Troubleshooting

Troubleshooting

Since SV² uses Cython, error messages may be cryptic. A Segmentation Fault typically indicates the input files are not formatted correctly.

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Pip install error

MemoryError

Solution:

$ pip install --no-cache-dir https://github.com/dantaki/SV2/releases/download/sv2v1.4.0/sv2-1.4.0.tar.gz

ImportError: No module named Cython.Build

Solution: reinstall cython

$ pip install cython --upgrade
$ pip install sv2

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Versions < 1.4.0 genotyping error

UserWarning: Trying to unpickle estimator SVC from version pre-0.18 when using version 0.18.1. This might lead to breaking code or invalid results. Use at your own risk.

Solution:

Install scikit-learn v0.17 pip install scikit-learn==0.17

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For any bugs or errors in SV² please contact Danny Antaki dantaki@ucsd.edu