subprocess.CalledProcessError when segmenting about cnvkit HOT 4 OPEN

Are there any blank fields in your .cnr file? Which columns do they occur in?

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Hi, thank you for replying. My cnr have NAs in weight columns. You can find the file here

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Hi @sainsachiko, after spending hours trying to debug the same issue, I was able to get it to run. Theres's some issue with the R env that DNACopy needs to run segmentation. so you'll have to run CNVkit from within an environment. I kept running into a compatibility issue with Conda until I used the yaml file on the repo to make it.

There are two ways you get CNVkit to run - i) Using the docker image and running everything in that container ii) Build a Conda env with the yaml file (NOTE - This yaml will work on Mac OS only, further I am on an Apple Silicon M2 chip, so that could further nuance the dependency list).

name: cnvkit
channels:
    - conda-forge
    - bioconda
    - defaults
dependencies:
    - python>=3.8
    - biopython >=1.80
    - matplotlib >=3.5.2
    - numpy >=1.24.2
    - pandas >=1.5.3
    - pyfaidx >=0.7.1
    - pytest
    - reportlab >=3.6.12
    - ruff
    - scikit-learn >=1.1.0
    - scipy >=1.10.1
    - tox

Once set up, don't forget to pip install CNVkit!

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@Sanat-Mishra

I am using the Docker image but still get the same error.

@etal

In my .cnr file, the weights column are empty for antitarget regions.

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