I installed cutadapt first using sudo apt install cutadapt, but it gave an old version (version 2.8). I then used pip to install cutadapt thinking it would also just upgrade what I already had. python3 -m pip install --user --upgrade cutadapt This installed the latest version (4.9).

Now the problem is, when I typed cutadapt --version it was showing me version 2.8. So I figured pip just installed it differently and I deleted the sudo apt install using sudo apt remove cutadapt.

But when I type cutadapt --version it is giving me an error now:

-bash: /usr/bin/cutadapt: No such file or directory

But if I type which cutadapt it shows:

/home/chauk/.local/bin/cutadapt

So there are two paths for cutadapt and I have no idea how to fix this as I thought removing the first install with sudo would have corrected it.