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problem with configuring cutadapt #404

gdaniella opened this issue Sep 25, 2019 · 3 comments


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@gdaniella gdaniella commented Sep 25, 2019

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\", line 193, in _run_module_as_main "__main__", mod_spec) File "c:\users\mine\appdata\local\programs\python\python37\lib\", line 85, in _run_code exec(code, run_globals) File "C:\Users\mine\AppData\Local\Programs\Python\Python37\Scripts\cutadapt.exe\", line 5, in <module> File "c:\users\mine\appdata\local\programs\python\python37\lib\site-packages\cutadapt\", line 71, in <module> from import full_report, minimal_report File "c:\users\mine\appdata\local\programs\python\python37\lib\site-packages\cutadapt\", line 10, in <module> from .filters import (NoFilter, PairedNoFilter, TooShortReadFilter, TooLongReadFilter, File "c:\users\mine\appdata\local\programs\python\python37\lib\site-packages\cutadapt\", line 21, in <module> from .utils import raise_open_files_limit File "c:\users\mine\appdata\local\programs\python\python37\lib\site-packages\cutadapt\", 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


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@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

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@marcelm marcelm commented Sep 26, 2019

I’ve fixed the problem now.


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@marcelm marcelm commented Sep 29, 2019

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

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