Repository navigation
Error: Could not find HHBlits database #191
Description
Hi, we are trying to use your package and are encountering an error when trying out an example. On running the command:
create_individual_features.py \
--fasta_paths=baits.fasta,example_1_sequences_shorter.fasta \
--data_dir=/home/balakumaran.c/alphafold_database/ \
--mgnify_database_path=/home/balakumaran.c/alphafold_database/mgnify/mgy_clusters_2018_12.fa \
--output_dir=/home/balakumaran.c/alphapulldown/output/ \
--save_msa_files=False \
--use_precomputed_msas=False \
--max_template_date="2022-03-30" \
--skip_existing=True \
We are encountering the following error: ValueError: Could not find HHBlits database /home/balakumaran.c/alphafold_database/uniref30/UniRef30_2021_03. The full error file is attached below.
Our database follows the format for the AlphaFold 2.3.0 database:
alphafold_database
|-- bfd
|-- mgnify
|-- params
|-- pdb70
|-- pdb_mmcif
| `-- mmcif_files
|-- pdb_seqres
|-- small_bfd
|-- uniclust30
| `-- uniclust30_2018_08
|-- uniprot
|-- uniref30
| `-- UniRef30_2021_03
`-- uniref90
and so I am uncertain about what the error could be. Could you please help me with the same?
The code is being run on a cluster on a GPU node with Red Hat Enterprise (Kernel Linux 3.10.0-327.el7.x86_64). The GPU is a Tesla K40m.
Thanks,
Abhirath.
Activity
dingquanyu commentedon Oct 25, 2023
Hi
Thanks for your interest in our package. There should be 7 files under the uniclust30 subfolder. Could you please double check the requirements by AlphaFold? Since this is irrelevant to the package itself, it will be moved to the discussion section.