NameError: name 'pickle' is not defined

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santosh

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Jul 26, 2021, 4:56:58 PMJul 26
to majiq_voila
Hi Everyone,

I got the following error while running majiq deltapsi. Could someone let me know what am I missing? Is this error due to not small number of LSV detected across groups?

Error/Warning:

2021-07-26 15:31:13,010 (PID:98450) - INFO - Parsing file: 0_MAJIQ_analysis/analysis_07_26_2021/Results/build_groups/SRR8181357.majiq
2021-07-26 15:31:13,042 (PID:98450) - INFO - Parsing file: 0_MAJIQ_analysis/analysis_07_26_2021/Results/build_groups/SRR8181358.majiq
2021-07-26 15:31:13,057 (PID:98450) - INFO - Parsing file: 0_MAJIQ_analysis/analysis_07_26_2021/Results/build_groups/SRR8181359.majiq
2021-07-26 15:31:13,076 (PID:98450) - INFO - Parsing file: 0_MAJIQ_analysis/analysis_07_26_2021/Results/build_groups/SRR8181360.majiq
2021-07-26 15:31:13,092 (PID:98450) - INFO - Parsing file: 0_MAJIQ_analysis/analysis_07_26_2021/Results/build_groups/SRR8181361.majiq
2021-07-26 15:31:13,109 (PID:98450) - INFO - Parsing file: 0_MAJIQ_analysis/analysis_07_26_2021/Results/build_groups/SRR8181362.majiq
2021-07-26 15:31:13,126 (PID:98450) - INFO - Parsing file: 0_MAJIQ_analysis/analysis_07_26_2021/Results/build_groups/SRR8181363.majiq
2021-07-26 15:31:13,146 (PID:98450) - INFO - Parsing file: 0_MAJIQ_analysis/analysis_07_26_2021/Results/build_groups/SRR8181364.majiq
2021-07-26 15:31:13,162 (PID:98450) - INFO - Parsing file: 0_MAJIQ_analysis/analysis_07_26_2021/Results/build_groups/SRR8181365.majiq
2021-07-26 15:31:13,179 (PID:98450) - INFO - Parsing file: 0_MAJIQ_analysis/analysis_07_26_2021/Results/build_groups/SRR8181366.majiq
2021-07-26 15:31:13,196 (PID:98450) - INFO - Parsing file: 0_MAJIQ_analysis/analysis_07_26_2021/Results/build_groups/SRR8181367.majiq
2021-07-26 15:31:13,216 (PID:98450) - INFO - Parsing file: 0_MAJIQ_analysis/analysis_07_26_2021/Results/build_groups/SRR8181368.majiq
2021-07-26 15:31:13,241 (PID:98450) - INFO - Parsing file: 0_MAJIQ_analysis/analysis_07_26_2021/Results/build_groups/SRR8181369.majiq
2021-07-26 15:31:13,255 (PID:98450) - INFO - Parsing file: 0_MAJIQ_analysis/analysis_07_26_2021/Results/build_groups/SRR8181370.majiq
2021-07-26 15:31:13,274 (PID:98450) - INFO - Parsing file: 0_MAJIQ_analysis/analysis_07_26_2021/Results/build_groups/SRR8181371.majiq
2021-07-26 15:31:13,294 (PID:98450) - INFO - Parsing file: 0_MAJIQ_analysis/analysis_07_26_2021/Results/build_groups/SRR8181372.majiq
2021-07-26 15:31:13,318 (PID:98450) - INFO - Parsing file: 0_MAJIQ_analysis/analysis_07_26_2021/Results/build_groups/SRR8181373.majiq
2021-07-26 15:31:13,336 (PID:98450) - INFO - Parsing file: 0_MAJIQ_analysis/analysis_07_26_2021/Results/build_groups/SRR8181374.majiq
2021-07-26 15:31:13,362 (PID:98450) - INFO - Parsing file: 0_MAJIQ_analysis/analysis_07_26_2021/Results/build_groups/SRR8181375.majiq
2021-07-26 15:31:13,390 (PID:98450) - INFO - Parsing file: 0_MAJIQ_analysis/analysis_07_26_2021/Results/build_groups/SRR8181376.majiq
2021-07-26 15:31:13,409 (PID:98450) - INFO - Group SLE: 5 LSVs
2021-07-26 15:31:13,412 (PID:98450) - INFO - Parsing file: 0_MAJIQ_analysis/analysis_07_26_2021/Results/build_groups/SRR8181377.majiq
2021-07-26 15:31:13,433 (PID:98450) - INFO - Parsing file: 0_MAJIQ_analysis/analysis_07_26_2021/Results/build_groups/SRR8181378.majiq
2021-07-26 15:31:13,450 (PID:98450) - INFO - Parsing file: 0_MAJIQ_analysis/analysis_07_26_2021/Results/build_groups/SRR8181379.majiq
2021-07-26 15:31:13,470 (PID:98450) - INFO - Parsing file: 0_MAJIQ_analysis/analysis_07_26_2021/Results/build_groups/SRR8181380.majiq
2021-07-26 15:31:13,498 (PID:98450) - INFO - Parsing file: 0_MAJIQ_analysis/analysis_07_26_2021/Results/build_groups/SRR8181381.majiq
2021-07-26 15:31:13,519 (PID:98450) - INFO - Parsing file: 0_MAJIQ_analysis/analysis_07_26_2021/Results/build_groups/SRR8181382.majiq
2021-07-26 15:31:13,551 (PID:98450) - INFO - Group Healthy: 5 LSVs
2021-07-26 15:31:13,552 (PID:98450) - INFO - Number quantifiable LSVs: 5
2021-07-26 15:31:13,552 (PID:98450) - INFO - Calculating prior matrix...
NameError: name 'pickle' is not defined
Exception ignored in: 'majiq.src.internals.psi.__load_default_prior'
NameError: name 'pickle' is not defined
/software/python/conda3/envs/majiq/lib/python3.7/site-packages/majiq/src/basic_pipeline.py:11: RuntimeWarning: divide by zero encountered in log
  return pipeline.run()
2021-07-26 15:31:13,627 (PID:98450) - INFO - Computation done, saving results....
2021-07-26 15:31:13,672 (PID:98450) - INFO - DeltaPSI calculation for SLE_Healthy ended successfully! Result can be found at 0_MAJIQ_analysis/analysis_07_26_2021/Results/dpsi/SLE_Healthy/

Paul Jewell

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Sep 10, 2021, 10:24:37 AMSep 10
to majiq_voila
Hi Santosh,

Reviewing this error message, I believe this specific internal function has been deprecated. (so your issue should be resolved) If you come across this issue again, could you try to reinstall again, and let me know which version shows from

$ majiq --version

?

Thanks.
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