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ValueError: No valid inputs were provided #75

Open merryxiang opened 7 months ago

merryxiang commented 7 months ago

I REALLY NEED YOUR HELP. I REALLY NEED RoseTTAFold-All-Atom. After completing the installation steps, I got an error message during runtime.I tried to change the path to an absolute path in "protein.yaml", but still received this error message. Can anyone tell me some possible solutions?

(RFAA) good@xy-server:/mnt/mydrive/RoseTTAFold-All-Atom$ sudo /home/good/mambaforge/bin/python -m rf2aa.run_inference --config-name protein Using the cif atom ordering for TRP. Error executing job with overrides: [] Traceback (most recent call last): File "/mnt/mydrive/RoseTTAFold-All-Atom/rf2aa/run_inference.py", line 206, in main runner.infer() File "/mnt/mydrive/RoseTTAFold-All-Atom/rf2aa/run_inference.py", line 153, in infer self.parse_inference_config() File "/mnt/mydrive/RoseTTAFold-All-Atom/rf2aa/run_inference.py", line 93, in parse_inference_config raw_data = merge_all(protein_inputs, na_inputs, sm_inputs, residues_to_atomize, deterministic=self.deterministic) File "/mnt/mydrive/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

Alain-chavanieu commented 7 months ago

Hello I have the same/close problem. Did you find th solution ? TY (RFAA) bash-4.4$ python -m rf2aa.run_inference --config-name protein Using the cif atom ordering for TRP. Error executing job with overrides: [] Traceback (most recent call last): File "/disk/IA/rfaa/mambaforge/envs/RFAA/lib/python3.10/runpy.py", line 196, in _run_module_as_main return _run_code(code, main_globals, None, File "/disk/IA/rfaa/mambaforge/envs/RFAA/lib/python3.10/runpy.py", line 86, in _run_code exec(code, run_globals) File "/disk/IA/rfaa/RoseTTAFold-All-Atom/rf2aa/run_inference.py", line 209, in main() File "/disk/IA/rfaa/mambaforge/envs/RFAA/lib/python3.10/site-packages/hydra/main.py", line 94, in decorated_main _run_hydra( File "/disk/IA/rfaa/mambaforge/envs/RFAA/lib/python3.10/site-packages/hydra/_internal/utils.py", line 394, in _run_hydra _run_app( File "/disk/IA/rfaa/mambaforge/envs/RFAA/lib/python3.10/site-packages/hydra/_internal/utils.py", line 457, in _run_app run_and_report( File "/disk/IA/rfaa/mambaforge/envs/RFAA/lib/python3.10/site-packages/hydra/_internal/utils.py", line 223, in run_and_report raise ex File "/disk/IA/rfaa/mambaforge/envs/RFAA/lib/python3.10/site-packages/hydra/_internal/utils.py", line 220, in run_and_report return func() File "/disk/IA/rfaa/mambaforge/envs/RFAA/lib/python3.10/site-packages/hydra/_internal/utils.py", line 458, in lambda: hydra.run( File "/disk/IA/rfaa/mambaforge/envs/RFAA/lib/python3.10/site-packages/hydra/internal/hydra.py", line 132, in run = ret.return_value File "/disk/IA/rfaa/mambaforge/envs/RFAA/lib/python3.10/site-packages/hydra/core/utils.py", line 260, in return_value raise self._return_value File "/disk/IA/rfaa/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 "/disk/IA/rfaa/RoseTTAFold-All-Atom/rf2aa/run_inference.py", line 206, in main runner.infer() File "/disk/IA/rfaa/RoseTTAFold-All-Atom/rf2aa/run_inference.py", line 153, in infer self.parse_inference_config() File "/disk/IA/rfaa/RoseTTAFold-All-Atom/rf2aa/run_inference.py", line 93, in parse_inference_config raw_data = merge_all(protein_inputs, na_inputs, sm_inputs, residues_to_atomize, deterministic=self.deterministic) File "/disk/IA/rfaa/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

epr7142 commented 6 months ago

I encountered the same issue when trying to use this title; it appears that it has to do with the way hydra is being configured in run_inference.py

For the following line 214: @hydra.main(version_base=None, config_path='config/inference')

Hydra will always try to run the .yaml stored inside of /rf2aa/config/inference. But the default configs that it ships with use relative paths which are not accurate, and its trying to load files in locations that don't exist.

Try modifying the paths to hardcoded full paths to your input fasta files.

job_name: "7u7w_protein" protein_inputs: A: fasta_file: /your/install/location/RoseTTAFold-All-Atom/examples/protein/7u7w_A.fasta