Majiq PSI calculation error

[Enze Liu]

Hi,

I was trying to calculate PSI using 'majiq psi' but got the following error msgs:

File "/N/slate/enzeliu/anaconda/majiq_env/bin/majiq", line 8, in <module>
    sys.exit(main())
  File "/N/slate/enzeliu/anaconda/majiq_env/lib/python3.10/site-packages/rna_majiq/run_majiq.py", line 641, in main
    args.func(args)
  File "rna_majiq/src/calc_psi.pyx", line 29, in rna_majiq.src.calc_psi.calcpsi
  File "/N/slate/enzeliu/anaconda/majiq_env/lib/python3.10/site-packages/rna_majiq/src/basic_pipeline.py", line 13, in pipeline_run
    return pipeline.run()
  File "rna_majiq/src/calc_psi.pyx", line 127, in rna_majiq.src.calc_psi.CalcPsi.run
  File "rna_majiq/src/calc_psi.pyx", line 67, in rna_majiq.src.calc_psi._core_calcpsi
  File "rna_majiq/src/io.pyx", line 405, in rna_majiq.src.io.extract_lsv_summary
  File "rna_majiq/src/io.pyx", line 409, in rna_majiq.src.io.extract_lsv_summary
  File "rna_majiq/src/io.pyx", line 329, in rna_majiq.src.io._extract_lsv_summary
  File "rna_majiq/src/io.pyx", line 330, in rna_majiq.src.io._extract_lsv_summary
  File "/N/slate/enzeliu/anaconda/majiq_env/lib/python3.10/site-packages/numpy/lib/_npyio_impl.py", line 490, in load
    raise ValueError("Cannot load file containing pickled data "
ValueError: Cannot load file containing pickled data when allow_pickle=False

And chaning allow_pickle=False to True in my numpy didn't solve the issue:

Traceback (most recent call last):
  File "/N/slate/enzeliu/anaconda/majiq_env/bin/majiq", line 8, in <module>
    sys.exit(main())
  File "/N/slate/enzeliu/anaconda/majiq_env/lib/python3.10/site-packages/rna_majiq/run_majiq.py", line 641, in main
    args.func(args)
  File "rna_majiq/src/calc_psi.pyx", line 29, in rna_majiq.src.calc_psi.calcpsi
  File "/N/slate/enzeliu/anaconda/majiq_env/lib/python3.10/site-packages/rna_majiq/src/basic_pipeline.py", line 13, in pipeline_run
    return pipeline.run()
  File "rna_majiq/src/calc_psi.pyx", line 127, in rna_majiq.src.calc_psi.CalcPsi.run
  File "rna_majiq/src/calc_psi.pyx", line 67, in rna_majiq.src.calc_psi._core_calcpsi
  File "rna_majiq/src/io.pyx", line 405, in rna_majiq.src.io.extract_lsv_summary
  File "rna_majiq/src/io.pyx", line 409, in rna_majiq.src.io.extract_lsv_summary
  File "rna_majiq/src/io.pyx", line 329, in rna_majiq.src.io._extract_lsv_summary
  File "rna_majiq/src/io.pyx", line 330, in rna_majiq.src.io._extract_lsv_summary
  File "/N/slate/enzeliu/anaconda/majiq_env/lib/python3.10/site-packages/numpy/lib/_npyio_impl.py", line 495, in load
    raise pickle.UnpicklingError(
_pickle.UnpicklingError: Failed to interpret file <_io.BufferedReader name='../0661-189_m28/oxfordnanopore/0661-189_m28_m6A_align_sorted.bam'> as a pickle

Can you guys give me some hints?

[bsl...@seas.upenn.edu]

Based on the last line of the last error you sent: 

_pickle.UnpicklingError: Failed to interpret file <_io.BufferedReader name='../0661-189_m28/oxfordnanopore/0661-189_m28_m6A_align_sorted.bam'> as a pickle

It looks like you might be trying to call "majiq psi" on bam file(s).

"majiq psi" should be called on the output of "majiq build", which are .majiq files. Please see, for example, this documentation:

https://biociphers.bitbucket.io/majiq-docs/getting-started-guide/quick-overview.html

Please let us know if you have additional issues.

Barry