` HHSearch failed` with no `stdout` or `stderr` output
Author: GentleInfantCreated Feb 15, 2024Updated May 21, 2026
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).
Source: google-deepmind/alphafold