ImportError:No module named cutadapt.scripts

[GoogleCodeExporter]

Hi,

I did:

cutadapt -ab GGTCATAGCTGTTTCCTG  E020002_1_A1.1.paired.fq > 
E020002_1_A1.1.paired.nolinker.fq

But it came out this error:

Traceback (most recent call last):
  File "/home/xin/local/bin/cutadapt", line 9, in <module>
    from cutadapt.scripts import cutadapt
ImportError: No module named cutadapt.scripts

The cutadapt version is cutadapt-1.2.1

Any help is very appreciated!

Original issue reported on code.google.com by xinyang6...@gmail.com on 5 Jun 2013 at 11:12

[GoogleCodeExporter]

How did you install cutadapt? Did you run 'python setup.py install'? It seems 
that something is strange with your Python installation. Can you run cutadapt 
from within the unpacked cutadapt-1.2.1 directory? Use the command 
'bin/cutadapt' to try this.

Also, your command line should have either '-a' or '-b', but not '-ab', as you 
wrote above.

Original comment by marcel.m...@tu-dortmund.de on 5 Jun 2013 at 12:15

[GoogleCodeExporter]

Thanks a lot! I ran 'python setup.py install --prefix=~/local' to install it. 
It works now using 'bin/cutadapt' within cutadapt-1.2.1 directory.

Original comment by xinyang6...@gmail.com on 5 Jun 2013 at 1:05

[GoogleCodeExporter]

Great! I'm closing this issue then.

Original comment by marcel.m...@tu-dortmund.de on 5 Jun 2013 at 2:29

• Changed state: WontFix

[GoogleCodeExporter]

i am trying to install cutadapt on server, (in my account) but I am getting 
same error. I tried your solutions, but still getting same error.
Traceback (most recent call last):
  File "./cutadapt", line 9, in <module>
    from cutadapt.scripts import cutadapt
  File "/project/sater/softwares/cutadapt-1.4.1/cutadapt/scripts/cutadapt.py", line 74, in <module>
    from cutadapt.adapters import Adapter, ColorspaceAdapter, BACK, FRONT, PREFIX, ANYWHERE
  File "/project/sater/softwares/cutadapt-1.4.1/cutadapt/adapters.py", line 4, in <module>
    from cutadapt import align, colorspace
  File "/project/sater/softwares/cutadapt-1.4.1/cutadapt/align.py", line 225, in <module>
    from cutadapt._align import globalalign_locate, compare_prefixes
ImportError: /project/sater/softwares/cutadapt-1.4.1/cutadapt/_align.so: 
undefined symbol: PyUnicodeUCS4_DecodeUTF8

Please suggest some solution.

thank you

Original comment by vrutants...@gmail.com on 15 Jul 2014 at 10:00

[GoogleCodeExporter]

Hi, sorry for the late reply, I wasn't working the last days.

I'm copying here from an e-mail I sent to someone else about the same problem:

cutadapt comes with a pre-compiled Python extension module, and it seems your 
Python version is different from the one I used to compile the module, so you 
will need to re-compile the module.

Please try this within the cutadapt-1.4.2 (or 1.4.1) directory:

python setup.py build_ext -i

This should rebuild the module.

The next cutadapt version will handle this more gracefully.

Original comment by marcel.m...@tu-dortmund.de on 21 Jul 2014 at 12:32

[GoogleCodeExporter]

Hi, I'm having the same problem. I already install Cutadapt on my server on my 
user, I can use it without problems, the problem is when I try to make it 
accessible for others users without installing it on every user. I already try 
to put /home/my_user/.local/bin/cutadapt on /etc/environment and make a soft 
link but the same error

Traceback (most recent call last):
  File "/home/genomica/.local/bin/cutadapt", line 9, in <module>
    from cutadapt.scripts import cutadapt
ImportError: No module named cutadapt.scripts

keeps appearing on the other users. Any help will be useful, thanks

Original comment by regina.c...@gmail.com on 31 Mar 2015 at 6:55

[GoogleCodeExporter]

Hi, I think that can be solved. Python packages that were installed into the 
/home/user/.local directory are actually not meant to be shared. It is possible 
to make it work, but there is a simpler way since you seem to have root access. 
Just run the pip command as root and without the --user parameter:

sudo pip install cutadapt

This installs cutadapt into /usr/local/bin , which should make it available to 
every user. Please get back to me if it doesn’t work!

Original comment by marcel.m...@tu-dortmund.de on 31 Mar 2015 at 9:01

[GoogleCodeExporter]

[deleted comment]

[GoogleCodeExporter]

thanks that really help! I put sudo pip install --upgrade cut adapt since it 
was already install, now it works! 

Original comment by regina.c...@gmail.com on 31 Mar 2015 at 10:10

[GoogleCodeExporter]

Great! I’ll see if I can add a section about this to the documentation.

Original comment by marcel.m...@tu-dortmund.de on 1 Apr 2015 at 8:18