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YeoLab / outrigger

Create a *de novo* alternative splicing database, validate splicing events, and quantify percent spliced-in (Psi) from RNA seq data
http://yeolab.github.io/outrigger/
BSD 3-Clause "New" or "Revised" License
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ValueError: Cannot mask with non-boolean array containing NA / NaN values error #102

Open titand98 opened 3 years ago

titand98 commented 3 years ago

Description

outrigger psi command did not execute

"""

The above exception was the direct cause of the following exception:

Traceback (most recent call last): File "/home/erpl/anaconda2/envs/outrigger-env/bin/outrigger", line 10, in sys.exit(main()) File "/home/erpl/anaconda2/envs/outrigger-env/lib/python3.6/site-packages/outrigger/commandline.py", line 1071, in main cl = CommandLine(sys.argv[1:]) File "/home/erpl/anaconda2/envs/outrigger-env/lib/python3.6/site-packages/outrigger/commandline.py", line 344, in init self.args.func() File "/home/erpl/anaconda2/envs/outrigger-env/lib/python3.6/site-packages/outrigger/commandline.py", line 356, in psi psi.execute() File "/home/erpl/anaconda2/envs/outrigger-env/lib/python3.6/site-packages/outrigger/commandline.py", line 1020, in execute **isoform_junctions) File "/home/erpl/anaconda2/envs/outrigger-env/lib/python3.6/site-packages/outrigger/psi/compute.py", line 661, in calculate_psi uneven_coverage_multiplier, n_jobs) File "/home/erpl/anaconda2/envs/outrigger-env/lib/python3.6/site-packages/outrigger/psi/compute.py", line 600, in _maybe_parallelize_psi for event_id, event_df in grouped) File "/home/erpl/anaconda2/envs/outrigger-env/lib/python3.6/site-packages/joblib/parallel.py", line 1054, in call self.retrieve() File "/home/erpl/anaconda2/envs/outrigger-env/lib/python3.6/site-packages/joblib/parallel.py", line 933, in retrieve self._output.extend(job.get(timeout=self.timeout)) File "/home/erpl/anaconda2/envs/outrigger-env/lib/python3.6/site-packages/joblib/_parallel_backends.py", line 542, in wrap_future_result return future.result(timeout=timeout) File "/home/erpl/anaconda2/envs/outrigger-env/lib/python3.6/concurrent/futures/_base.py", line 432, in result return self.get_result() File "/home/erpl/anaconda2/envs/outrigger-env/lib/python3.6/concurrent/futures/_base.py", line 384, in get_result raise self._exception ValueError: Cannot mask with non-boolean array containing NA / NaN values

Steps to Reproduce

  1. I executed outrigger index which gave me results
  2. I tried to do outrigger psi Notably I have star output SJ.out.tab for bulk and single cells in same file.

Expected behavior: psi output

Actual behavior: ValueError: Cannot mask with non-boolean array containing NA / NaN values

Versions

command line- outrigger psi -i /home/erpl/sayak/study/STAR_defaultopt_notrimming/SJ.out_folder/outrigger_output/index/ -o /home/erpl/sayak/study/STAR_defaultopt_notrimming/SJ.out_folder/outrigger_output/ os -ubuntu 19.04