deepTools : No module named cycler

Question

[mbk0asis]

Hello,

I'm getting an error message below after upgrading my system to Ubuntu 20.04 when executed 'deepTools' including 'bamCoverage', 'plotHeatmap' and etc.

Traceback (most recent call last):
  File "/usr/local/bin/plotHeatmap", line 5, in <module>
    from deeptools.plotHeatmap import main
  File "/usr/local/lib/python2.7/dist-packages/deeptools/plotHeatmap.py", line 8, in <module>
    import matplotlib
  File "/usr/local/lib/python2.7/dist-packages/matplotlib/__init__.py", line 130, in <module>
    from matplotlib.rcsetup import defaultParams, validate_backend, cycler
  File "/usr/local/lib/python2.7/dist-packages/matplotlib/rcsetup.py", line 33, in <module>
    from cycler import Cycler, cycler as ccycler
ImportError: No module named cycler

It seemed like a compatibility problem between python 2 and 3.

So I tried to completely remove 'deepTools' using pip/pip3 and install again.

But I got another error.

$ sudo pip3 uninstall deeptools    

Found existing installation: deepTools 3.3.2
Not uninstalling deeptools at /usr/lib/python3/dist-packages, outside environment /usr
Can't uninstall 'deepTools'. No files were found to uninstall.

Anyone has any idea? I'm completely lost...

Answer 1

[ATpoint]

python2.7 <=> pip3

See the issue? You have a python2 vs. python3 conflict. How did you install python3 in the first place?

[mbk0asis]

Sorry for late reply. I just upgrade Ubuntu to 20.04 which had python3 as a default interpreter, so I installed 2.7 later with apt python2. Thank you!

[ATpoint]

Python3 is fine, current deeptools in on Python3, I'd remove the python2 stuff completely and then repeat the installation as described in the deeptools manual.

[mbk0asis]

Thank you, ATpoint! It worked after removing python2 in the system.