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CNVKIT import errors

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
• 5,764 views • link
updated by GenoMax GenoMax • written by alons alons

Try to install using virtualenv and pip, currently (2018-01-22) PyPI hosts the same version as the GitHub repository.

• 0 views • link
written by h.mon h.mon

` 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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updated by WouterDeCoster WouterDeCoster • written by rashi.naresh • rashi.naresh

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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written by julian.dangelo • julian.dangelo

hi all i am having similar errors with installation of cnvkit (for mac)...and cannot seem to figure it out...would anyone kindly please help?

base) torunp01@LEVIND19-I27R5K test % make
python3 ../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 4, in <module>
    from cnvlib import commands
  File "/Users/torunp01/opt/miniconda3/gatk/cnvkit/cnvlib/__init__.py", line 1, in <module>
    from skgenome.tabio import write
  File "/Users/torunp01/opt/miniconda3/gatk/cnvkit/skgenome/__init__.py", line 1, in <module>
    from . import tabio
  File "/Users/torunp01/opt/miniconda3/gatk/cnvkit/skgenome/tabio/__init__.py", line 10, in <module>
    import pandas as pd
ModuleNotFoundError: No module named 'pandas'
make: *** [build/reference-picard.cnn] Error 1
• 0 views • link
updated by GenoMax GenoMax • written by ptoru001 • ptoru001

2 answers

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

• 0 views • link
written by Eric T. Eric T.

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

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written by alons alons

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

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written by WouterDeCoster WouterDeCoster

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

• 0 views • link
written by julian.dangelo • julian.dangelo

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.

• 0 views • link
written by WouterDeCoster WouterDeCoster

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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written by alons alons

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