Don't know how to handle unstranded transcript

[lydiayliu]

  
  Command exit status:
    1
  
  Command output:
    [ 2022-10-21 01:52:55 ] moPepGen callVariant started
    [ 2022-10-21 01:54:48 ] Reference indices loaded.
    [ 2022-10-21 01:54:48 ] Using GVF file: ACH-000005_mutation_VEP.gvf
    [ 2022-10-21 01:54:48 ] Using GVF file: ACH-000005_fusion_STARFusion.gvf
    [ 2022-10-21 01:54:48 ] Variants sorted
  
  Command error:
    2022-10-21 01:54:51,471     INFO worker.py:1518 -- Started a local Ray instance.
    Traceback (most recent call last):
      File "/usr/local/bin/moPepGen", line 8, in <module>
        sys.exit(main())
      File "/usr/local/lib/python3.8/site-packages/moPepGen/cli/__main__.py", line 89, in main
        args.func(args)
      File "/usr/local/lib/python3.8/site-packages/moPepGen/cli/call_variant_peptide.py", line 351, in call_variant_peptide
        results = ray.get([wrapper_remote.remote(d) for d in dispatches])
      File "/usr/local/lib/python3.8/site-packages/ray/_private/client_mode_hook.py", line 105, in wrapper
        return func(*args, **kwargs)
      File "/usr/local/lib/python3.8/site-packages/ray/_private/worker.py", line 2275, in get
        raise value.as_instanceof_cause()
    ray.exceptions.RayTaskError(ValueError): ray::wrapper_remote() (pid=2016, ip=172.17.0.3)
      File "/usr/local/lib/python3.8/site-packages/moPepGen/cli/call_variant_peptide.py", line 248, in wrapper_remote
        return call_variant_peptides_wrapper(*dispatch)
      File "/usr/local/lib/python3.8/site-packages/moPepGen/cli/call_variant_peptide.py", line 201, in call_variant_peptides_wrapper
        donor_breakpoint_genomic = reference_data.anno.coordinate_transcript_to_genomic(
      File "/usr/local/lib/python3.8/site-packages/moPepGen/gtf/GenomicAnnotation.py", line 230, in coordinate_transcript_to_genomic
        raise ValueError("Don't know how to handle unstranded transcript.")
    ValueError: Don't know how to handle unstranded transcript.
  
  Work dir:
    work/5b/f45d0bb4042ceedc096c9419dc6420
  
  Tip: view the complete command output by changing to the process work dir and entering the command `cat .command.out`
  

The meta pipeline workdir is here: /hot/project/method/AlgorithmDevelopment/ALGO-000074-moPepGen/CCLE/processed/noncanonical-database/call-nonCanonicalPeptide/work/ec/65d49c722d22150b20235322bfdea0

But unfortunately the actual scratch is on the worker node