tomo name error if the name starts with a 0 in TS alignment Relion5

[ASKrebs]

I am running into a bug during TS alignment when my tiltseries is named with 00s at the beginning and the name consists only of digits. When I change the name (rlnTomoName) in the star files to also contain letters, it runs. So the name 00255 doesn't work but TS00255 does.

A short command where it doesn't work is: relion_python_tomo_align_tilt_series IMOD:fiducials --nominal-fiducial-diameter-nanometers 10 --tilt-series-star-file CtfFind/tilt_series_ctf.star --output-directory AlignTiltSeries/ --pipeline_control AlignTiltSeries/

I get the following (shortened due to max.characters) error message in the terminal:

[09:35:26] Extracting metadata for tilt series. cli_fiducials.py:29 /opt/conda/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( /opt/conda/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') /opt/conda/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( /opt/conda/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') /opt/conda/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( /opt/conda/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') /opt/conda/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( /opt/conda/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') /opt/conda/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( /opt/conda/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') /opt/conda/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( /opt/conda/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') /opt/conda/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( /opt/conda/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) ────────────────────────────────╮ │ /opt/conda/envs/relion-5.0/lib/python3.10/site-packages/pandas/core/indexes/base.py:3802 in │ │ get_loc │ │ │ │ 3799 │ │ """ │ │ 3800 │ │ casted_key = self._maybe_cast_indexer(key) │ │ 3801 │ │ try: │ │ ❱ 3802 │ │ │ return self._engine.get_loc(casted_key) │ │ 3803 │ │ except KeyError as err: │ │ 3804 │ │ │ if isinstance(casted_key, slice) or ( │ │ 3805 │ │ │ │ isinstance(casted_key, abc.Iterable) │ │ │ │ ╭──────────────────────────────── locals ────────────────────────────────╮ │ │ │ casted_key = '00255' │ │ │ │ key = '00255' │ │ │ │ self = Index([255, 256, 257], dtype='int64', name='rlnTomoName') │ │ │ ╰────────────────────────────────────────────────────────────────────────╯ │ │ │ │ in pandas._libs.index.IndexEngine.get_loc:153 │ │ │ │ in pandas._libs.index.IndexEngine.get_loc:161 │ │ │ │ in pandas._libs.index.Int64Engine._check_type:70 │ ╰──────────────────────────────────────────────────────────────────────────────────────────────────╯ KeyError: '00255'

The above exception was the direct cause of the following exception:

╭─────────────────────────────── Traceback (most recent call last) ────────────────────────────────╮ │ in fiducials_cli:2 │ │ ╭───────────────────────────────────── locals ─────────────────────────────────────╮ │ │ │ nominal_fiducial_diameter_nanometers = 10.0 │ │ │ │ output_directory = PosixPath('AlignTiltSeries') │ │ │ │ pipeline_control = PosixPath('AlignTiltSeries') │ │ │ │ tilt_series_star_file = PosixPath('CtfFind/tilt_series_ctf.star') │ │ │ │ tomogram_name = None │ │ │ ╰──────────────────────────────────────────────────────────────────────────────────╯ │ │ │ │ /opt/conda/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_ARGUMENT.name) │ │ ❱ 75 │ │ │ func(*args, **kwargs) │ │ 76 │ │ │ if job_directory is not None and pipeline_directory is not None: │ │ 77 │ │ │ │ write_job_success_file(job_directory) │ │ 78 │ │ except BaseException: │ │ │ │ ╭─────────────────────────────────────────── locals ───────────────────────────────────────────╮ │ │ │ args = () │ │ │ │ func = <function fiducials_cli at 0x7f0082679ea0> │ │ │ │ job_directory = PosixPath('AlignTiltSeries') │ │ │ │ kwargs = { │ │ │ │ │ 'tilt_series_star_file': PosixPath('CtfFind/tilt_series_ctf.star'), │ │ │ │ │ 'output_directory': PosixPath('AlignTiltSeries'), │ │ │ │ │ 'nominal_fiducial_diameter_nanometers': 10.0, │ │ │ │ │ 'tomogram_name': None │ │ │ │ } │ │ │ │ pipeline_directory = PosixPath('AlignTiltSeries') │ │ │ ╰──────────────────────────────────────────────────────────────────────────────────────────────╯ │ │ │ │ /opt/conda/envs/relion-5.0/lib/python3.10/site-packages/tomography_python_programs/align_tilt_se │ │ ries/imod/cli_fiducials.py:33 in fiducials_cli │ │ │ │ 30 │ tilt_series_set = RlnTiltSeriesSet.from_star_file( │ │ 31 │ │ filename=tilt_series_star_file, tilt_series_id=tomogram_name │ │ 32 │ ) │ │ ❱ 33 │ for global_data, tilt_series in tilt_series_set: │ │ 34 │ │ console.log(f'Aligning {tilt_series.name}...') │ │ 35 │ │ align_single_tilt_series( │ │ 36 │ │ │ tilt_series=tilt_series, │ │ │ │ ╭─────────────────────────────────────────── locals ───────────────────────────────────────────╮ │ │ │ nominal_fiducial_diameter_nanometers = 10.0 │ │ │ │ output_directory = PosixPath('AlignTiltSeries') │ │ │ │ tilt_series_set = RlnTiltSeriesSet( │ │ │ │ │ global_data= rlnTomoName rlnVoltage │ │ │ │ rlnSphericalAberration rlnAmplitudeContrast │ │ │ │ rlnMicrographOriginalPixelSize rlnTomoHand │ │ │ │ rlnTomoTiltSeriesPixelSize │ │ │ │ rlnTomoName │ │ │ │ 255 255 300.0 │ │ │ │ 2.7 0.07 │ │ │ │ 1.7005 1.0 1.7005 │ │ │ │ 256 256 300.0 │ │ │ │ 2.7 0.07 │ │ │ │ 1.7005 1.0 1.7005 │ │ │ │ 257 257 300.0 │ │ │ │ 2.7 0.07 │ │ │ │ 1.7005 1.0 1.7005, │ │ │ │ │ tilt_series=[ │ │ │ │ │ │ RlnTiltSeries( │ │ │ │ │ │ │ name='00255', │ │ │ │ │ │ │ data= rlnMicrographMovieName │ │ │ │ rlnTomoTiltMovieFrameCount │ │ │ │ rlnTomoNominalStageTiltAngle │ │ │ │ rlnTomoNominalTiltAxisAngle ... rlnCtfAstigmatism │ │ │ │ rlnDefocusAngle rlnCtfFigureOfMerit │ │ │ │ rlnCtfMaxResolution │ │ │ │ 0 data/data/TS_02001-0.0.tif │ │ │ │ 12 -0.01135 │ │ │ │ 85.7 ... 275.392578 88.783653 │ │ │ │ 0.045798 8.291962 │ │

[...]

│ │ 40 data/data/TS_03_041_60.0.tif │ │ │ │ 12 59.98280 │ │ │ │ 85.7 ... 457.650391 -81.486980 │ │ │ │ 0.016579 14.756881 │ │ │ │ │ │ │ │ [41 rows x 19 columns] │ │ │ │ │ │ ), │ │ │ │ │ │ RlnTiltSeries( │ │ │ │ │ │ │ name='00257', │ │ │ │ │ │ │ data= rlnMicrographMovieName │ │ │ │ rlnTomoTiltMovieFrameCount │ │ │ │ rlnTomoNominalStageTiltAngle │ │ │ │ rlnTomoNominalTiltAxisAngle ... rlnCtfAstigmatism │ │ │ │ rlnDefocusAngle rlnCtfFigureOfMerit │ │ │ │ rlnCtfMaxResolution │ │ │ │ 0 data/data/TS_04001-0.0.tif │ │ │ │ 12 -0.01035 │ │ │ │ 85.7 ... 232.371094 -7.723870 │ │ │ │ 0.056624 7.195504 │ │

[...]

│ │ 40 data/data/TS_04_041_60.0.tif │ │ │ │ 12 59.98680 │ │ │ │ 85.7 ... 488.773438 -72.590830 │ │ │ │ 0.013987 9.262298 │ │ │ │ │ │ │ │ [41 rows x 19 columns] │ │ │ │ │ │ ) │ │ │ │ │ ] │ │ │ │ ) │ │ │ │ tilt_series_star_file = PosixPath('CtfFind/tilt_series_ctf.star') │ │ │ │ tomogram_name = None │ │ │ ╰──────────────────────────────────────────────────────────────────────────────────────────────╯ │ │ │ │ /opt/conda/envs/relion-5.0/lib/python3.10/site-packages/tomography_python_programs/_metadata_mod │ │ els/relion/tilt_series_set.py:95 in │ │ │ │ 92 │ │ return self.tilt_series[self._tilt_series_names.index(tilt_series_id)] │ │ 93 │ │ │ 94 │ def iter(self) -> Iterable[Tuple[pd.Series, RlnTiltSeries]]: │ │ ❱ 95 │ │ return ((self.global_data.loc[tilt_series.name], tilt_series) for │ │ 96 │ │ │ │ tilt_series in self.tilt_series) │ │ 97 │ │ │ │ ╭─────────────────────────────────────────── locals ───────────────────────────────────────────╮ │ │ │ .0 = <list_iterator object at 0x7f0082935540> │ │ │ │ self = RlnTiltSeriesSet( │ │ │ │ │ global_data= rlnTomoName rlnVoltage rlnSphericalAberration │ │ │ │ rlnAmplitudeContrast rlnMicrographOriginalPixelSize rlnTomoHand │ │ │ │ rlnTomoTiltSeriesPixelSize │ │ │ │ rlnTomoName │ │ │ │ 255 255 300.0 2.7 │ │ │ │ 0.07 1.7005 1.0 1.7005 │ │ │ │ 256 256 300.0 2.7 │ │ │ │ 0.07 1.7005 1.0 1.7005 │ │ │ │ 257 257 300.0 2.7 │ │ │ │ 0.07 1.7005 1.0 1.7005, │ │ │ │ │ tilt_series=[ │ │ │ │ │ │ RlnTiltSeries( │ │ │ │ │ │ │ name='00255', │ │ │ │ │ │ │ data= rlnMicrographMovieName rlnTomoTiltMovieFrameCount │ │ │ │ rlnTomoNominalStageTiltAngle rlnTomoNominalTiltAxisAngle ... │ │ │ │ rlnCtfAstigmatism rlnDefocusAngle rlnCtfFigureOfMerit rlnCtfMaxResolution │ │ │ │ 0 data/data/TS_02001-0.0.tif 12 │ │ │ │ -0.01135 85.7 ... 275.392578 88.783653 │ │

[..]

│ │ -42.784290 0.019736 25.000000 │ │ │ │ 40 data/data/TS_02_041_60.0.tif 12 │ │ │ │ 59.98430 85.7 ... 569.316406 -58.727370 │ │ │ │ 0.013299 25.000000 │ │ │ │ │ │ │ │ [41 rows x 19 columns] │ │ │ │ │ │ ), │ │ │ │ │ │ RlnTiltSeries( │ │ │ │ │ │ │ name='00256', │ │ │ │ │ │ │ data= rlnMicrographMovieName rlnTomoTiltMovieFrameCount │ │ │ │ rlnTomoNominalStageTiltAngle rlnTomoNominalTiltAxisAngle ... │ │ │ │ rlnCtfAstigmatism rlnDefocusAngle rlnCtfFigureOfMerit rlnCtfMaxResolution │ │ │ │ 0 data/data/TS_03001-0.0.tif 12 │ │ │ │ -0.01535 85.7 ... 470.345703 -62.573570 │ │ │ │ 0.043402 5.213509 │ │

[..]

│ │ 40 data/data/TS_04_041_60.0.tif 12 │ │ │ │ 59.98680 85.7 ... 488.773438 -72.590830 │ │ │ │ 0.013987 9.262298 │ │ │ │ │ │ │ │ [41 rows x 19 columns] │ │ │ │ │ │ ) │ │ │ │ │ ] │ │ │ │ ) │ │ │ │ tilt_series = RlnTiltSeries( │ │ │ │ │ name='00255', │ │ │ │ │ data= rlnMicrographMovieName rlnTomoTiltMovieFrameCount │ │ │ │ rlnTomoNominalStageTiltAngle rlnTomoNominalTiltAxisAngle ... │ │ │ │ rlnCtfAstigmatism rlnDefocusAngle rlnCtfFigureOfMerit rlnCtfMaxResolution │ │ │ │ 0 data/data/TS_02001-0.0.tif 12 │ │ │ │ -0.01135 85.7 ... 275.392578 88.783653 │ │ │ │ 0.045798 8.291962 │ │ │ │ 1 data/data/TS_02_002_3.0.tif 12 │ │ │ │ 2.98478 85.7 ... 520.529297 -52.787060 │ │ │ │ 0.035346 6.263712 │ │

[...]

│ │ 40 data/data/TS_02_041_60.0.tif 12 │ │ │ │ 59.98430 85.7 ... 569.316406 -58.727370 │ │ │ │ 0.013299 25.000000 │ │ │ │ │ │ │ │ [41 rows x 19 columns] │ │ │ │ ) │ │ │ ╰──────────────────────────────────────────────────────────────────────────────────────────────╯ │ │ │ │ /opt/conda/envs/relion-5.0/lib/python3.10/site-packages/pandas/core/indexing.py:1192 in │ │ getitem │ │ │ │ 1189 │ │ │ │ │ 1190 │ │ │ maybe_callable = com.apply_if_callable(key, self.obj) │ │ 1191 │ │ │ maybe_callable = self._check_deprecated_callable_usage(key, maybe_callable) │ │ ❱ 1192 │ │ │ return self._getitem_axis(maybe_callable, axis=axis) │ │ 1193 │ │ │ 1194 │ def _is_scalar_access(self, key: tuple): │ │ 1195 │ │ raise NotImplementedError() │ │ │ │ ╭─────────────────────────────────── locals ───────────────────────────────────╮ │ │ │ axis = 0 │ │ │ │ key = '00255' │ │ │ │ maybe_callable = '00255' │ │ │ │ self = <pandas.core.indexing._LocIndexer object at 0x7f00826868e0> │ │ │ ╰──────────────────────────────────────────────────────────────────────────────╯ │ │ │ │ /opt/conda/envs/relion-5.0/lib/python3.10/site-packages/pandas/core/indexing.py:1432 in │ │ _getitem_axis │ │ │ │ 1429 │ │ │ │ 1430 │ │ # fall thru to straight lookup │ │ 1431 │ │ self._validate_key(key, axis) │ │ ❱ 1432 │ │ return self._get_label(key, axis=axis) │ │ 1433 │ │ │ 1434 │ def _get_slice_axis(self, slice_obj: slice, axis: AxisInt): │ │ 1435 │ │ """ │ │ │ │ ╭─────────────────────────────── locals ───────────────────────────────╮ │ │ │ axis = 0 │ │ │ │ key = '00255' │ │ │ │ labels = Index([255, 256, 257], dtype='int64', name='rlnTomoName') │ │ │ │ self = <pandas.core.indexing._LocIndexer object at 0x7f00826868e0> │ │ │ ╰──────────────────────────────────────────────────────────────────────╯ │ │ │ │ /opt/conda/envs/relion-5.0/lib/python3.10/site-packages/pandas/core/indexing.py:1382 in │ │ _get_label │ │ │ │ 1379 │ │ │ 1380 │ def _get_label(self, label, axis: AxisInt): │ │ 1381 │ │ # GH#5567 this will fail if the label is not present in the axis. │ │ ❱ 1382 │ │ return self.obj.xs(label, axis=axis) │ │ 1383 │ │ │ 1384 │ def _handle_lowerdim_multi_index_axis0(self, tup: tuple): │ │ 1385 │ │ # we have an axis0 multi-index, handle or raise │ │ │ │ ╭────────────────────────────── locals ───────────────────────────────╮ │ │ │ axis = 0 │ │ │ │ label = '00255' │ │ │ │ self = <pandas.core.indexing._LocIndexer object at 0x7f00826868e0> │ │ │ ╰─────────────────────────────────────────────────────────────────────╯ │ │ │ │ /opt/conda/envs/relion-5.0/lib/python3.10/site-packages/pandas/core/generic.py:4295 in xs │ │ │ │ 4292 │ │ │ │ else: │ │ 4293 │ │ │ │ │ new_index = index[loc] │ │ 4294 │ │ else: │ │ ❱ 4295 │ │ │ loc = index.getloc(key) │ │ 4296 │ │ │ │ │ 4297 │ │ │ if isinstance(loc, np.ndarray): │ │ 4298 │ │ │ │ if loc.dtype == np.bool: │ │ │ │ ╭─────────────────────────────────────────── locals ───────────────────────────────────────────╮ │ │ │ axis = 0 │ │ │ │ drop_level = True │ │ │ │ index = Index([255, 256, 257], dtype='int64', name='rlnTomoName') │ │ │ │ key = '00255' │ │ │ │ labels = Index([255, 256, 257], dtype='int64', name='rlnTomoName') │ │ │ │ level = None │ │ │ │ self = │ │ │ rlnTomoName rlnVoltage rlnSphericalAberration │ │ │ │ rlnAmplitudeContrast rlnMicrographOriginalPixelSize rlnTomoHand │ │ │ │ rlnTomoTiltSeriesPixelSize │ │ │ │ rlnTomoName │ │ │ │ 255 255 300.0 2.7 │ │ │ │ 0.07 1.7005 1.0 1.7005 │ │ │ │ 256 256 300.0 2.7 │ │ │ │ 0.07 1.7005 1.0 1.7005 │ │ │ │ 257 257 300.0 2.7 │ │ │ │ 0.07 1.7005 1.0 1.7005 │ │ │ ╰──────────────────────────────────────────────────────────────────────────────────────────────╯ │ │ │ │ /opt/conda/envs/relion-5.0/lib/python3.10/site-packages/pandas/core/indexes/base.py:3809 in │ │ get_loc │ │ │ │ 3806 │ │ │ │ and any(isinstance(x, slice) for x in casted_key) │ │ 3807 │ │ │ ): │ │ 3808 │ │ │ │ raise InvalidIndexError(key) │ │ ❱ 3809 │ │ │ raise KeyError(key) from err │ │ 3810 │ │ except TypeError: │ │ 3811 │ │ │ # If we have a listlike key, _check_indexing_error will raise │ │ 3812 │ │ │ # InvalidIndexError. Otherwise we fall through and re-raise │ │ │ │ ╭──────────────────────────────── locals ────────────────────────────────╮ │ │ │ casted_key = '00255' │ │ │ │ key = '00255' │ │ │ │ self = Index([255, 256, 257], dtype='int64', name='rlnTomoName') │ │ │ ╰────────────────────────────────────────────────────────────────────────╯ │ ╰──────────────────────────────────────────────────────────────────────────────────────────────────╯ KeyError: '00255'

---------------------------------- PYTHON ERROR --------------------------------- Has RELION been provided a Python interpreter with the correct environment? The interpreter can be passed to RELION either during Cmake configuration by using the Cmake flag -DPYTHON_EXE_PATH=<path/to/python/interpreter>.

Using python executable: /opt/conda/envs/relion-5.0/bin/python

[EuanPyle]

Hi, Can you paste the tilt_series.star file here please? The one which contains rlnTomoName Thanks

[ASKrebs]

Sure. I am copying the one that caused the error:

data_global

loop_ _rlnTomoName #1 _rlnTomoTiltSeriesStarFile #2 _rlnVoltage #3 _rlnSphericalAberration #4 _rlnAmplitudeContrast #5 _rlnMicrographOriginalPixelSize #6 _rlnTomoHand #7 _rlnTomoTiltSeriesPixelSize #8 00255 CtfFind/MotionCorr/ImportTomo/tilt_series/00255.star 300.000000 2.700000 0.070000 1.700500 1.000000 1.700500 00256 CtfFind/MotionCorr/ImportTomo/tilt_series/00256.star 300.000000 2.700000 0.070000 1.700500 1.000000 1.700500 00257 CtfFind/MotionCorr/ImportTomo/tilt_series/00257.star 300.000000 2.700000 0.070000 1.700500 1.000000 1.700500

[EuanPyle]

thanks, I'll try to replicate the issue

[ASKrebs]

Maybe the tiltseries star file (#2 in the loop of the star file before ie 00255.star) might help you too. I am pasting it below with only the first input line. To get rid of the error, I need to change the data_00255 to the name with letters too.

data_00255

loop_ _rlnMicrographMovieName #1 _rlnTomoTiltMovieFrameCount #2 _rlnTomoNominalStageTiltAngle #3 _rlnTomoNominalTiltAxisAngle #4 _rlnMicrographPreExposure #5 _rlnTomoNominalDefocus #6 _rlnCtfPowerSpectrum #7 _rlnMicrographName #8 _rlnMicrographMetadata #9 _rlnAccumMotionTotal #10 _rlnAccumMotionEarly #11 _rlnAccumMotionLate #12 _rlnCtfImage #13 _rlnDefocusU #14 _rlnDefocusV #15 _rlnCtfAstigmatism #16 _rlnDefocusAngle #17 _rlnCtfFigureOfMerit #18 _rlnCtfMaxResolution #19 data/data/TS_02001-0.0.tif 12 -0.01135 85.700000 3.246490 -2.25000 MotionCorr/data/data/TS_02001-0_0_PS.mrc MotionCorr/data/data/TS_02001-0_0.mrc MotionCorr/data/data/TS_02001-0_0.star 1.496300 0.000000 1.496300 CtfFind/MotionCorr/data/data/TS_02001-0_0_PS.ctf:mrc 22144.326172 21868.933594 275.392578 88.783653 0.045798 8.291962

[EuanPyle]

thanks, I've replicated the error myself so I'll do a little digging, thanks for the report!

[EuanPyle]

Ok, I've found the issue, it's actually not a RELION bug, it's a bug with a starfile reader which RELION uses. Either way, good spot! Should be fixed at some point, but for now, just name your mdoc files with a prefix like TS_.

Thanks

[EuanPyle]

Sorry for taking so long with this, it required fixes across multiple projects, it should be fixed within a few days