epic2 run error - Expected 72 from C header, got 88 from PyObject

[mbassalbioinformatics]

Hi After installing epic2, when attempting to run just a version check i get the following

/home/m/anaconda2/envs/python3_velocyto/lib/python3.7/importlib/_bootstrap.py:219: RuntimeWarning: pysam.libcalignedsegment.PileupColumn size changed, may indicate binary incompatibility. Expected 72 from C header, got 88 from PyObject
  return f(*args, **kwds)

Thoughts?

[endrebak]

I hear that a lot. I will have to ask on the bioconda issues page. Will do it tomorrow. For now a fix is to create a new environment and install epic2 there.

Or you could try conda uninstall pysam; conda uninstall epic2; conda install epic2 but that might delete more packages than you hoped to do.

[mbassalbioinformatics]

tried setting up a new env as suggested, still the same issue when attempting to run epic2. Ill wait to see what solution youre able to find from the bioconda forums. Thanks.

[mbassalbioinformatics]

Ok what seems to work is the following, rather than setting up by running the command

conda install -c bioconda epic2

setup a new environment manually install pysam and Cython then epic2

conda create -n <name> python=3
pip install pysam
pip install Cython
(may need to) pip install epic2

hope this helps.

[endrebak]

From epic2 0.0.40 and onwards, this should never be a problem. Uploading to bioconda now :)