Python Command Failed:

Jianghua Cai

• January 24, 2023 09:01

I use geneious prime to design CRISPR target more than one year. it worked very well. but recetnly, when I use geneious prime to design CRISPR target, it comes out "Python Command Failed:"

com.biomatters.geneious.publicapi.plugin.DocumentOperationException
at com.biomatters.plugins.crispr.Scoring.m.a(PythonUtilities.java:553)
at com.biomatters.plugins.crispr.Scoring.l.a(PythonModule.java:314)
at com.biomatters.plugins.crispr.Scoring.g.a(Doench2016Runner.java:140)
at com.biomatters.plugins.crispr.Scoring.g.a(Doench2016Runner.java:62)
at com.biomatters.plugins.crispr.Scoring.i.b(Doench2016ScoringAlgorithm.java:61)
at com.biomatters.plugins.crispr.Scoring.c.a(CRISPRScoringAlgorithm.java:200)
at com.biomatters.plugins.crispr.d.a(CRISPRManager.java:168)
at com.biomatters.plugins.crispr.d.a(CRISPRManager.java:68)
at com.biomatters.plugins.crispr.CRISPRAnnotationGenerator.generate(CRISPRAnnotationGenerator.java:61)
at com.biomatters.plugins.sequenceviewer.annotations.aE.b(SequenceViewerAnnotationGenerators.java:180)
at com.biomatters.geneious.common.operations.c.c(OperationsUtilities.java:165)
at com.biomatters.geneious.common.operations.c.b(OperationsUtilities.java:162)
at com.biomatters.geneious.common.operations.b$c.a(OperationsUtilities.java:141)
at com.biomatters.geneious.common.operations.b$d.a(OperationsUtilities.java:168)
at com.biomatters.plugins.sequenceviewer.annotations.aD.run(SequenceViewerAnnotationGenerators.java:210)
at java.base/java.lang.Thread.run(Thread.java:829)
Caused by: com.biomatters.geneious.publicapi.plugin.DocumentOperationException: Please wait failed with error code 1
C:\Users\caijhua\AppData\Local\Geneious\geneious_python\Biomatters-Azimuth\venv\bin\sklearn\base.py:310: UserWarning: Trying to unpickle estimator DummyRegressor from version 0.23.2 when using version 0.24.1. This might lead to breaking code or invalid results. Use at your own risk.
warnings.warn(
C:\Users\caijhua\AppData\Local\Geneious\geneious_python\Biomatters-Azimuth\venv\bin\sklearn\base.py:310: UserWarning: Trying to unpickle estimator DecisionTreeRegressor from version 0.23.2 when using version 0.24.1. This might lead to breaking code or invalid results. Use at your own risk.
warnings.warn(
C:\Users\caijhua\AppData\Local\Geneious\geneious_python\Biomatters-Azimuth\venv\bin\sklearn\base.py:310: UserWarning: Trying to unpickle estimator GradientBoostingRegressor from version 0.23.2 when using version 0.24.1. This might lead to breaking code or invalid results. Use at your own risk.
warnings.warn(
Traceback (most recent call last):
File "C:\Users\caijhua\AppData\Local\Geneious\geneious_python\Biomatters-Azimuth\venv\bin\azimuth\cli_predict.py", line 19, in
predictions = predict(np.array(options.sequences), None, None)
File "C:\Users\caijhua\AppData\Local\Geneious\geneious_python\Biomatters-Azimuth\venv\bin\azimuth\model_comparison.py", line 630, in predict
feature_sets = feat.featurize_data(Xdf, learn_options, pandas.DataFrame(), gene_position, pam_audit=pam_audit,
File "C:\Users\caijhua\AppData\Local\Geneious\geneious_python\Biomatters-Azimuth\venv\bin\azimuth\features\featurization.py", line 68, in featurize_data
feature_sets["Tm"] = Tm_feature(data, pam_audit, learn_options=None)
File "C:\Users\caijhua\AppData\Local\Geneious\geneious_python\Biomatters-Azimuth\venv\bin\azimuth\features\featurization.py", line 381, in Tm_feature
featarray[i,0] = Tm.Tm_staluc(seq, rna=rna) #30mer Tm
AttributeError: module 'Bio.SeqUtils.MeltingTemp' has no attribute 'Tm_staluc'

at com.biomatters.geneious.privateApi.ExecutionForOperation.execute(ExecutionForOperation.java:72)
at com.biomatters.plugins.crispr.Scoring.m.a(PythonUtilities.java:547)
... 15 more

 

Could you tell me how to manage this?

Thanks in advance.

 

 

1

• Official comment

  

  Jonas Kuhn

  • April 03, 2023 21:32

  Hi Chamilka,

  Which version of Geneious are you using?

  For a more detailed analysis it might be best to contact support (via the 'Help' menu in Geneious) and include log files.

  Regards, Jonas
• 

  Tom Edwards

  • January 24, 2023 21:06

  Hi Jianghua,

  This problem should be fixed in the latest version of Geneious, let us know if you are still running into any issues after trying CRISPR on the latest version :)

  Cheers,
  Tom

  0
• 

  Chamilka Ratnayake

  • March 30, 2023 02:02

  I still encounter this problem. How to resolve this?

  0

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