Could not find HHBlits database

[Neutrino0532]

Traceback (most recent call last):
  File "run_alphafold.py", line 338, in <module>
    app.run(main)
  File "/home/yulab/anaconda3/envs/af2/lib/python3.8/site-packages/absl/app.py", line 312, in run
    _run_main(main, args)
  File "/home/yulab/anaconda3/envs/af2/lib/python3.8/site-packages/absl/app.py", line 258, in _run_main
    sys.exit(main(argv))
  File "run_alphafold.py", line 273, in main
    data_pipeline = pipeline.DataPipeline(
  File "/home/yulab/software/alphafold/alphafold/data/pipeline.py", line 101, in __init__
    self.hhblits_bfd_uniclust_runner = hhblits.HHBlits(
  File "/home/yulab/software/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 /data1/AF2_data/uniclust30/UniRef30_2020_02

in file run_alphafold.py, change line 77 to the following code will fix it.

    DOWNLOAD_DIR, 'uniclust30', 'UniRef30_2020_02', 'UniRef30_2020_02')

[kuixu]

Have you solved the problem?

It seems that maybe your 'uniclust30' is named 'uniclust30_2018_08', while the code is 'uniclust30_2020_02'. The simplest way is to comment line77, and uncomment line78.

alphafold/run_alphafold.py

Lines 76 to 78 in b64fb84

	uniclust30_database_path = os.path.join(
	DOWNLOAD_DIR, 'uniclust30', 'UniRef30_2020_02')
	#DOWNLOAD_DIR, 'uniclust30', 'uniclust30_2018_08', 'uniclust30_2018_08')

[Neutrino0532]

Have you solved the problem?

It seems that maybe your 'uniclust30' is named 'uniclust30_2018_08', while the code is 'uniclust30_2020_02'. The simplest way is to comment line77, and uncomment line78.

alphafold/run_alphafold.py

Lines 76 to 78 in b64fb84

	uniclust30_database_path = os.path.join(
	DOWNLOAD_DIR, 'uniclust30', 'UniRef30_2020_02')
	#DOWNLOAD_DIR, 'uniclust30', 'uniclust30_2018_08', 'uniclust30_2018_08')

The problem has been solved. The error occurs with incorrect database structure, so modifying codes to adapt to database structure works.

[karlaarz]

Hi! I installed alphafold following the non_docker option using the reduced version of the databases (reduced_dbs mode) and I'm finding a similar 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, lines 76 and 77 look different from the ones mentioned here:

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

Is there any other solution?

Thanks!