BUG in RELION 5: Denoise fails with an assert command

[Amy1809]

I am following the Relion 5 pipeline starting from the very beginning. When I proceed to the frist step (training setp) in denoising, Relion5 gives me an error saying that the it could not find the training model in my denoise job output. I have cryoCARE installed, and I have set 'Generate tomograms for denoising' to Yes in both motion correction and tomogram reconstruction stages, so I don't know why this happens.

Environment:

• OS: [linux-64]
• RELION version [RELION-5.0-beta-3-commit-7d79f3]

Job options:

• Type of job: [Denoise tomograms]
• Full command
  which relion_python_tomo_denoise cryoCARE:train --tomogram-star-file Tomograms/job038/tomograms.star --output-directory Denoise/job039/ --gpu 0 --training-tomograms Position_1:Position_1_2:Position_2_2:Position_3_3:Position_6 --number-training-subvolumes 1200 --subvolume-sidelength 72 --pipeline_control Denoise/job039/

Error message:

/bin/sh: 1: cryoCARE_train.py: Permission denied
╭───────────────────── Traceback (most recent call last) ──────────────────────╮
│ in cryoCARE_train:2                                                          │
│ ╭───────────────────────────────── locals ─────────────────────────────────╮ │
│ │                        gpu = [0]                                         │ │
│ │ number_training_subvolumes = 1200                                        │ │
│ │           output_directory = PosixPath('Denoise/job039')                 │ │
│ │           pipeline_control = PosixPath('Denoise/job039')                 │ │
│ │       subvolume_sidelength = 72                                          │ │
│ │         tomogram_star_file = PosixPath('Tomograms/job038/tomograms.star… │ │
│ │         training_tomograms = 'Position_1:Position_1_2:Position_2_2:Posi… │ │
│ ╰──────────────────────────────────────────────────────────────────────────╯ │
│                                                                              │
│ /home/anaconda3/envs/relion-5.0/lib/python3.10/site-packages/tomogra │
│ phy_python_programs/_utils/relion.py:75 in pipeline_job                      │
│                                                                              │
│   72 │   │   │   job_directory.mkdir(parents=True, exist_ok=True)            │
│   73 │   │   try:                                                            │
│   74 │   │   │   pipeline_directory = kwargs.pop(PIPELINE_CONTROL_KEYWORD_AR │
│ ❱ 75 │   │   │   func(*args, **kwargs)                                       │
│   76 │   │   │   if job_directory is not None and pipeline_directory is not  │
│   77 │   │   │   │   write_job_success_file(job_directory)                   │
│   78 │   │   except BaseException:                                           │
│                                                                              │
│ ╭───────────────────────────────── locals ─────────────────────────────────╮ │
│ │               args = ()                                                  │ │
│ │               func = <function cryoCARE_train at 0x7ea90d26c8b0>         │ │
│ │      job_directory = PosixPath('Denoise/job039')                         │ │
│ │             kwargs = {                                                   │ │
│ │                      │   'tomogram_star_file':                           │ │
│ │                      PosixPath('Tomograms/job038/tomograms.star'),       │ │
│ │                      │   'output_directory':                             │ │
│ │                      PosixPath('Denoise/job039'),                        │ │
│ │                      │   'training_tomograms':                           │ │
│ │                      'Position_1:Position_1_2:Position_2_2:Position_3_3… │ │
│ │                      │   'number_training_subvolumes': 1200,             │ │
│ │                      │   'subvolume_sidelength': 72,                     │ │
│ │                      │   'gpu': [0]                                      │ │
│ │                      }                                                   │ │
│ │ pipeline_directory = PosixPath('Denoise/job039')                         │ │
│ ╰──────────────────────────────────────────────────────────────────────────╯ │
│                                                                              │
│ /home/anaconda3/envs/relion-5.0/lib/python3.10/site-packages/tomogra │
│ phy_python_programs/denoise/cryoCARE/train.py:147 in cryoCARE_train          │
│                                                                              │
│   144 │   │   console.log(f'Denoising model can be found in {output_director │
│   145 │   else:                                                              │
│   146 │   │   e = f'Could not find denoise model ({MODEL_NAME}.tar.gz) in {o │
│ ❱ 147 │   │   raise RuntimeError(e)                                          │
│   148 │                                                                      │
│   149 │   console.save_html(str(output_directory / 'log.html'), clear=False) │
│   150 │   console.save_text(str(output_directory / 'log.txt'), clear=False)  │
│                                                                              │
│ ╭───────────────────────────────── locals ─────────────────────────────────╮ │
│ │                        cmd = 'cryoCARE_train.py --conf                   │ │
│ │                              Denoise/job039/external/training/train_con… │ │
│ │                          e = 'Could not find denoise model               │ │
│ │                              (denoising_model.tar.gz) in Denoise/job039. │ │
│ │                              Trainin'+20                                 │ │
│ │                 even_tomos = [                                           │ │
│ │                              │                                           │ │
│ │                              'Tomograms/job038/tomograms/rec_Position_1… │ │
│ │                              │                                           │ │
│ │                              'Tomograms/job038/tomograms/rec_Position_1… │ │
│ │                              │                                           │ │
│ │                              'Tomograms/job038/tomograms/rec_Position_2… │ │
│ │                              │                                           │ │
│ │                              'Tomograms/job038/tomograms/rec_Position_3… │ │
│ │                              │                                           │ │
│ │                              'Tomograms/job038/tomograms/rec_Position_6… │ │
│ │                              ]                                           │ │
│ │                global_star = │   rlnTomoName  ...                        │ │
│ │                              rlnTomogramHProjectionalf2                  │ │
│ │                              0    Position_1  ...                        │ │
│ │                              Tomograms/job038/projections/rec_Position_… │ │
│ │                              1  Position_1_2  ...                        │ │
│ │                              Tomograms/job038/projections/rec_Position_… │ │
│ │                              2  Position_2_2  ...                        │ │
│ │                              Tomograms/job038/projections/rec_Position_… │ │
│ │                              3  Position_3_3  ...                        │ │
│ │                              Tomograms/job038/projections/rec_Position_… │ │
│ │                              4    Position_6  ...                        │ │
│ │                              Tomograms/job038/projections/rec_Position_… │ │
│ │                                                                          │ │
│ │                              [5 rows x 17 columns]                       │ │
│ │                        gpu = [0]                                         │ │
│ │ number_training_subvolumes = 1200                                        │ │
│ │                  odd_tomos = [                                           │ │
│ │                              │                                           │ │
│ │                              'Tomograms/job038/tomograms/rec_Position_1… │ │
│ │                              │                                           │ │
│ │                              'Tomograms/job038/tomograms/rec_Position_1… │ │
│ │                              │                                           │ │
│ │                              'Tomograms/job038/tomograms/rec_Position_2… │ │
│ │                              │                                           │ │
│ │                              'Tomograms/job038/tomograms/rec_Position_3… │ │
│ │                              │                                           │ │
│ │                              'Tomograms/job038/tomograms/rec_Position_6… │ │
│ │                              ]                                           │ │
│ │           output_directory = PosixPath('Denoise/job039')                 │ │
│ │       subvolume_sidelength = 72                                          │ │
│ │            tilt_series_dir = PosixPath('Denoise/job039/tilt_series')     │ │
│ │               tomogram_dir = PosixPath('Denoise/job039/tomograms')       │ │
│ │         tomogram_star_file = PosixPath('Tomograms/job038/tomograms.star… │ │
│ │          train_config_json = {                                           │ │
│ │                              │   'train_data':                           │ │
│ │                              'Denoise/job039/external/training',         │ │
│ │                              │   'epochs': 100,                          │ │
│ │                              │   'steps_per_epoch': 200,                 │ │
│ │                              │   'batch_size': 16,                       │ │
│ │                              │   'unet_kern_size': 3,                    │ │
│ │                              │   'unet_n_depth': 3,                      │ │
│ │                              │   'unet_n_first': 16,                     │ │
│ │                              │   'learning_rate': 0.0004,                │ │
│ │                              │   'model_name': 'denoising_model',        │ │
│ │                              │   'path': 'Denoise/job039',               │ │
│ │                              │   ... +2                                  │ │
│ │                              }                                           │ │
│ │     train_data_config_json = {                                           │ │
│ │                              │   'even': [                               │ │
│ │                              │   │                                       │ │
│ │                              'Tomograms/job038/tomograms/rec_Position_1… │ │
│ │                              │   │                                       │ │
│ │                              'Tomograms/job038/tomograms/rec_Position_1… │ │
│ │                              │   │                                       │ │
│ │                              'Tomograms/job038/tomograms/rec_Position_2… │ │
│ │                              │   │                                       │ │
│ │                              'Tomograms/job038/tomograms/rec_Position_3… │ │
│ │                              │   │                                       │ │
│ │                              'Tomograms/job038/tomograms/rec_Position_6… │ │
│ │                              │   ],                                      │ │
│ │                              │   'odd': [                                │ │
│ │                              │   │                                       │ │
│ │                              'Tomograms/job038/tomograms/rec_Position_1… │ │
│ │                              │   │                                       │ │
│ │                              'Tomograms/job038/tomograms/rec_Position_1… │ │
│ │                              │   │                                       │ │
│ │                              'Tomograms/job038/tomograms/rec_Position_2… │ │
│ │                              │   │                                       │ │
│ │                              'Tomograms/job038/tomograms/rec_Position_3… │ │
│ │                              │   │                                       │ │
│ │                              'Tomograms/job038/tomograms/rec_Position_6… │ │
│ │                              │   ],                                      │ │
│ │                              │   'patch_shape': [72, 72, 72],            │ │
│ │                              │   'num_slices': 1200,                     │ │
│ │                              │   'split': 0.9,                           │ │
│ │                              │   'tilt_axis': 'Y',                       │ │
│ │                              │   'n_normalization_samples': 120,         │ │
│ │                              │   'path':                                 │ │
│ │                              'Denoise/job039/external/training',         │ │
│ │                              │   'overwrite': 'True'                     │ │
│ │                              }                                           │ │
│ │               training_dir = PosixPath('Denoise/job039/external/trainin… │ │
│ │         training_tomograms = [                                           │ │
│ │                              │   'Position_1',                           │ │
│ │                              │   'Position_1_2',                         │ │
│ │                              │   'Position_2_2',                         │ │
│ │                              │   'Position_3_3',                         │ │
│ │                              │   'Position_6'                            │ │
│ │                              ]                                           │ │
│ │    training_tomograms_star = │   rlnTomoName  ...                        │ │
│ │                              rlnTomogramHProjectionalf2                  │ │
│ │                              0    Position_1  ...                        │ │
│ │                              Tomograms/job038/projections/rec_Position_… │ │
│ │                              1  Position_1_2  ...                        │ │
│ │                              Tomograms/job038/projections/rec_Position_… │ │
│ │                              2  Position_2_2  ...                        │ │
│ │                              Tomograms/job038/projections/rec_Position_… │ │
│ │                              3  Position_3_3  ...                        │ │
│ │                              Tomograms/job038/projections/rec_Position_… │ │
│ │                              4    Position_6  ...                        │ │
│ │                              Tomograms/job038/projections/rec_Position_… │ │
│ │                                                                          │ │
│ │                              [5 rows x 17 columns]                       │ │
│ ╰──────────────────────────────────────────────────────────────────────────╯ │
╰──────────────────────────────────────────────────────────────────────────────╯
RuntimeError: Could not find denoise model (denoising_model.tar.gz) in 
Denoise/job039. Training has likely failed.

And here is the .out file

 Beginning to train denoise model.                         train.py:97
/bin/sh: 1: cryoCARE_extract_train_data.py: Permission denied

Any suggestions or advice will be helpful.