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kylessmith / SomVarIUS

Somatic variant identification from unpaired samples
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IndexError: list index out of range #6

Open Varunachander opened 5 years ago

Varunachander commented 5 years ago

Hi, I encountered an issue using Somvarius:

storing chromosome/dbsnp intersection in memory... Traceback (most recent call last): File "/hgsccl/next-gen/scratch/chander/software/bin/SomVarIUS", line 4, in import('pkg_resources').run_script('SomVarIUS==1.2', 'SomVarIUS') File "build/bdist.linux-x86_64/egg/pkg_resources.py", line 517, in run_script File "build/bdist.linux-x86_64/egg/pkg_resources.py", line 1430, in run_script File "/hgsccl/next-gen/scratch/chander/software/lib/python2.7/site-packages/SomVarIUS-1.2-py2.7-linux-x86_64.egg/EGG-INFO/scripts/SomVarIUS", line 265, in

File "/hgsccl/next-gen/scratch/chander/software/lib/python2.7/site-packages/SomVarIUS-1.2-py2.7-linux-x86_64.egg/EGG-INFO/scripts/SomVarIUS", line 196, in get_mutations

File "SomVarIUS_calling.pyx", line 597, in write_mutations (SomVarIUS/SomVarIUS_calling.c:11842) File "SomVarIUS_calling.pyx", line 328, in SomVarIUS_calling.filter_regions (SomVarIUS/SomVarIUS_calling.c:7614) IndexError: list index out of range

Any thoughts what is going on? Best, Varuna

pllittle commented 4 years ago

Hi,

I didn't have trouble running somvarius without CNV input, but when I did run it with CNV input, I received the following error in the log output.

Traceback (most recent call last): File "/opt/conda/bin/SomVarIUS", line 4, in import('pkg_resources').run_script('SomVarIUS==1.2', 'SomVarIUS') File "/opt/conda/lib/python2.7/site-packages/pkg_resources/init.py", line 666, in run_script self.require(requires)[0].run_script(script_name, ns) File "/opt/conda/lib/python2.7/site-packages/pkg_resources/init.py", line 1469, in run_script exec(script_code, namespace, namespace) File "/opt/conda/lib/python2.7/site-packages/SomVarIUS-1.2-py2.7-linux-x86_64.egg/EGG-INFO/scripts/SomVarIUS", line 265, in

File "/opt/conda/lib/python2.7/site-packages/SomVarIUS-1.2-py2.7-linux-x86_64.egg/EGG-INFO/scripts/SomVarIUS", line 196, in get_mutations

File "SomVarIUS/SomVarIUS_calling.pyx", line 586, in write_mutations IndexError: list index out of range

Best, Paul