FileNotFoundError

[marctormo]

Hello,

We are encountering an error when attempting to run OpenFold on our cluster to predict the structure of a dimer. The job fails with the following FileNotFoundError:

Traceback (most recent call last):
  File "/aplic/noarch/software/openfold/1-Miniconda3-23.9.0-0/run_pretrained_openfold.py", line 493, in <module>
    main(args)
  File "/aplic/noarch/software/openfold/1-Miniconda3-23.9.0-0/run_pretrained_openfold.py", line 283, in main
    for model, output_directory in model_generator:
  File "/data/samanthafs/homes/aplic/noarch/software/openfold/1-Miniconda3-23.9.0-0/openfold/utils/script_utils.py", line 66, in load_models_from_command_line
    import_jax_weights_(
  File "/data/samanthafs/homes/aplic/noarch/software/openfold/1-Miniconda3-23.9.0-0/openfold/utils/import_weights.py", line 650, in import_jax_weights_
    data = np.load(npz_path)
  File "/homes/aplic/noarch/software/Miniconda3/23.9.0-0/envs/openfold_env/lib/python3.10/site-packages/numpy/lib/npyio.py", line 427, in load
    fid = stack.enter_context(open(os_fspath(file), "rb"))
FileNotFoundError: [Errno 2] No such file or directory: 'openfold/resources/params/params_model_1_ptm_multimer_v3.npz'

We have downloaded the AlphaFold2 parameter files using download_alphafold_params.sh and linked them to the openfold/resources/params/ directory. The contents of this directory are:

[manager@marvin2 aplic_db]$ ls -alh /aplic/noarch/software/openfold/1-Miniconda3-23.9.0-0/openfold/resources/params/
total 5.3G
drwxrwxr-x 2 manager manager 4.0K Mar 19 11:10 .
drwxrwxr-x 3 manager manager 4.0K Mar 19 11:08 ..
-rw-rw-r-- 1 manager manager  19K Mar 24  2020 LICENSE
-rw-rw-r-- 1 manager manager 356M Nov 22  2022 params_model_1_multimer_v3.npz
-rw-rw-r-- 1 manager manager 356M Jul 19  2021 params_model_1.npz
-rw-rw-r-- 1 manager manager 356M Jul 19  2021 params_model_1_ptm.npz
-rw-rw-r-- 1 manager manager 356M Nov 22  2022 params_model_2_multimer_v3.npz
-rw-rw-r-- 1 manager manager 356M Jul 19  2021 params_model_2.npz
-rw-rw-r-- 1 manager manager 356M Jul 19  2021 params_model_2_ptm.npz
-rw-rw-r-- 1 manager manager 356M Nov 22  2022 params_model_3_multimer_v3.npz
-rw-rw-r-- 1 manager manager 355M Jul 19  2021 params_model_3.npz
-rw-rw-r-- 1 manager manager 355M Jul 19  2021 params_model_3_ptm.npz
-rw-rw-r-- 1 manager manager 356M Nov 22  2022 params_model_4_multimer_v3.npz
-rw-rw-r-- 1 manager manager 355M Jul 19  2021 params_model_4.npz
-rw-rw-r-- 1 manager manager 355M Jul 19  2021 params_model_4_ptm.npz
-rw-rw-r-- 1 manager manager 356M Nov 22  2022 params_model_5_multimer_v3.npz
-rw-rw-r-- 1 manager manager 355M Jul 19  2021 params_model_5.npz
-rw-rw-r-- 1 manager manager 355M Jul 19  2021 params_model_5_ptm.npz

These files appear to match those expected from the AlphaFold2 parameter download, as referenced here: https://sbgrid.org/wiki/examples/alphafold2.md.

However, the error message indicates that params_model_1_ptm_multimer_v3.npz is missing, even though we have params_model_1_multimer_v3.npz and params_model_1_ptm.npz.

Could you please advise on why run_pretrained_openfold.py is requesting params_model_1_ptm_multimer_v3.npz? Is there a configuration or parameter setting that might be causing this discrepancy?

Thank you for your assistance. Marc

[jnwei]

Hi,

There is a small typo with the multimer model specification: Try specifying model_1_multimer_v3instead of params_model_1_ptm_multimer_v3 (no ptm for multimer models).