed download). In current/bfd the permission flag are -rw----r-x for all the files, whereas in 2022-02-02/bfd some file permissions are -rw-------.

If I run alphafold with the --db_preset=reduced_dbs flag I have no problems, since the small_bfd/ dataset is used and permissions are fine (i.e., -rw-r--r--).

I hope this helps.

Yes you're right, as the db was not ready yet I didn't run the chmod, it should be ok now.