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dry-run / annotation-only run of clinvar VCF crashes at peddy #236

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alkc opened this issue Oct 1, 2024 · 0 comments
Open

dry-run / annotation-only run of clinvar VCF crashes at peddy #236

alkc opened this issue Oct 1, 2024 · 0 comments

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@alkc
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alkc commented Oct 1, 2024

with the following error, as mentioned by Viktor:

Traceback (most recent call last):                                                                  
  File "/opt/conda/envs/py3-env/lib/python3.7/runpy.py", line 193, in _run_module_as_main           
    "__main__", mod_spec)                                                                           
  File "/opt/conda/envs/py3-env/lib/python3.7/runpy.py", line 85, in _run_code                      
    exec(code, run_globals)                                                                         
  File "/opt/conda/envs/py3-env/lib/python3.7/site-packages/peddy/__main__.py", line 14, in <module>
    sys.exit(cli())                                                                                 
  File "/opt/conda/envs/py3-env/lib/python3.7/site-packages/click/core.py", line 829, in __call__   
    return self.main(*args, **kwargs)                                                               
  File "/opt/conda/envs/py3-env/lib/python3.7/site-packages/click/core.py", line 782, in main       
    rv = self.invoke(ctx)                                                                           
  File "/opt/conda/envs/py3-env/lib/python3.7/site-packages/click/core.py", line 1066, in invoke    
    return ctx.invoke(self.callback, **ctx.params)                                                  
  File "/opt/conda/envs/py3-env/lib/python3.7/site-packages/click/core.py", line 610, in invoke     
    return callback(*args, **kwargs)                                                                
  File "/opt/conda/envs/py3-env/lib/python3.7/site-packages/peddy/cli.py", line 209, in peddy       
    in ("ped_check", "het_check", "sex_check")]):                                                   
  File "/opt/conda/envs/py3-env/lib/python3.7/site-packages/peddy/cli.py", line 43, in run          
    prefix=prefix, **kwargs)                                                                        
  File "/opt/conda/envs/py3-env/lib/python3.7/site-packages/peddy/peddy.py", line 866, in het_check 
    sites, min_depth=min_depth)                                                                     
  File "cyvcf2/cyvcf2.pyx", line 76, in cyvcf2.cyvcf2.par_het                                       
  File "cyvcf2/cyvcf2.pyx", line 743, in cyvcf2.cyvcf2.VCF._finish_het                              
IndexError: index 0 is out of bounds for axis 0 with size 0                                         

the interesting part of the pipeline run has completed at this point, would just be nice to have a cleaner finish for dry runs.

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