Version 1.5.19 crashing

[tzhughes]

Hi @moonso

Did what you recommend which was to get the latest version but now getting the following error "UnboundLocalError: local variable 'variant_chrom' referenced before assignment" when running the latest version.

I got the latest version by:

• download zip file of master branch
• unzip and cd into dir
• python setup.py install -f
• check

> genmod --version
genmode version: 1.5.19

• running code below

genmod annotate --family_file /Volumes/jbod/proj_alex/repoAlex/fam/alexander.fam --family_type ped --vep --outfile alexander.variantsOnly.ug.vqsrAndHard.SNPEFFtopImpact.vepAllAndTopImpacts.genmod.vcf ../../010_alignments/alexander.variantsOnly.ug.vqsrAndHard.SNPEFFtopImpact.vepAllAndTopImpacts.vcf

Traceback (most recent call last):
  File "/Library/Frameworks/Python.framework/Versions/2.7/bin/genmod", line 5, in <module>
    pkg_resources.run_script('genmod==1.5.19', 'genmod')
  File "build/bdist.macosx-10.6-intel/egg/pkg_resources.py", line 492, in run_script
  File "build/bdist.macosx-10.6-intel/egg/pkg_resources.py", line 1350, in run_script
  File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/genmod-1.5.19-py2.7.egg/EGG-INFO/scripts/genmod", line 556, in <module>
    run_genmod()
  File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/click-3.3-py2.7.egg/click/core.py", line 610, in __call__
    return self.main(*args, **kwargs)
  File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/click-3.3-py2.7.egg/click/core.py", line 590, in main
    rv = self.invoke(ctx)
  File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/click-3.3-py2.7.egg/click/core.py", line 936, in invoke
    return _process_result(sub_ctx.command.invoke(sub_ctx))
  File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/click-3.3-py2.7.egg/click/core.py", line 782, in invoke
    return ctx.invoke(self.callback, **ctx.params)
  File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/click-3.3-py2.7.egg/click/core.py", line 416, in invoke
    return callback(*args, **kwargs)
  File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/click-3.3-py2.7.egg/click/decorators.py", line 64, in new_func
    return ctx.invoke(f, obj, *args[1:], **kwargs)
  File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/click-3.3-py2.7.egg/click/core.py", line 416, in invoke
    return callback(*args, **kwargs)
  File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/genmod-1.5.19-py2.7.egg/EGG-INFO/scripts/genmod", line 415, in annotate
    var_annotator.annotate()
  File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/genmod-1.5.19-py2.7.egg/genmod/variant_annotator.py", line 95, in annotate
    self.annotate_variant(variant)
  File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/genmod-1.5.19-py2.7.egg/genmod/variant_annotator.py", line 266, in annotate_variant
    if len(self.exon_trees[variant_chrom].find_range(variant_interval)):
UnboundLocalError: local variable 'variant_chrom' referenced before assignment
Process VariantPrinter-33:
Traceback (most recent call last):
  File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/multiprocessing/process.py", line 258, in _bootstrap
    self.run()
  File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/genmod-1.5.19-py2.7.egg/genmod/variant_printer.py", line 42, in run
    next_result = self.task_queue.get()
  File "<string>", line 2, in get
  File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/multiprocessing/managers.py", line 759, in _callmethod
    kind, result = conn.recv()
EOFError

[moonso]

Ok I think this one has to do with the vep option. Will have a look at it tomorrow.

[moonso]

Fixed the problem with vep annotation. Solved in version 1.5.20