Problem with cutadapt installation

[StephaniePi83]

Hi,
I'm trying to use cutadapt. I have python 2.7 installed;
I run :

python setup.py build_ext -i

which return :

running build_ext

and when i do, i have the following error :

/home/stephanie/Téléchargements/cutadapt-1.0/cutadapt --help
Traceback (most recent call last):
  File "/home/stephanie/Téléchargements/cutadapt-1.0/cutadapt", line 78, in <module>
    from cutadapt import align, seqio
  File "/home/stephanie/Téléchargements/cutadapt-1.0/lib/cutadapt/align.py", line 222, in <module>
    from cutadapt.calign import globalalign, globalalign_locate
ImportError: /home/stephanie/Téléchargements/cutadapt-1.0/lib/cutadapt/calign.so: wrong ELF class: ELFCLASS64

How can i solve this problem ?
Thank in advance for your help

[GenoMax]

What OS are you running and on what platform? This could be a 32-bit/64-bit library incompatibility issue.

[StephaniePi83]

I have a virtual box installed on my PC (windows 7) with ubuntu.
To answer your question :
DISTRIB_ID=Ubuntu
DISTRIB_RELEASE=11.10
DISTRIB_CODENAME=oneiric
DISTRIB_DESCRIPTION="Ubuntu 11.10"

[GenoMax]

Is it a 32-bit or 64-bit install of Ubuntu? Did you install python separately?

I wonder if you can use windows version of python and run cutadapt through that.

I have a virtual box installed on my PC (windows 7) with ubuntu.
To answer your question :
DISTRIB_ID=Ubuntu
DISTRIB_RELEASE=11.10
DISTRIB_CODENAME=oneiric
DISTRIB_DESCRIPTION="Ubuntu 11.10"

[StephaniePi83]

In fact i have ubuntu and i have python2.7 installed on it;
it's 64 bits

[GenoMax]

This may be a long shot but look at the last post in this thread: http://stackoverflow.com/questions/5...dule-named-md5

The bit about ia32 library.

[StephaniePi83]

yes i try to do

apt-get install ia32-libs

but it does'nt work ...
I think that the problem occur at the begining of the installation

python setup.py build
running build
running build_py
running build_ext
building 'cutadapt.calign' extension
gcc -pthread -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall -Wstrict-prototypes -fPIC -I/usr/include/python2.7 -c lib/cutadapt/calignmodule.c -o build/temp.linux-i686-2.7/lib/cutadapt/calignmodule.o
lib/cutadapt/calignmodule.c:23:20: erreur fatale: Python.h : Aucun fichier ou dossier de ce type
compilation terminée.
error: command 'gcc' failed with exit status 1

[GenoMax]

I think you need to install the python-dev environment.

apt-get install python-dev

[StephaniePi83]

I've done it but the problem is not fixed; i don't understand ...

[GenoMax]

What is the latest error message? Are you still getting the error with gcc?

I've done it but the problem is not fixed; i don't understand ...

[evallespin]

Hi StephaniePi83, I'm having the same problem and I'm not able to resolve it... have you got the solution now? thanks,

Elena

[StephaniePi83]

Hi Elena, i don't fixe this problem, i just run cutadapt and it work ...
Does it work for you ?

[evallespin]

Thanks for you quickly answer!

I'm able to run cutadapt, but later I have again the same problem:

[sudo] password for genmed13:
SIOCADDRT: El archivo ya existe
genmed13@genmed13-HP-Compaq-dc5800-Microtower:~$ cd Descargas/
genmed13@genmed13-HP-Compaq-dc5800-Microtower:~/Descargas$ cd cutadapt-1.0
genmed13@genmed13-HP-Compaq-dc5800-Microtower:~/Descargas/cutadapt-1.0$ ./cutadapt --help
Traceback (most recent call last):
File "./cutadapt", line 78, in <module>
from cutadapt import align, seqio
File "/home/genmed13/Descargas/cutadapt-1.0/lib/cutadapt/align.py", line 222, in <module>
from cutadapt.calign import globalalign, globalalign_locate
ImportError: /home/genmed13/Descargas/cutadapt-1.0/lib/cutadapt/calign.so: wrong ELF class: ELFCLASS64
genmed13@genmed13-HP-Compaq-dc5800-Microtower:~/Descargas/cutadapt-1.0$ python setup.py build_ext -i
running build_ext
genmed13@genmed13-HP-Compaq-dc5800-Microtower:~/Descargas/cutadapt-1.0$ ./cutadapt -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC /Escritorio/s_G1_L001_I1_001_mate1.fastq -o /Escritorio/s_G1_L001_I1_001_mate1_trimmed.fastq
Traceback (most recent call last):
File "./cutadapt", line 78, in <module>
from cutadapt import align, seqio
File "/home/genmed13/Descargas/cutadapt-1.0/lib/cutadapt/align.py", line 222, in <module>
from cutadapt.calign import globalalign, globalalign_locate
ImportError: /home/genmed13/Descargas/cutadapt-1.0/lib/cutadapt/calign.so: wrong ELF class: ELFCLASS64

[StephaniePi83]

Try with "cutadapt" without "./"

[evallespin]

(Thanks for helping me! you are the only one )

It dosen't work...

genmed13@genmed13-HP-Compaq-dc5800-Microtower:~/Descargas/cutadapt-1.0$ cutadapt -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC /Escritorio/s_G1_L001_I1_001_mate1.fastq -o /Escritorio/s_G1_L001_I1_001_mate1_trimmed.fastq
cutadapt: no se encontró la orden
genmed13@genmed13-HP-Compaq-dc5800-Microtower:~/Descargas/cutadapt-1.0$