'make test' fails in DREME

[CharlesEGrant]

Several users have reported that 'make test' and 'make check' fail during the test of DREME. The error reported is 

Quote:

dreme -norc -oc results/dreme -v 1 -noxslt -p Klf1-200-100.s &>> $all_messages  File "/meme/scripts/dreme", line 176  with open(eps_file, 'w') as eps_fh:  ^  SyntaxError: invalid syntax

This error indicates that the version of Python found by MEME is not recent enough for use with the MEME Suite. As noted in the installation guide, MEME requires either Python 2.6 or 2.7. This message indicates that the local version of Python is 2.5 or older. 

You'll need to install 2.6 or 2.7 version of python, and re-run 'configure', 'make', and 'make install'. 

Note that by default, MEME will try to use the first version of Python that it finds in your execution PATH. If you have multiple versions of Python on your system you can specify which one MEME should use using the '--with-python=<path to python>' option to the configure script.

[James Johnson]

Can you post some more information like the contents of the config.log file generated by configure?

[Laura Sloofman]

James, 

I got a similar error for fasta-dinucleotide-shuffle test:

esting fasta-center . . .

  fasta-center -len 100 < Klf1-200.s 1> results/fasta-center1/fasta-center_Oi6f9_stdout 2> $error_messages

  SUCCESS

  *******************************************************************************

  Testing fasta-dinucleotide-shuffle . . .

  fasta-dinucleotide-shuffle -f Klf1-200-100.s -t -dinuc 1> results/fasta-dinucleotide-shuffle1/fasta-dinucleotide-shuffle_4njKL_stdout 2> $error_messages

  Traceback (most recent call last):

    File "/home/sinhas/sloofma2/software/meme_4.10.0/scripts/fasta-dinucleotide-shuffle", line 6, in ?

      import sequence

    File "/home/sinhas/sloofma2/software/meme_4.10.0/scripts/sequence.py", line 660

      with open(template_file, 'r') as template_fh:

              ^

  SyntaxError: invalid syntax

  -------------------------------------------------------------------------------

  fasta-dinucleotide-shuffle exited with value 1 indicating failure.

  FAIL

[CharlesEGrant]

Hi Laura,

Have you checked that your version of Python is 2.6 or 2.7? You can check the version by running the command

python --version

If it turns out that the version of Python you are running is 2.6 or 2.7 could you attach a copy of the config.log file?

[Hima vyshnavi.a.]

Hi charles,
                 Even i had the same problem and i have the python version 2.7 installed in my linux system. And how can i run a file in meme?

[CharlesEGrant]

Hi Hima,

Could you upload a copy of the 'config.log' file from the root directory of your MEME Suite distribution directory? That would help us diagnose the problem.

Could you also try running the following three commands and forward us the results:

which dreme

which python

python --version