` HHSearch failed` with no `stdout` or `stderr` output

[GentleInfant]

Running a job is failing with

I0214 13:38:24.695471 140207840163648 utils.py:36] Started HHsearch query
I0214 13:38:24.777242 140207840163648 utils.py:40] Finished HHsearch query in 0.082 seconds
Traceback (most recent call last):
  File "/app/alphafold/run_alphafold.py", line 468, in <module>
    app.run(main)
  File "/opt/conda/lib/python3.8/site-packages/absl/app.py", line 312, in run
    _run_main(main, args)
  File "/opt/conda/lib/python3.8/site-packages/absl/app.py", line 258, in _run_main
    sys.exit(main(argv))
  File "/app/alphafold/run_alphafold.py", line 443, in main
    predict_structure(
  File "/app/alphafold/run_alphafold.py", line 196, in predict_structure
    feature_dict = data_pipeline.process(
  File "/app/alphafold/alphafold/data/pipeline.py", line 188, in process
    pdb_templates_result = self.template_searcher.query(uniref90_msa_as_a3m)
  File "/app/alphafold/alphafold/data/tools/hhsearch.py", line 94, in query
    raise RuntimeError(
RuntimeError: HHSearch failed:
stdout:


stderr:

I'm using the singularity image but the developer on git says it's an issue with alphafold he can't fix. I'm pretty sure I tried adding the -DHAVEX_AVX2=1 but it didn't help. (feel free to suggest I try again if you think that's what it is - I've tried a lot of things!). I don't believe it's ever worked on this machine (I'm not the only one trying to get it to work).

I'm running the image as a slurm job with 64G memory (I saw another ticket that mentioned they hadn't assigned enough memory but 64G was the amount of memory on a bare metal install on a different machine that has alphafold working).

[gioodm]

Hi! I'm running into a similar problem running ColabFold with singularity (https://github.com/sokrypton/ColabFold/wiki/Running-ColabFold-in-Docker).. it predicts some of the structures in the fasta file, while others run into this issue.

Did you manage to find a solution? how did you install it using the -DHAVEX_AVX2=1 flag?

[GentleInfant]

Nope, no solutions have been forthcoming :/

The way I tried to do it was to edit the Singularity.def file and according to the instructions here add it to the cmake call, for me that's line 48: && cmake -DCMAKE_INSTALL_PREFIX=/opt/hhsuite .. \ -> && cmake -DHAVEX_AVX2=1 -DCMAKE_INSTALL_PREFIX=/opt/hhsuite .. \. Then rebuild the image.

[wtroy2]

I am still having this problem. Has anyone found a solution?

Ive used it in the past and not has this problem but on fresh installs I get it

[gioodm]

Not sure if this is a viable solutions for you, but my workaround was to just not use HHsearch by removing the —template option

[JuergenUniVie]

I hope a solution can be found for this....