jmProteins2024
commented
5 months ago We figured this out. There were some permission issues on the folders where we installed it on a cluster.
Closed jmProteins2024 closed 5 months ago
jmProteins2024
commented
5 months ago We figured this out. There were some permission issues on the folders where we installed it on a cluster.
Hi,
We are trying to run the protein small molecule example
/mambaforge/envs/RFAA/bin/python -m rf2aa.run_inference --config-name protein_sm
and are getting the following error:
Using the cif atom ordering for TRP. Error executing job with overrides: [] Traceback (most recent call last): File "/p/work1/projects/RXbioinfo/SOFTWARE/mambaforge/envs/RFAA/lib/python3.10/runpy.py", line 196, in _run_module_as_main return _run_code(code, main_globals, None, File "/p/work1/projects/RXbioinfo/SOFTWARE/mambaforge/envs/RFAA/lib/python3.10/runpy.py", line 86, in _run_code exec(code, run_globals) File "/p/work1/projects/RXbioinfo/SOFTWARE/RoseTTAFold-All-Atom/rf2aa/run_inference.py", line 211, in
main()
File "/p/work1/projects/RXbioinfo/SOFTWARE/mambaforge/envs/RFAA/lib/python3.10/site-packages/hydra/main.py", line 94, in decorated_main
_run_hydra(
File "/p/work1/projects/RXbioinfo/SOFTWARE/mambaforge/envs/RFAA/lib/python3.10/site-packages/hydra/_internal/utils.py", line 394, in _run_hydra
_run_app(
File "/p/work1/projects/RXbioinfo/SOFTWARE/mambaforge/envs/RFAA/lib/python3.10/site-packages/hydra/_internal/utils.py", line 457, in _run_app
run_and_report(
File "/p/work1/projects/RXbioinfo/SOFTWARE/mambaforge/envs/RFAA/lib/python3.10/site-packages/hydra/_internal/utils.py", line 223, in run_and_report
raise ex
File "/p/work1/projects/RXbioinfo/SOFTWARE/mambaforge/envs/RFAA/lib/python3.10/site-packages/hydra/_internal/utils.py", line 220, in run_and_report
return func()
File "/p/work1/projects/RXbioinfo/SOFTWARE/mambaforge/envs/RFAA/lib/python3.10/site-packages/hydra/_internal/utils.py", line 458, in
lambda: hydra.run(
File "/p/work1/projects/RXbioinfo/SOFTWARE/mambaforge/envs/RFAA/lib/python3.10/site-packages/hydra/internal/hydra.py", line 132, in run
= ret.return_value
File "/p/work1/projects/RXbioinfo/SOFTWARE/mambaforge/envs/RFAA/lib/python3.10/site-packages/hydra/core/utils.py", line 260, in return_value
raise self._return_value
File "/p/work1/projects/RXbioinfo/SOFTWARE/mambaforge/envs/RFAA/lib/python3.10/site-packages/hydra/core/utils.py", line 186, in run_job
ret.return_value = task_function(task_cfg)
File "/p/work1/projects/RXbioinfo/SOFTWARE/RoseTTAFold-All-Atom/rf2aa/run_inference.py", line 208, in main
runner.infer()
File "/p/work1/projects/RXbioinfo/SOFTWARE/RoseTTAFold-All-Atom/rf2aa/run_inference.py", line 154, in infer
self.parse_inference_config()
File "/p/work1/projects/RXbioinfo/SOFTWARE/RoseTTAFold-All-Atom/rf2aa/run_inference.py", line 94, in parse_inference_config
raw_data = merge_all(protein_inputs, na_inputs, sm_inputs, residues_to_atomize, deterministic=self.deterministic)
File "/p/work1/projects/RXbioinfo/SOFTWARE/RoseTTAFold-All-Atom/rf2aa/data/merge_inputs.py", line 174, in merge_all
raise ValueError("No valid inputs were provided")
ValueError: No valid inputs were provided
Do you know what we could be doing wrong. The files are in the correct folders.
Thanks so much for your help,
Josh