ReNOVo implementation... ValueError: Length of values (14751) does not match length of index (14755)

[se2cheeese]

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]

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]

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?