Denoise Tomograms with continue Flag

[FlorianBeckOle]

Denoise Tomograms denoises all tomogramms again instead of just denoise the new reconstructed tomograms although the job was continued. Finally the job crashes as the tomogram list already exists (For the denoise trainining it behaves the same)

thanks for helping

Florian

Environment:

• OS: Sles15
• MPI runtime: impi/2018.4
• RELION relion5.0-beta-3
• Memory: 768GB
• GPU: NVIDIA L40S

Dataset: -2 tomograms with 60 tilts

Job options:

• Type of job: Denoise tomogram
• Number of MPI processes:-
• Number of threads: -

which relion_python_tomo_denoise cryoCARE:predict --tomogram-star-file Tomograms/job006/tomograms.star --cryocare-path /fs/pool/pool-bmapps/hpcl8/app/soft/CRYO-CARE/0.2/conda3/envs/cryocare_11/bin/ --output-directory Denoise/job008/ --gpu 0 --model-file Denoise/job007/denoising_model.tar.gz --n-tiles 4 4 4 --pipeline_control Denoise/job008/

Error message: Currently Loaded Modulefiles: 1) intel/18.0.5(default) 2) impi/2018.4(default) 3) RELION/5.0-beta-3NC
/fs/pool/pool-bmapps/hpcl8/app/soft/RELION/5.0-beta-3/conda3/envs/relion-5.0/lib/python3.10/site-packages/starfile/parser.py:177: FutureWarning: The 'delim_whitespace' keyword in pd.read_csv is deprecated and will be removed in a future version. Use sep='\s+' instead df = pd.read_csv( /fs/pool/pool-bmapps/hpcl8/app/soft/RELION/5.0-beta-3/conda3/envs/relion-5.0/lib/python3.10/site-packages/starfile/parser.py:194: FutureWarning: errors='ignore' is deprecated and will raise in a future version. Use to_numeric without passing errors and catch exceptions explicitly instead self.dataframes[key] = df.apply(pd.to_numeric, errors='ignore') ╭───────────────────── Traceback (most recent call last) ──────────────────────╮ │ in cryoCARE_predict:2 │ │ ╭───────────────────────────────── locals ─────────────────────────────────╮ │ │ │ cryocare_path = PosixPath('/fs/pool/pool-bmapps/hpcl8/app/soft/CRY… │ │ │ │ gpu = [0] │ │ │ │ model_file = PosixPath('Denoise/job007/denoising_model.tar.gz') │ │ │ │ n_tiles = (4, 4, 4) │ │ │ │ output_directory = PosixPath('Denoise/job008') │ │ │ │ pipeline_control = PosixPath('Denoise/job008') │ │ │ │ tomogram_name = None │ │ │ │ tomogram_star_file = PosixPath('Tomograms/job006/tomograms.star') │ │ │ ╰──────────────────────────────────────────────────────────────────────────╯ │ │ │ │ /fs/pool/pool-bmapps/hpcl8/app/soft/RELION/5.0-beta-3/conda3/envs/relion-5.0 │ │ /lib/python3.10/site-packages/tomography_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_predict at 0x14be79a45240> │ │ │ │ job_directory = PosixPath('Denoise/job008') │ │ │ │ kwargs = { │ │ │ │ │ 'tomogram_star_file': │ │ │ │ PosixPath('Tomograms/job006/tomograms.star'), │ │ │ │ │ 'output_directory': │ │ │ │ PosixPath('Denoise/job008'), │ │ │ │ │ 'model_file': │ │ │ │ PosixPath('Denoise/job007/denoising_model.tar.gz'), │ │ │ │ │ 'cryocare_path': │ │ │ │ PosixPath('/fs/pool/pool-bmapps/hpcl8/app/soft/CRY… │ │ │ │ │ 'n_tiles': (4, 4, 4), │ │ │ │ │ 'tomogram_name': None, │ │ │ │ │ 'gpu': [0] │ │ │ │ } │ │ │ │ pipeline_directory = PosixPath('Denoise/job008') │ │ │ ╰──────────────────────────────────────────────────────────────────────────╯ │ │ │ │ /fs/pool/pool-bmapps/hpcl8/app/soft/RELION/5.0-beta-3/conda3/envs/relion-5.0 │ │ /lib/python3.10/site-packages/tomography_python_programs/denoise/cryoCARE/pr │ │ edict.py:141 in cryoCARE_predict │ │ │ │ 138 │ │ output_directory=output_directory, │ │ 139 │ │ tomo_name=tomogram_name │ │ 140 │ ) │ │ ❱ 141 │ save_global_star( │ │ 142 │ │ global_star=global_star, │ │ 143 │ │ output_directory=output_directory, │ │ 144 │ ) │ │ │ │ ╭───────────────────────────────── locals ─────────────────────────────────╮ │ │ │ cmd = '/fs/pool/pool-bmapps/hpcl8/app/soft/CRYO-CARE/0.2… │ │ │ │ cryocare_path = '/fs/pool/pool-bmapps/hpcl8/app/soft/CRYO-CARE/0.2… │ │ │ │ even_tomos = [ │ │ │ │ │ │ │ │ │ 'Tomograms/job006/tomograms/rec_Position_1_half1.m… │ │ │ │ │ │ │ │ │ 'Tomograms/job006/tomograms/rec_Position_36_half1.… │ │ │ │ ] │ │ │ │ global_star = rlnTomoName ... │ │ │ │ rlnTomoReconstructedTomogramDenoised │ │ │ │ 0 Position_1 ... │ │ │ │ Denoise/job008/tomograms/rec_Position_1.mrc │ │ │ │ 1 Position_36 ... │ │ │ │ Denoise/job008/tomograms/rec_Position_36.mrc │ │ │ │ │ │ │ │ [2 rows x 17 columns] │ │ │ │ gpu = [0] │ │ │ │ model_file = PosixPath('Denoise/job007/denoising_model.tar.gz') │ │ │ │ n_tiles = (4, 4, 4) │ │ │ │ odd_tomos = [ │ │ │ │ │ │ │ │ │ 'Tomograms/job006/tomograms/rec_Position_1_half2.m… │ │ │ │ │ │ │ │ │ 'Tomograms/job006/tomograms/rec_Position_36_half2.… │ │ │ │ ] │ │ │ │ output_directory = PosixPath('Denoise/job008') │ │ │ │ predict_executable = '/fs/pool/pool-bmapps/hpcl8/app/soft/CRYO-CARE/0.2… │ │ │ │ predict_json = { │ │ │ │ │ 'path': │ │ │ │ 'Denoise/job007/denoising_model.tar.gz', │ │ │ │ │ 'even': [ │ │ │ │ │ │ │ │ │ │ 'Tomograms/job006/tomograms/rec_Position_1_half1.m… │ │ │ │ │ │ │ │ │ │ 'Tomograms/job006/tomograms/rec_Position_36_half1.… │ │ │ │ │ ], │ │ │ │ │ 'odd': [ │ │ │ │ │ │ │ │ │ │ 'Tomograms/job006/tomograms/rec_Position_1_half2.m… │ │ │ │ │ │ │ │ │ │ 'Tomograms/job006/tomograms/rec_Position_36_half2.… │ │ │ │ │ ], │ │ │ │ │ 'n_tiles': [4, 4, 4], │ │ │ │ │ 'output': 'Denoise/job008/tomograms', │ │ │ │ │ 'overwrite': 'True', │ │ │ │ │ 'gpu_id': [0] │ │ │ │ } │ │ │ │ tilt_series_dir = PosixPath('Denoise/job008/tilt_series') │ │ │ │ tomogram_dir = PosixPath('Denoise/job008/tomograms') │ │ │ │ tomogram_name = None │ │ │ │ tomogram_star_file = PosixPath('Tomograms/job006/tomograms.star') │ │ │ │ training_dir = PosixPath('Denoise/job008/external/training') │ │ │ ╰──────────────────────────────────────────────────────────────────────────╯ │ │ │ │ /fs/pool/pool-bmapps/hpcl8/app/soft/RELION/5.0-beta-3/conda3/envs/relion-5.0 │ │ /lib/python3.10/site-packages/tomography_python_programs/denoise/cryoCARE/_u │ │ tils.py:168 in save_global_star │ │ │ │ 165 │ """ │ │ 166 │ Saves global star file (tomograms.star) in output directory. │ │ 167 │ """ │ │ ❱ 168 │ starfile.write({'global': global_star}, f'{output_directory}/tomog │ │ 169 │ │ 170 def rename_predicted_tomograms( │ │ 171 │ even_tomos: List, │ │ │ │ ╭───────────────────────────────── locals ─────────────────────────────────╮ │ │ │ global_star = rlnTomoName ... │ │ │ │ rlnTomoReconstructedTomogramDenoised │ │ │ │ 0 Position_1 ... │ │ │ │ Denoise/job008/tomograms/rec_Position_1.mrc │ │ │ │ 1 Position_36 ... │ │ │ │ Denoise/job008/tomograms/rec_Position_36.mrc │ │ │ │ │ │ │ │ [2 rows x 17 columns] │ │ │ │ output_directory = PosixPath('Denoise/job008') │ │ │ ╰──────────────────────────────────────────────────────────────────────────╯ │ │ │ │ /fs/pool/pool-bmapps/hpcl8/app/soft/RELION/5.0-beta-3/conda3/envs/relion-5.0 │ │ /lib/python3.10/site-packages/starfile/functions.py:41 in write │ │ │ │ 38 │ data can be a single dataframe, a list of dataframes or a dict of d │ │ 39 │ float format defaults to 6 digits after the decimal point │ │ 40 │ """ │ │ ❱ 41 │ StarWriter(data, filename=filename, float_format=float_format, over │ │ 42 │ │ │ na_rep=na_rep, sep=sep, force_loop=force_loop) │ │ 43 │ │ │ │ ╭───────────────────────────────── locals ─────────────────────────────────╮ │ │ │ data = { │ │ │ │ │ 'global': rlnTomoName ... │ │ │ │ rlnTomoReconstructedTomogramDenoised │ │ │ │ 0 Position_1 ... │ │ │ │ Denoise/job008/tomograms/rec_Position_1.mrc │ │ │ │ 1 Position_36 ... │ │ │ │ Denoise/job008/tomograms/rec_Position_36.mrc │ │ │ │ │ │ │ │ [2 rows x 17 columns] │ │ │ │ } │ │ │ │ filename = 'Denoise/job008/tomograms.star' │ │ │ │ float_format = '%.6f' │ │ │ │ force_loop = True │ │ │ │ na_rep = '' │ │ │ │ overwrite = False │ │ │ │ sep = '\t' │ │ │ ╰──────────────────────────────────────────────────────────────────────────╯ │ │ │ │ /fs/pool/pool-bmapps/hpcl8/app/soft/RELION/5.0-beta-3/conda3/envs/relion-5.0 │ │ /lib/python3.10/site-packages/starfile/writer.py:24 in init │ │ │ │ 21 │ │ │ │ filename: PathLike, overwrite: bool = False, float_fo │ │ 22 │ │ │ │ sep: str = '\t', na_rep: str = '', force_loop: bo │ │ 23 │ │ self.overwrite = overwrite │ │ ❱ 24 │ │ self.filename = filename │ │ 25 │ │ self.dataframes = dataframes │ │ 26 │ │ self.float_format = float_format │ │ 27 │ │ self.sep = sep │ │ │ │ ╭───────────────────────────────── locals ─────────────────────────────────╮ │ │ │ dataframes = { │ │ │ │ │ 'global': rlnTomoName ... │ │ │ │ rlnTomoReconstructedTomogramDenoised │ │ │ │ 0 Position_1 ... │ │ │ │ Denoise/job008/tomograms/rec_Position_1.mrc │ │ │ │ 1 Position_36 ... │ │ │ │ Denoise/job008/tomograms/rec_Position_36.mrc │ │ │ │ │ │ │ │ [2 rows x 17 columns] │ │ │ │ } │ │ │ │ filename = 'Denoise/job008/tomograms.star' │ │ │ │ float_format = '%.6f' │ │ │ │ force_loop = True │ │ │ │ na_rep = '' │ │ │ │ overwrite = False │ │ │ │ self = <starfile.writer.StarWriter object at 0x14be79bd6fe0> │ │ │ │ sep = '\t' │ │ │ ╰──────────────────────────────────────────────────────────────────────────╯ │ │ │ │ /fs/pool/pool-bmapps/hpcl8/app/soft/RELION/5.0-beta-3/conda3/envs/relion-5.0 │ │ /lib/python3.10/site-packages/starfile/writer.py:82 in filename │ │ │ │ 79 │ def filename(self, filename: Union[Path, str]): │ │ 80 │ │ self._filename = Path(filename) │ │ 81 │ │ if not self.file_writable: │ │ ❱ 82 │ │ │ raise FileExistsError('to overwrite an existing file set o │ │ 83 │ │ │ 84 │ @property │ │ 85 │ def file_exists(self): │ │ │ │ ╭───────────────────────────── locals ─────────────────────────────╮ │ │ │ filename = 'Denoise/job008/tomograms.star' │ │ │ │ self = <starfile.writer.StarWriter object at 0x14be79bd6fe0> │ │ │ ╰──────────────────────────────────────────────────────────────────╯ │ ╰──────────────────────────────────────────────────────────────────────────────╯ FileExistsError: to overwrite an existing file set overwrite=True srun: error: hpcl9302: task 0: Exited with exit code 2 srun: Terminating StepId=559313.0

[xingxingjiukunkun]

did you know how to download or find the denoise model cryoCARE,if you could tell me i will very thankful

Denoise Tomograms denoises all tomogramms again instead of just denoise the new reconstructed tomograms although the job was continued. Finally the job crashes as the tomogram list already exists (For the denoise trainining it behaves the same)

thanks for helping

Florian

Environment:

• OS: Sles15
• MPI runtime: impi/2018.4
• RELION relion5.0-beta-3
• Memory: 768GB
• GPU: NVIDIA L40S

Dataset: -2 tomograms with 60 tilts

Job options:

• Type of job: Denoise tomogram
• Number of MPI processes:-
• Number of threads: -

which relion_python_tomo_denoise cryoCARE:predict --tomogram-star-file Tomograms/job006/tomograms.star --cryocare-path /fs/pool/pool-bmapps/hpcl8/app/soft/CRYO-CARE/0.2/conda3/envs/cryocare_11/bin/ --output-directory Denoise/job008/ --gpu 0 --model-file Denoise/job007/denoising_model.tar.gz --n-tiles 4 4 4 --pipeline_control Denoise/job008/

Error message: Currently Loaded Modulefiles:

1. intel/18.0.5(default) 2) impi/2018.4(default) 3) RELION/5.0-beta-3NC /fs/pool/pool-bmapps/hpcl8/app/soft/RELION/5.0-beta-3/conda3/envs/relion-5.0/lib/python3.10/site-packages/starfile/parser.py:177: FutureWarning: The 'delim_whitespace' keyword in pd.read_csv is deprecated and will be removed in a future version. Use sep='\s+' instead df = pd.read_csv( /fs/pool/pool-bmapps/hpcl8/app/soft/RELION/5.0-beta-3/conda3/envs/relion-5.0/lib/python3.10/site-packages/starfile/parser.py:194: FutureWarning: errors='ignore' is deprecated and will raise in a future version. Use to_numeric without passing errors and catch exceptions explicitly instead self.dataframes[key] = df.apply(pd.to_numeric, errors='ignore') ╭───────────────────── Traceback (most recent call last) ──────────────────────╮ │ in cryoCARE_predict:2 │ │ ╭───────────────────────────────── locals ─────────────────────────────────╮ │ │ │ cryocare_path = PosixPath('/fs/pool/pool-bmapps/hpcl8/app/soft/CRY… │ │ │ │ gpu = [0] │ │ │ │ model_file = PosixPath('Denoise/job007/denoising_model.tar.gz') │ │ │ │ n_tiles = (4, 4, 4) │ │ │ │ output_directory = PosixPath('Denoise/job008') │ │ │ │ pipeline_control = PosixPath('Denoise/job008') │ │ │ │ tomogram_name = None │ │ │ │ tomogram_star_file = PosixPath('Tomograms/job006/tomograms.star') │ │ │ ╰──────────────────────────────────────────────────────────────────────────╯ │ │ │ │ /fs/pool/pool-bmapps/hpcl8/app/soft/RELION/5.0-beta-3/conda3/envs/relion-5.0 │ │ /lib/python3.10/site-packages/tomography_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_predict at 0x14be79a45240> │ │ │ │ job_directory = PosixPath('Denoise/job008') │ │ │ │ kwargs = { │ │ │ │ │ 'tomogram_star_file': │ │ │ │ PosixPath('Tomograms/job006/tomograms.star'), │ │ │ │ │ 'output_directory': │ │ │ │ PosixPath('Denoise/job008'), │ │ │ │ │ 'model_file': │ │ │ │ PosixPath('Denoise/job007/denoising_model.tar.gz'), │ │ │ │ │ 'cryocare_path': │ │ │ │ PosixPath('/fs/pool/pool-bmapps/hpcl8/app/soft/CRY… │ │ │ │ │ 'n_tiles': (4, 4, 4), │ │ │ │ │ 'tomogram_name': None, │ │ │ │ │ 'gpu': [0] │ │ │ │ } │ │ │ │ pipeline_directory = PosixPath('Denoise/job008') │ │ │ ╰──────────────────────────────────────────────────────────────────────────╯ │ │ │ │ /fs/pool/pool-bmapps/hpcl8/app/soft/RELION/5.0-beta-3/conda3/envs/relion-5.0 │ │ /lib/python3.10/site-packages/tomography_python_programs/denoise/cryoCARE/pr │ │ edict.py:141 in cryoCARE_predict │ │ │ │ 138 │ │ output_directory=output_directory, │ │ 139 │ │ tomo_name=tomogram_name │ │ 140 │ ) │ │ ❱ 141 │ save_global_star( │ │ 142 │ │ global_star=global_star, │ │ 143 │ │ output_directory=output_directory, │ │ 144 │ ) │ │ │ │ ╭───────────────────────────────── locals ─────────────────────────────────╮ │ │ │ cmd = '/fs/pool/pool-bmapps/hpcl8/app/soft/CRYO-CARE/0.2… │ │ │ │ cryocare_path = '/fs/pool/pool-bmapps/hpcl8/app/soft/CRYO-CARE/0.2… │ │ │ │ even_tomos = [ │ │ │ │ │ │ │ │ │ 'Tomograms/job006/tomograms/rec_Position_1_half1.m… │ │ │ │ │ │ │ │ │ 'Tomograms/job006/tomograms/rec_Position_36_half1.… │ │ │ │ ] │ │ │ │ global_star = rlnTomoName ... │ │ │ │ rlnTomoReconstructedTomogramDenoised │ │ │ │ 0 Position_1 ... │ │ │ │ Denoise/job008/tomograms/rec_Position_1.mrc │ │ │ │ 1 Position_36 ... │ │ │ │ Denoise/job008/tomograms/rec_Position_36.mrc │ │ │ │ │ │ │ │ [2 rows x 17 columns] │ │ │ │ gpu = [0] │ │ │ │ model_file = PosixPath('Denoise/job007/denoising_model.tar.gz') │ │ │ │ n_tiles = (4, 4, 4) │ │ │ │ odd_tomos = [ │ │ │ │ │ │ │ │ │ 'Tomograms/job006/tomograms/rec_Position_1_half2.m… │ │ │ │ │ │ │ │ │ 'Tomograms/job006/tomograms/rec_Position_36_half2.… │ │ │ │ ] │ │ │ │ output_directory = PosixPath('Denoise/job008') │ │ │ │ predict_executable = '/fs/pool/pool-bmapps/hpcl8/app/soft/CRYO-CARE/0.2… │ │ │ │ predict_json = { │ │ │ │ │ 'path': │ │ │ │ 'Denoise/job007/denoising_model.tar.gz', │ │ │ │ │ 'even': [ │ │ │ │ │ │ │ │ │ │ 'Tomograms/job006/tomograms/rec_Position_1_half1.m… │ │ │ │ │ │ │ │ │ │ 'Tomograms/job006/tomograms/rec_Position_36_half1.… │ │ │ │ │ ], │ │ │ │ │ 'odd': [ │ │ │ │ │ │ │ │ │ │ 'Tomograms/job006/tomograms/rec_Position_1_half2.m… │ │ │ │ │ │ │ │ │ │ 'Tomograms/job006/tomograms/rec_Position_36_half2.… │ │ │ │ │ ], │ │ │ │ │ 'n_tiles': [4, 4, 4], │ │ │ │ │ 'output': 'Denoise/job008/tomograms', │ │ │ │ │ 'overwrite': 'True', │ │ │ │ │ 'gpu_id': [0] │ │ │ │ } │ │ │ │ tilt_series_dir = PosixPath('Denoise/job008/tilt_series') │ │ │ │ tomogram_dir = PosixPath('Denoise/job008/tomograms') │ │ │ │ tomogram_name = None │ │ │ │ tomogram_star_file = PosixPath('Tomograms/job006/tomograms.star') │ │ │ │ training_dir = PosixPath('Denoise/job008/external/training') │ │ │ ╰──────────────────────────────────────────────────────────────────────────╯ │ │ │ │ /fs/pool/pool-bmapps/hpcl8/app/soft/RELION/5.0-beta-3/conda3/envs/relion-5.0 │ │ /lib/python3.10/site-packages/tomography_python_programs/denoise/cryoCARE/_u │ │ tils.py:168 in save_global_star │ │ │ │ 165 │ """ │ │ 166 │ Saves global star file (tomograms.star) in output directory. │ │ 167 │ """ │ │ ❱ 168 │ starfile.write({'global': global_star}, f'{output_directory}/tomog │ │ 169 │ │ 170 def rename_predicted_tomograms( │ │ 171 │ even_tomos: List, │ │ │ │ ╭───────────────────────────────── locals ─────────────────────────────────╮ │ │ │ global_star = rlnTomoName ... │ │ │ │ rlnTomoReconstructedTomogramDenoised │ │ │ │ 0 Position_1 ... │ │ │ │ Denoise/job008/tomograms/rec_Position_1.mrc │ │ │ │ 1 Position_36 ... │ │ │ │ Denoise/job008/tomograms/rec_Position_36.mrc │ │ │ │ │ │ │ │ [2 rows x 17 columns] │ │ │ │ output_directory = PosixPath('Denoise/job008') │ │ │ ╰──────────────────────────────────────────────────────────────────────────╯ │ │ │ │ /fs/pool/pool-bmapps/hpcl8/app/soft/RELION/5.0-beta-3/conda3/envs/relion-5.0 │ │ /lib/python3.10/site-packages/starfile/functions.py:41 in write │ │ │ │ 38 │ data can be a single dataframe, a list of dataframes or a dict of d │ │ 39 │ float format defaults to 6 digits after the decimal point │ │ 40 │ """ │ │ ❱ 41 │ StarWriter(data, filename=filename, float_format=float_format, over │ │ 42 │ │ │ na_rep=na_rep, sep=sep, force_loop=force_loop) │ │ 43 │ │ │ │ ╭───────────────────────────────── locals ─────────────────────────────────╮ │ │ │ data = { │ │ │ │ │ 'global': rlnTomoName ... │ │ │ │ rlnTomoReconstructedTomogramDenoised │ │ │ │ 0 Position_1 ... │ │ │ │ Denoise/job008/tomograms/rec_Position_1.mrc │ │ │ │ 1 Position_36 ... │ │ │ │ Denoise/job008/tomograms/rec_Position_36.mrc │ │ │ │ │ │ │ │ [2 rows x 17 columns] │ │ │ │ } │ │ │ │ filename = 'Denoise/job008/tomograms.star' │ │ │ │ float_format = '%.6f' │ │ │ │ force_loop = True │ │ │ │ na_rep = '' │ │ │ │ overwrite = False │ │ │ │ sep = '\t' │ │ │ ╰──────────────────────────────────────────────────────────────────────────╯ │ │ │ │ /fs/pool/pool-bmapps/hpcl8/app/soft/RELION/5.0-beta-3/conda3/envs/relion-5.0 │ │ /lib/python3.10/site-packages/starfile/writer.py:24 in init │ │ │ │ 21 │ │ │ │ filename: PathLike, overwrite: bool = False, float_fo │ │ 22 │ │ │ │ sep: str = '\t', na_rep: str = '', force_loop: bo │ │ 23 │ │ self.overwrite = overwrite │ │ ❱ 24 │ │ self.filename = filename │ │ 25 │ │ self.dataframes = dataframes │ │ 26 │ │ self.float_format = float_format │ │ 27 │ │ self.sep = sep │ │ │ │ ╭───────────────────────────────── locals ─────────────────────────────────╮ │ │ │ dataframes = { │ │ │ │ │ 'global': rlnTomoName ... │ │ │ │ rlnTomoReconstructedTomogramDenoised │ │ │ │ 0 Position_1 ... │ │ │ │ Denoise/job008/tomograms/rec_Position_1.mrc │ │ │ │ 1 Position_36 ... │ │ │ │ Denoise/job008/tomograms/rec_Position_36.mrc │ │ │ │ │ │ │ │ [2 rows x 17 columns] │ │ │ │ } │ │ │ │ filename = 'Denoise/job008/tomograms.star' │ │ │ │ float_format = '%.6f' │ │ │ │ force_loop = True │ │ │ │ na_rep = '' │ │ │ │ overwrite = False │ │ │ │ self = <starfile.writer.StarWriter object at 0x14be79bd6fe0> │ │ │ │ sep = '\t' │ │ │ ╰──────────────────────────────────────────────────────────────────────────╯ │ │ │ │ /fs/pool/pool-bmapps/hpcl8/app/soft/RELION/5.0-beta-3/conda3/envs/relion-5.0 │ │ /lib/python3.10/site-packages/starfile/writer.py:82 in filename │ │ │ │ 79 │ def filename(self, filename: Union[Path, str]): │ │ 80 │ │ self._filename = Path(filename) │ │ 81 │ │ if not self.file_writable: │ │ ❱ 82 │ │ │ raise FileExistsError('to overwrite an existing file set o │ │ 83 │ │ │ 84 │ @Property │ │ 85 │ def file_exists(self): │ │ │ │ ╭───────────────────────────── locals ─────────────────────────────╮ │ │ │ filename = 'Denoise/job008/tomograms.star' │ │ │ │ self = <starfile.writer.StarWriter object at 0x14be79bd6fe0> │ │ │ ╰──────────────────────────────────────────────────────────────────╯ │ ╰──────────────────────────────────────────────────────────────────────────────╯ FileExistsError: to overwrite an existing file set overwrite=True srun: error: hpcl9302: task 0: Exited with exit code 2 srun: Terminating StepId=559313.0