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Subject:

relion 5: relion_python_tomo_align_tilt_series error

From:

Hiroko Takazaki <[log in to unmask]>

Reply-To:

Hiroko Takazaki <[log in to unmask]>

Date:

Tue, 16 Apr 2024 22:37:23 +0900

Content-Type:

text/plain

Parts/Attachments:
Parts/Attachments

text/plain (291 lines) 

Hi All,

Now, I am doing subtomogram tutorial using relion5.

I got an error when I run 'relion_python_tomo_align_tilt_series' using 
both IMOD and AreTomo.
The results of the execution are as follows.
Should I install IMOD and AreTomo?
If I install them, how should I set their PATH?

Best Regards,
Hiroko Takazaki

##### IMOD error #####
relion_python_tomo_align_tilt_series IMOD:fiducials 
--nominal-fiducial-diameter-nanometers 10  --tilt-series-star-file 
ExcludeTiltImages/job004/selected_tilt_series.star --output-directory 
AlignTiltSeries/job005/  --pipeline_control AlignTiltSeries/job005/
[21:54:41] Extracting metadata for tilt series. cli_fiducials.py:29
/opt/anaconda3/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/anaconda3/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/anaconda3/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/anaconda3/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/anaconda3/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/anaconda3/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/anaconda3/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/anaconda3/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/anaconda3/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/anaconda3/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/anaconda3/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/anaconda3/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/anaconda3/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/anaconda3/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/anaconda3/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/anaconda3/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/anaconda3/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/anaconda3/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/anaconda3/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/anaconda3/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/anaconda3/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/anaconda3/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')
            Aligning TS_01... cli_fiducials.py:39
[21:54:41] Running IMOD alignment align_tilt_series.py:44
[21:54:42] ERROR: alignment for TS_01 failed with error:No IMOD 
installation found. align_tilt_series.py:65
[21:54:42] Aligning TS_03... cli_fiducials.py:39
[21:54:42] Running IMOD alignment align_tilt_series.py:44
[21:54:42] ERROR: alignment for TS_03 failed with error:No IMOD 
installation found. align_tilt_series.py:65
            Aligning TS_43... cli_fiducials.py:39
[21:54:42] Running IMOD alignment align_tilt_series.py:44
[21:54:43] ERROR: alignment for TS_43 failed with error:No IMOD 
installation found. align_tilt_series.py:65
[21:54:43] Aligning TS_45... cli_fiducials.py:39
[21:54:43] Running IMOD alignment align_tilt_series.py:44
[21:54:43] ERROR: alignment for TS_45 failed with error:No IMOD 
installation found. align_tilt_series.py:65
            Aligning TS_54... cli_fiducials.py:39
[21:54:43] Running IMOD alignment align_tilt_series.py:44
[21:54:43] ERROR: alignment for TS_54 failed with error:No IMOD 
installation found. align_tilt_series.py:65
            Writing aligned_tilt_series.star cli_fiducials.py:51

##### AreTomo error #####
relion_python_tomo_align_tilt_series AreTomo 
--sample-thickness-nanometers 200 --tilt-series-star-file 
ExcludeTiltImages/job004/selected_tilt_series.star --output-directory 
AlignTiltSeries/job005/  --pipeline_control AlignTiltSeries/job005/
[21:59:44] Extracting metadata from STAR file cli.py:29
/opt/anaconda3/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/anaconda3/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/anaconda3/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/anaconda3/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/anaconda3/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/anaconda3/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/anaconda3/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/anaconda3/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/anaconda3/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/anaconda3/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/anaconda3/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/anaconda3/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/anaconda3/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/anaconda3/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/anaconda3/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/anaconda3/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/anaconda3/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/anaconda3/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/anaconda3/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/anaconda3/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/anaconda3/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/anaconda3/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')
            Aligning TS_01... cli.py:35
[21:59:44] Running AreTomo on TS_01 align_tilt_series.py:44
[21:59:45] ERROR: alignment for TS_01 failed align_tilt_series.py:70
[21:59:45] Aligning TS_03... cli.py:35
[21:59:45] Running AreTomo on TS_03 align_tilt_series.py:44
[21:59:45] ERROR: alignment for TS_03 failed align_tilt_series.py:70
            Aligning TS_43... cli.py:35
[21:59:45] Running AreTomo on TS_43 align_tilt_series.py:44
[21:59:46] ERROR: alignment for TS_43 failed align_tilt_series.py:70
[21:59:46] Aligning TS_45... cli.py:35
[21:59:46] Running AreTomo on TS_45 align_tilt_series.py:44
[21:59:46] ERROR: alignment for TS_45 failed align_tilt_series.py:70
            Aligning TS_54... cli.py:35
[21:59:46] Running AreTomo on TS_54 align_tilt_series.py:44
[21:59:47] ERROR: alignment for TS_54 failed align_tilt_series.py:70
[21:59:47] Writing aligned_tilt_series.star cli.py:45

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