Comments (3)
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.
Lines 76 to 78 in b64fb84
The problem has been solved. The error occurs with incorrect database structure, so modifying codes to adapt to database structure works.
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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.
Lines 76 to 78 in b64fb84
from alphafold.
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!
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Related Issues (19)
- Wrong order of conda packages? HOT 2
- --preset reduced_dbs not available flag HOT 1
- Setting working directory in install_on_local.sh HOT 1
- Issue in installing the software HOT 1
- database/pdb_mmcif/raw/*/*.cif': No such file or directory HOT 3
- can't find file to patch at input line 5
- ValueError: Could not find CIFs in /data01/xukui/alphafold/pdb_mmcif/mmcif_files HOT 1
- jaxlib.xla_extension.XlaRuntimeError
- FileNotFoundError: [Errno 2] No such file or directory: '../AlphaLink2/alphafold/all_data/pdb_mmcif/mmcif_files/4fxg.cif'
- pip3 install requirement are not compatible
- let pip3 install requirements without versions HOT 1
- Only 1 GPU is used
- download_pdb_mmcif.sh has the rsyncs commented-out, then fails
- stereo_chemical_props.txt is not found HOT 2
- Could not find CIFs HOT 4
- Running output
- Unable to initialize backend 'gpu' HOT 7
- Core dumpled
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