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Re: lumpy-sv / Python

Hi Ken,

[ CCing the list since this is pretty much public]

On Tue, 12 Jan, 2021, 1:37 pm Ken Yamaguchi, <ken@knowledgesynthesis.com> wrote:
Hi Andreas and Nilesh,

If I run lumpyexpress on bullseye (with just lumpy-sv and dependencies installed), I get

    Sourcing executables from /etc/lumpy-sv/lumpyexpress.config ...

    Checking for required python modules (/usr/bin/python3)...
    Traceback (most recent call last):
      File "<string>", line 1, in <module>
    AttributeError: module 'importlib' has no attribute 'util'

Same behavior on unstable. Some searching makes me think it's related to Python 3.9, and the LUMPY README says LUMPY Express requires Python 2.7.

Thanks a lot for investigating this. However, not being a bioinformatics I do not have an idea as to what data is exactly fit for lumpy-sv to do an analysis on.

Would you mind sharing

* The (processed) data files that you're trying to run lumpyexpress on?

* The exact command that you invoked?

This will help me debug this further.

Thanks again for testing, which might have gone un-noticed otherwise.


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