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.py:138] HHblits failed. HHblits stderr begin:
E0207 18:12:26.269661 46988191018688 hhblits.py:141] - 18:12:26.220 ERROR: Could find neither hhm_db nor a3m_db!
E0207 18:12:26.269691 46988191018688 hhblits.py:142] 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
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
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.,
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.