When running with docker, ordinary users may encounter permission problems when creating the output directory. You need to manually mkdir -p $HOME/alphafold3/input $HOME/alphafold3/output chmod -R 777 $HOME/alphafold3/output

[hezhiqiang8909]

Found local devices: [CudaDevice(id=0)]
Building model from scratch...
Processing 1 fold inputs.
Processing fold input 2PV7
Checking we can load the model parameters...
Running data pipeline...
Processing chain A
Processing chain A took 1415.38 seconds
Processing chain B
Processing chain B took 0.07 seconds
Output directory: /root/af_output/2pv7
Writing model input JSON to /root/af_output/2pv7
Traceback (most recent call last):
  File "/app/alphafold/run_alphafold.py", line 706, in <module>
    app.run(main)
  File "/alphafold3_venv/lib/python3.11/site-packages/absl/app.py", line 308, in run
    _run_main(main, args)
  File "/alphafold3_venv/lib/python3.11/site-packages/absl/app.py", line 254, in _run_main
    sys.exit(main(argv))
             ^^^^^^^^^^
  File "/app/alphafold/run_alphafold.py", line 691, in main
    process_fold_input(
  File "/app/alphafold/run_alphafold.py", line 552, in process_fold_input
    write_fold_input_json(fold_input, output_dir)
  File "/app/alphafold/run_alphafold.py", line 416, in write_fold_input_json
    os.makedirs(output_dir, exist_ok=True)
  File "<frozen os>", line 225, in makedirs
PermissionError: [Errno 13] Permission denied: '/root/af_output/2pv7'

[jsspencer]

I can't reproduce this with docker 27.3.1 -- if the specified output directory does not exist, then it is created with appropriate permissions and ownership.