New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Problem with fivepseq install #1

Open

Markestine opened this issue Dec 14, 2021 · 1 comment

Markestine commented Dec 14, 2021

Hi,
I try to install fivepseq1.0 with pip3 and python3.8.
I followed the instructions in the README and everything is fine.

But when I test my installation, I have this error
AttributeError: module 'pysam.libcalignmentfile' has no attribute 'PileupColumn'

Do you have any suggestions to fix this trouble?

Thanks in advance,
fivepseq_error.txt

janoppelt commented Jul 31, 2023 •

edited

Loading

It may be related to the version of pysam you installed. You want to have pysam version less than 0.17.0. See this related comment from cgat.

Something like this could work:

pip3 install  --force-reinstall "pysam<0.17.0"
pip3 install  --force-reinstall plastid

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment