Could not find HHBlits database

[karlaarz]

Hi! I installed alphafold following the non_docker option using the reduced version of the databases (reduced_dbs mode), and I have this error:

bash run_alphafold.sh -d /home/k.ruiz/alphafold_data -o /home/k.ruiz/rnaseq/alphafold/output -f /home/k.ruiz/rnaseq/alphafold/input/MSTRG.4643.1_3_RBP3.fasta -t 2020-05-14

I0725 12:53:28.340466 140062189004608 templates.py:857] Using precomputed obsolete pdbs /home/k.ruiz/alphafold_data/pdb_mmcif/obsolete.dat.
E0725 12:53:28.343733 140062189004608 hhblits.py:82] Could not find HHBlits database /home/k.ruiz/alphafold_data/bfd/bfd_metaclust_clu_complete_id30_c90_final_seq.sorted_opt
Traceback (most recent call last):
  File "/home/k.ruiz/alphafold-2.2.0/run_alphafold.py", line 422, in <module>
    app.run(main)
  File "/home/k.ruiz/miniconda3/envs/alphafold/lib/python3.8/site-packages/absl/app.py", line 312, in run
    _run_main(main, args)
  File "/home/k.ruiz/miniconda3/envs/alphafold/lib/python3.8/site-packages/absl/app.py", line 258, in _run_main
    sys.exit(main(argv))
  File "/home/k.ruiz/alphafold-2.2.0/run_alphafold.py", line 338, in main
    monomer_data_pipeline = pipeline.DataPipeline(
  File "/home/k.ruiz/alphafold-2.2.0/alphafold/data/pipeline.py", line 138, in __init__
    self.hhblits_bfd_uniclust_runner = hhblits.HHBlits(
  File "/home/k.ruiz/alphafold-2.2.0/alphafold/data/tools/hhblits.py", line 83, in __init__
    raise ValueError(f'Could not find HHBlits database {database_path}')
ValueError: Could not find HHBlits database /home/k.ruiz/alphafold_data/bfd/bfd_metaclust_clu_complete_id30_c90_final_seq.sorted_opt

However, when I try to edit the run_alphafold.py file following this thread, lines 76 and 77 look different from the ones mentioned there, as my run_alphafold.py looks like:

flags.DEFINE_string('uniclust30_database_path', None, 'Path to the Uniclust30 '
                    'database for use by HHblits.')

Is there any other solution?

Thanks!

[Old-Shatterhand]

Hi @karlaarz

sorry for the late response. For me, this sounds like you didn't install the datasets properly. Have you checked if there are files in /home/k.ruiz/alphafold_data/bfd/ that have the prefix bfd_metaclust_clu_complete_id30_c90_final_seq.sorted_opt and varying extensions?

If this does not help, you can try to reinstall the databases.

Best, Roman

[addsg]

Hi @karlaarz
I have met the same problem as you. For me, you can add -c reduced_dbs in you command

[karlaarz]

Hi @addsg thanks for your comment! :)

[apal6]

Hi,

I have the same error and still not able to fix it. Would you mind helping me?

File "/scratch/groups/alphafold/alphafold/data/tools/hhblits.py", line 83, in __init__ raise ValueError(f'Could not find HHBlits database {database_path}') ValueError: Could not find HHBlits database /scratch/groups/uniref30/uniref30.fasta

Thank you in advance.

[addsg]

hi, if you download reduced_dbs instead of bfd database, you can try to add -c reduced_dbs in you command. If conditions permit， I suggest you to download bfd because it will provide lots of convenient in the following steps.