Dreme always crashing

[DJEKIDEL MOHAMED NADHIR]

Hello everybody,

I am running the meme-chip tool and it always crashes at the end of the execution of dreme, with the following error message

dreme -v 1 -oc E-GEOD-33664.processed.1/LongCenteredPETs/GSM832461_IHH025T_hg19_memechip/dreme_out -p E-GEOD-33664.processed.1/LongCenteredPETs/GSM832461_IHH025T_hg19_memechip/seqs-centere$

Traceback (most recent call last):

  File "/data/home/nadhir/Packages/MEME_suite/meme_4.9.0/bin/dreme", line 1921, in <module>

    if __name__ == '__main__': main()

  File "/data/home/nadhir/Packages/MEME_suite/meme_4.9.0/bin/dreme", line 1873, in main

    given_only)

  File "/data/home/nadhir/Packages/MEME_suite/meme_4.9.0/bin/dreme", line 1218, in find_print

    minw, maxw, ethresh, log_add_pthresh, given_only)

  File "/data/home/nadhir/Packages/MEME_suite/meme_4.9.0/bin/dreme", line 335, in output_best_re

    logo_out.output_logo(pwm, motif_num, best_re, False)

  File "/data/home/nadhir/Packages/MEME_suite/meme_4.9.0/bin/dreme", line 200, in output_logo

    png_maker = subprocess.Popen(args)

  File "/data/software/Python/Python-2.7.3/lib/python2.7/subprocess.py", line 679, in __init__

    errread, errwrite)

  File "/data/software/Python/Python-2.7.3/lib/python2.7/subprocess.py", line 1249, in _execute_child

    raise child_exception

OSError: [Errno 2] No such file or directory

the error comes after running for a long-time 

Thanks in advance

[James Johnson]

I think the error message means that it couldn't run GhostScript. You can probably fix it by installing GhostScript or ImageMagick (which includes GhostScript) and then reconfiguring/installing the MEME Suite install.

1. Install Ghostscript
2. Change to MEME Suite distribution directory
   
3. make clean
4. ./configure your_ parameters_here
5. make
6. make install
   

It looks like DREME is failing when it tries to create the motif logos in portable network graphic (PNG) format. Internally the logos are generated in Encapsulated Postscript format and then the external program ghostscript is called to do the conversion. When I wrote that bit of code I intended it to print "Failed to create PNG file. Have you got ghostscript installed?" but it seems that I got something wrong. I will see that the bug is fixed for the next release.