Skip to content
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.

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 configuring cutadapt #404

Closed
gdaniella opened this issue Sep 25, 2019 · 3 comments

Comments

@gdaniella
Copy link

@gdaniella gdaniella commented Sep 25, 2019

Hi,
A little new to this. Have been trying to follow DADA2's ITS pipeline which requires cutadapt. Have installed python (v3.7.4), and used pip to install cutadapt (v2.5):
pip install cutadapt
received the following:

Collecting cutadapt
Requirement already satisfied: xopen~=0.8.1 in c:\users\mine\appdata\local\programs\python\python37\lib\site-packages (from cutadapt) (0.8.2)
Requirement already satisfied: dnaio~=0.3.0 in c:\users\mine\appdata\local\programs\python\python37\lib\site-packages (from cutadapt) (0.3)
Installing collected packages: cutadapt
Successfully installed cutadapt-2.5

However, when typing cutadapt on the cmd, getting this massage:
Traceback (most recent call last): File "c:\users\mine\appdata\local\programs\python\python37\lib\runpy.py", line 193, in _run_module_as_main "__main__", mod_spec) File "c:\users\mine\appdata\local\programs\python\python37\lib\runpy.py", line 85, in _run_code exec(code, run_globals) File "C:\Users\mine\AppData\Local\Programs\Python\Python37\Scripts\cutadapt.exe\__main__.py", line 5, in <module> File "c:\users\mine\appdata\local\programs\python\python37\lib\site-packages\cutadapt\__main__.py", line 71, in <module> from cutadapt.report import full_report, minimal_report File "c:\users\mine\appdata\local\programs\python\python37\lib\site-packages\cutadapt\report.py", line 10, in <module> from .filters import (NoFilter, PairedNoFilter, TooShortReadFilter, TooLongReadFilter, File "c:\users\mine\appdata\local\programs\python\python37\lib\site-packages\cutadapt\filters.py", line 21, in <module> from .utils import raise_open_files_limit File "c:\users\mine\appdata\local\programs\python\python37\lib\site-packages\cutadapt\utils.py", line 4, in <module> import resource ModuleNotFoundError: No module named 'resource'
Expected to get a list of arguments, general info, etc.
And when running DADA2 pipeline R cannot call on cutadapt and no output is produced.

Thanks so much for your help

@marcelm

This comment has been minimized.

Copy link
Owner

@marcelm marcelm commented Sep 25, 2019

Indeed, it appears as if he resource module is not available on Windows. I don’t test Cutadapt on Windows, so haven’t noticed this.

I can fix this so that the module is not used on Windows. Until then, you can just use Cutadapt 2.4 instead. It doesn’t need the resource module.

@marcelm marcelm closed this in 012caad Sep 25, 2019
@marcelm

This comment has been minimized.

Copy link
Owner

@marcelm marcelm commented Sep 26, 2019

I’ve fixed the problem now.

@marcelm

This comment has been minimized.

Copy link
Owner

@marcelm marcelm commented Sep 29, 2019

And for others finding this issue: Use pip install cutadapt==2.4 to get version 2.4.

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Projects
None yet
2 participants
You can’t perform that action at this time.