Error ELFCLASS64

[GoogleCodeExporter]

Hello, I'm really struggling with Cutadapt... I don't know how to continue with 
this error:

[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

What can I do?

Thanks...

Original issue reported on code.google.com by evalles...@gmail.com on 9 Jul 2012 at 11:41

[GoogleCodeExporter]

Please try to delete the calign.so file and re-run the build_ext command line.

Original comment by marcel.m...@tu-dortmund.de on 9 Jul 2012 at 1:33

[GoogleCodeExporter]

Done... but...

genmed13@genmed13:~/cutadapt-1.0$ ./cutadapt -a 
AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC /Desktop/FastqFiles/s_G1_L001_I1_001.fastq 
-o /Desktop/FastqFiles/s_G1_L001_I1_001_trimmed.fastq 
Traceback (most recent call last):
  File "./cutadapt", line 78, in <module>
    from cutadapt import align, seqio
  File "/home/genmed13/cutadapt-1.0/lib/cutadapt/align.py", line 222, in <module>
    from cutadapt.calign import globalalign, globalalign_locate
ImportError: No module named calign

Thanks!

Original comment by evalles...@gmail.com on 10 Jul 2012 at 10:26

[GoogleCodeExporter]

Sorry, you said and re-run the build_ext command line...

genmed13@genmed13:~/cutadapt-1.0$ python setup.py build_ext -irunning build_ext
building 'cutadapt.calign' extension
creating build
creating build/temp.linux-i686-2.7
creating build/temp.linux-i686-2.7/lib
creating build/temp.linux-i686-2.7/lib/cutadapt
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: fatal error: Python.h: No such file or 
directory
compilation terminated.
error: command 'gcc' failed with exit status 1

Original comment by evalles...@gmail.com on 10 Jul 2012 at 10:31

[GoogleCodeExporter]

Please see here:
http://code.google.com/p/cutadapt/wiki/documentation#gcc_failed_with_exit_status
_1

In short: Install the python-dev package.

I'll add this to the README as well (the FAQ is quite well hidden I admit).

Original comment by marcel.m...@tu-dortmund.de on 10 Jul 2012 at 11:44

[GoogleCodeExporter]

I've fixed it! thanks!!

Original comment by evalles...@gmail.com on 11 Jul 2012 at 8:47

[GoogleCodeExporter]

Glad I could help :-)

Original comment by marcel.m...@tu-dortmund.de on 11 Jul 2012 at 10:26

• Changed state: Done