Running the Openfold Inference for PDB 6KWC

[TonnarCastellano]

I am confused as to why its asking for a separate pdb's cif file

(openfold_env) MATTERHORN ~/workdir/openfold/bin $ ./first_test/predict_test_prealigned.sh 
[2025-06-23 15:57:36,689] [INFO] [real_accelerator.py:203:get_accelerator] Setting ds_accelerator to cuda (auto detect)
Warning: The default cache directory for DeepSpeed Triton autotune, ~/.triton/autotune, appears to be on an NFS system. While this is generally acceptable, if you experience slowdowns or hanging when DeepSpeed exits, it is recommended to set the TRITON_CACHE_DIR environment variable to a non-NFS path.
 [WARNING]  async_io requires the dev libaio .so object and headers but these were not found.
 [WARNING]  async_io: please install the libaio-devel package with yum
 [WARNING]  If libaio is already installed (perhaps from source), try setting the CFLAGS and LDFLAGS environment variables to where it can be found.
~/anaconda3/envs/openfold_env/lib/python3.10/site-packages/deepspeed/runtime/zero/linear.py:49: FutureWarning: `torch.cuda.amp.custom_fwd(args...)` is deprecated. Please use `torch.amp.custom_fwd(args..., device_type='cuda')` instead.
  def forward(ctx, input, weight, bias=None):
~/anaconda3/envs/openfold_env/lib/python3.10/site-packages/deepspeed/runtime/zero/linear.py:67: FutureWarning: `torch.cuda.amp.custom_bwd(args...)` is deprecated. Please use `torch.amp.custom_bwd(args..., device_type='cuda')` instead.
  def backward(ctx, grad_output):
INFO:~/anaconda3/envs/openfold_env/lib/python3.10/site-packages/openfold-2.2.0-py3.10-linux-x86_64.egg/openfold/utils/script_utils.py:Successfully loaded JAX parameters at openfold/resources/params/params_model_1_ptm.npz...
INFO:~/workdir/openfold/bin/./openfold/run_pretrained_openfold.py:Using precomputed alignments for 6KWC_1 at ./first_test/out/alignments...
Traceback (most recent call last):
  File "~/workdir/openfold/bin/./openfold/run_pretrained_openfold.py", line 500, in <module>
    main(args)
  File "~/workdir/openfold/bin/./openfold/run_pretrained_openfold.py", line 300, in main
    feature_dict = generate_feature_dict(
  File "~/workdir/openfold/bin/./openfold/run_pretrained_openfold.py", line 152, in generate_feature_dict
    feature_dict = data_processor.process_fasta(
  File "~/anaconda3/envs/openfold_env/lib/python3.10/site-packages/openfold-2.2.0-py3.10-linux-x86_64.egg/openfold/data/data_pipeline.py", line 889, in process_fasta
    template_features = make_template_features(
  File "~/anaconda3/envs/openfold_env/lib/python3.10/site-packages/openfold-2.2.0-py3.10-linux-x86_64.egg/openfold/data/data_pipeline.py", line 57, in make_template_features
    templates_result = template_featurizer.get_templates(
  File "~/anaconda3/envs/openfold_env/lib/python3.10/site-packages/openfold-2.2.0-py3.10-linux-x86_64.egg/openfold/data/templates.py", line 1158, in get_templates
    result = _process_single_hit(
  File "~/anaconda3/envs/openfold_env/lib/python3.10/site-packages/openfold-2.2.0-py3.10-linux-x86_64.egg/openfold/data/templates.py", line 866, in _process_single_hit
    cif_string = _read_file(cif_path)
  File "~/anaconda3/envs/openfold_env/lib/python3.10/site-packages/openfold-2.2.0-py3.10-linux-x86_64.egg/openfold/data/templates.py", line 820, in _read_file
    with open(path, 'r') as f:
FileNotFoundError: [Errno 2] No such file or directory: './first_test/input_cifs/2dfb.cif'

[abhinavb22]

I think it is looking for PDB templates, and you may have set the PDB path to ./first_test/input_cifs ?