majiq psi error

[Enze Liu]

Hi,

I tried to run the following command:

majiq build my_annotation.gff3 -o my_build -c majiq_build_config.ini

majiq psi -o psi -j 8 --name PDX S1.bam S2.bam S3.bam

I got following error msgs when running 'majiq psi':

Traceback (most recent call last):
  File "/N/slate/enzeliu/majiq/bin/majiq", line 8, in <module>
    sys.exit(main())
             ^^^^^^
  File "/N/slate/enzeliu/majiq/lib/python3.11/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/majiq/lib/python3.11/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/majiq/lib/python3.11/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

I installed majiq in a virtural environment with numpy=1.21.6

Thanks

[San Jewell]

Hello,

I can't say I'm sure exactly how this error came about but it looks like you are running $ majiq psi  ; with bam files as input. Instead, the processed majiq files from your run of $ majiq build  ; should be used instead. Please see this page for an overview of the file extensions through the build process: https://biociphers.bitbucket.io/majiq-docs/getting-started-guide/quick-overview.html

Thanks,

-San