problem installing cutadapt

Question

[Javad]

Dear all,

I have difficulty installing cutadapt on my system. After installing cutadapt with pip3 install --user --upgrade cutadapt and running cutadapt --version, I get the following error that don't know how to address it.

Traceback (most recent call last):
  File "./cutadapt", line 5, in <module>
    from cutadapt.__main__ import main
ModuleNotFoundError: No module named 'cutadapt.__main__'

Installing with conda leads to the same type of error. Any idea is highly appreciated.

Thanks in advance.

[ATpoint]

Output of python --version?

[Javad]

Hi.

Python 3.7.4

[ATpoint]

Hmm, if you install with a package manager you should not need to use ./ at all. Can you simply type cutadapt and which cutadapt?

[Ido Tamir]

start using conda, it helps a bit: https://bioconda.github.io/user/install.html#install-conda

[Javad]

Hi, As I said above, conda doesn't help. It leads to the same error.

[Ido Tamir]

sorry, did not read, but that is very wierd. Did you use a new conda environment? did you activate the new environment? look at $PATH, $PYTHONPATH , which cutadapt if there are discrepancies that would explain the problem. i.e. which version does get picked up

[Asaf]

You should initiate a new virtual environment in python, activate it and install with pip