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

usegalaxy.eu support
1

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

2

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
3

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?

4

Hi @Ulises_Mancini

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

5

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
6

Hi,

we have update Alphafold2 on the EU server to the latest version and also the underlying database.

Please try to new version 2.3.1 (Galaxy | Europe)

Happy research!
Bjoern

1 Like
7

Hi,
I’m getting the exact same error. Any way to solve this?
Thank you

1 Like
8

Welcome, @Julian_Martinez_Maye

Current Alphafold availability is…

Did the error come up at UseGalaxy.eu? If you haven’t tried there yet, please do and let us know how that goes :slight_smile:

9

Thanks for the quick answer. Yes, the problem seems to come up in the UseGalaxy.eu page.
Best,
Julián

10

Ok, thanks for clarifying.

Please submit a bug report from that red error dataset to report the problem to the EU administrators. You can include a link to this topic in the comments for context.

cc @bjoern.gruening @gallardoalba

11

As of today, this problem should be solved on usegalaxy.eu, at least for the latest version of the tool (2.3.1+galaxy2). We are still running some more test cases for the latest version as well as for the older ones to make sure that this error is not arising in older versions of the tool.

1 Like