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mazzalab-ieo / renovo

Clinical machine-learning based interpreter of germline mutations.
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ReNOVo implementation... ValueError: Length of values (14751) does not match length of index (14755) #1

Open se2cheeese opened 2 years ago

se2cheeese commented 2 years ago

Hello, I tried to run your tool but come up with the following error. Could you help me to solve this problem?

Thank you.

ReNOVo implementation... sys:1: DtypeWarning: Columns (8,9,13,14,35,38,41,44,47,50,53,56,59,64,65,85,86,87,88,118,119,120,121) have mixed types.Specify dtype option on import or set low_memory=False. sys:1: DtypeWarning: Columns (8,9,13,14,35,38,41,44,47,50,53,56,59,60,64,65,85,86,87,88,118,119,120,121) have mixed types.Specify dtype option on import or set low_memory=False. Traceback (most recent call last): File "./Scripts/Renovo_implementation.py", line 70, in original_input["RENOVO_Class"]=RENOVO_Class File "/gpfs/home/salee/.local/lib/python3.6/site-packages/pandas/core/frame.py", line 3044, in setitem self._set_item(key, value) File "/gpfs/home/salee/.local/lib/python3.6/site-packages/pandas/core/frame.py", line 3120, in _set_item value = self._sanitize_column(key, value) File "/gpfs/home/salee/.local/lib/python3.6/site-packages/pandas/core/frame.py", line 3768, in _sanitize_column value = sanitize_index(value, self.index) File "/gpfs/home/salee/.local/lib/python3.6/site-packages/pandas/core/internals/construction.py", line 748, in sanitize_index "Length of values " ValueError: Length of values (14751) does not match length of index (14755) DONE!

Output generated! in ./TEST/ReNOVo_output/test_ReNOVo_and_ANNOVAR_implemented.txt

removed ./TEST/temporary/... removed ./TEST/ReNOVo_output/...

Thanks for using ReNOVo!

mazzalab-ieo commented 2 years ago

Hi, sorry for the late reply. You have probably already solved the problem but I try to answer anyway. Not being able to see the input dataset I think it is a problem due to repeated genetic variants. One thing that can happen is that after the conversion of the file to avinput by annovar some lines are repeated, or there are malformatted lines. These are only hypotheses based on the reported error (the number of genetic variants processed does not correspond to the number of genetic variants given in input)

se2cheeese commented 2 years ago

Thanks for the reply. Unfortunately, I couldn't solve the problem yet. I also thought the problem might be related to duplicates, so I checked duplications before running the tool and modified my vcf file in several ways, which finally failed. Do you have any suggestions to tackle this problem?