NameError: name 'pickle' is not defined

[santosh]

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]

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.