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a-slide / pycoQC

pycoQC computes metrics and generates Interactive QC plots from the sequencing summary report generated by Oxford Nanopore technologies basecaller (Albacore/Guppy)
https://a-slide.github.io/pycoQC/
GNU General Public License v3.0
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No module named 'pysam.libchtslib #116

Closed ganiatgithub closed 4 years ago

ganiatgithub commented 4 years ago

Describe the bug Hi, I just started to work with pycoQC, I run into the error of "No module named 'pysam.libchtslib" when running pycoQC in jupyter notebook.

To Reproduce

conda create -n pycoQC python=3.6 conda activate pycoQC pip install pycoQC pip3 install notebook jupyter notebook

Screenshots

Screen Shot 2020-05-05 at 9 58 40 pm

Desktop (please complete the following information):

Additional context I did confirm that the package libchtslib is present at the system path that I feed to jupyter:

(pycoQC) uqgni1-7329:pysam uqgni1$ ls /opt/anaconda3/envs/pycoQC/lib/python3.6/site-packages/pysam | grep "libchtslib" libchtslib.cpython-36m-darwin.so libchtslib.pxd

Any tips on trouble shooting?

Thank you!

a-slide commented 4 years ago

Hi @ganiatgithub I am not sure I can do anything about that, it seems to be a pysam library issue. Can you tell me which version of pysam is installed in your environment ?

import pysam
pysam.__version__

Thanks

ganiatgithub commented 4 years ago

Hi, it is 0.15.3

ganiatgithub commented 4 years ago

As a matter of fact, I worked it out in command line, so you may close this now :)

a-slide commented 4 years ago

Great thanks