CNVKIT import errors
2
1
Entering edit mode
3.8 years ago
alons ▴ 270

Hi all,

I'm trying to run CNVkit (from source, in linux) after following the installation instructions on the github page but running into import errors which seem to be rare as I couldn't find any references online:

Traceback (most recent call last):
  File "cnvkit.py", line 8, in <module>
    from cnvlib import commands
  File "/home/alon/Desktop/BioinformaticsPrograms/cnvkit/cnvlib/__init__.py", line 4, in <module>
    from .cmdutil import read_cna as read
  File "/home/alon/Desktop/BioinformaticsPrograms/cnvkit/cnvlib/cmdutil.py", line 9, in <module>
    from .cnary import CopyNumArray as CNA
  File "/home/alon/Desktop/BioinformaticsPrograms/cnvkit/cnvlib/cnary.py", line 14, in <module>
    from .segmetrics import segment_mean
ImportError: No module named segmetrics

Will greatly appreciate any help!

Alon

cnvkit cnv python linux • 2.2k views
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1
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Try to install using virtualenv and pip, currently (2018-01-22) PyPI hosts the same version as the GitHub repository.

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1
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` I have the sane error:

python ../cnvkit.py import-picard picard/p2-20_5.antitargetcoverage.csv picard/p2-20_5.targetcoverage.csv picard/p2-5_5.antitargetcoverage.csv picard/p2-5_5.targetcoverage.csv picard/p2-9_5.antitargetcoverage.csv picard/p2-9_5.targetcoverage.csv -d build/
Traceback (most recent call last):
  File "../cnvkit.py", line 8, in <module>
    from cnvlib import commands
  File "/Users/rashinaresh/cnvkit/cnvlib/__init__.py", line 4, in <module>
    from .cmdutil import read_cna as read
  File "/Users/rashinaresh/cnvkit/cnvlib/cmdutil.py", line 9, in <module>
    from .cnary import CopyNumArray as CNA
  File "/Users/rashinaresh/cnvkit/cnvlib/cnary.py", line 14, in <module>
    from .segmetrics import segment_mean
ModuleNotFoundError: No module named 'cnvlib.segmetrics'
make: *** [build/reference-picard.cnn] Error 1 `
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1
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Having the same issue as you both. Please post solution if anyone of you figure it out (I will as well).

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2
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3.8 years ago
Eric T. ★ 2.7k

This is fixed now. Sorry for the trouble, I forgot to check in a new file while refactoring.

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0
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Great! Thank you. Seems to be working now, running it.

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2
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3.8 years ago

Try the installation with conda. That's likely to solve many of your installation-related issues for many tools.

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1
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After removing all of the cnvkit files associated with the download via pip, I installed conda and used conda to get the cnvkit.py script which then worked fine. Seems that ONLY the conda method of installation works properly.

Thank you for the suggestion WouterDeCoster

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1
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Conda is going to change how you do your installations. Always try conda first, rather than building stuff manually.

I have moved my comment so you can mark is as 'accepted' and mark this question as solved.

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0
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I would but I think the developer of CNVkit (Eric T.) would want to see this first, get his input on it, might be a potential bug. He's pretty active in this forum.

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