AlphaFold2 Error - Could not find HHsearch database /data/pdb70/pdb70

I tried running a FASTA sequence on AlphaFold2 and it showed me this error:

E0902 16:02:23.065268 22797118093120 hhsearch.py:56] Could not find HHsearch database /data/pdb70/pdb70
Traceback (most recent call last):
File “/app/alphafold/run_alphafold.py”, line 445, in
app.run(main)
File “/opt/conda/lib/python3.7/site-packages/absl/app.py”, line 312, in run
_run_main(main, args)
File “/opt/conda/lib/python3.7/site-packages/absl/app.py”, line 258, in _run_main
sys.exit(main(argv))
File “/app/alphafold/run_alphafold.py”, line 353, in main
databases=[FLAGS.pdb70_database_path])
File “/app/alphafold/alphafold/data/tools/hhsearch.py”, line 57, in init
raise ValueError(f’Could not find HHsearch database {database_path}')
ValueError: Could not find HHsearch database /data/pdb70/pdb70

This is the sequence I tried to run:

33
MPAPAPLLIILRRRIRKQAHAHSKGGGGSMR
TSYLLLFTLCLLLSEMASGGNFLTGLGHRSD
HYNCVSSGGQCLYSACPIFTKIQGTCYRGKA
KCCKEAAAKFPGVGFPGVGFPGVGKPKPKPL
GIYVYVRRKKSLSGCYWCLKKFSWWDPGFFI
KKGLPIRASRLVFKKKRRCAVLLYKKVIFSN
ISNWVYKKRLGNGTFYKKLQVQFAVFKKNSP
YIPYLLKKSFQAWLTNQPYKKCAQLRYLVFK
KFIAVIPAANFKKYAIALVAELLKKMNITGY
TDAYKKLLLAITSNIVKKLIKGNFLEYVKKS
LSGCYWCLIKKIYVYVRRCVLKKFAVFGILP
CVKKDSQFTLIKPYKKPLGLWARVLAEALII
GFSWWDPGFFIIAAYSFQAWLTNQPYASFMV
AAYFIAVIPAANFPGVLLTQAAYSVIFSNIS
NWVYAAYTVYFLPNSIITNVFFIAAYMVSLI
YLASFLFKSSSTAAAYRLISTALKARALSLD
SAAYRRRLANSLRLATVIYGKAAYEIRWSFT
LNCSASDSEAAYEYVRILMRKLLLQITRHHH
HHH

Please let me know if there is an error with my input or within the tool
Thank you

Hi @sunag_parasu,
the problem is caused by the tool itself. I suggest you to try to run your analysis in the Australian Galaxy server; you can apply in the following link: AlphaFold 2.0.

Regards

1 Like

The problem is that if we don’t have an email from an Australian institution, we can’t apply to that server. Any other option?

Hi @Ulises_Mancini

The AU server is the only public Galaxy server option that I know of.

Hi Jenn
To access the Alphafold 2.0 tool on the Australian server, you need to register with an email from an Australian institution.
Search in google “Galaxy Australia AlphaFold 2.0 Access Request”
Best!

1 Like