FIMO job failed with input motifs from MEME

[zhou...@googlemail.com]

Hi guys,

The result HTML page of MEME was saved as meme.html setted as' web page, complete', later it was precossed to FIMO but the job failed and I got the following message:
'

Job Failed

---

The output from your job will be found here: http://nbcr-222.ucsd.edu/opal-jobs/appFIMO_4.9.013752749837741259394617

The following information may help your system administrator solve the problem

Message: Execution failed - process exited with value 1
Output code: 4'
'
In the link it is:

FIMO Job - Error

You may bookmark this page and return to it later.

Results

• Input Motifs
• Error Messages

Status Messages

• Parsing arguments
• Arguments ok
• Starting fimo
  fimo --oc . --verbosity 1 --bgfile db/mus_musculus.na.bfile --thresh 0.0001 meme.html db/mus_musculus.na
• fimo exited with error code 1

'
Inside of the 'Error Messages' is:'

Errors from MEME HTML parser:
MEME version is too old to be parsed by this parser.
FATAL: No motifs could be read.

'

ps: the online version of both programmes were used for the analysis.

Any help and comments are appreciated!

Best regards,
Qifeng

[James Johnson]

Your motifs look like they were generated by version 4.4.0 of the MEME Suite but the stated version in the file is 3.0.12. We've never released a version 3.0.12 and MEME certainly looked a lot different before version 4.4.0.

Prior to version 4.4.0 the HTML motifs were read by the same parser that read the text motif files however when we changed the HTML format for release 4.4.0 we also added a special parser for the HTML format and it checks that the version is 4.4.0 or larger before attempting to read the file. So the parser that should be reading the file thinks that it shouldn't because the version is too old. If you change the version to 4.4.0 then it will quite happly read the file.

To change the version number do a find and replace in the file for the text:
3.0.12
and replace it with:
4.4.0
Also note that we recommend you save MEME Suite output files as "Web Page, HTML only" as the web browser records things that have been written by Javascript which can break the page.

ps: the online version of both programmes were used for the analysis.

It looks like you ran MEME on a galaxy instance? They've stuffed up their install somehow by messing with the version number. Also the release they're running is version 4.4.0 (judging by the release date) so it is rather out of date as there have been 7 major releases since then!

[CharlesEGrant]

Hi Qifeng,

It looks like the MEME input file was generated on a local web server, not on the public MEME server at NBCR. The served named in the MEME file is:

http://liuweiguo/meme/cgi-bin/meme_request.cgi

The format of the MEME file looks roughly correct, and from a relatively current version, but the embedded version tag says that it was produced by MEME version 3.0.12 which would have been from almost 10  years ago! If you are using a locally modified version of the MEME tools you may run into problems if you try to process the output files on the public server. In this case I was able to get FIMO to accept the MEME input file simply by setting the version number to 4.9.0. In your MEME files I changed the line

<input name="version" value="MEME version 3.0.12" type="hidden">

to 

<input name="version" value="MEME version 4.9.0" type="hidden">

I also noticed that that the motifs in the input files seem to be simple repeats. Is this what you are looking for? You may need to run RepeatMaker (http://www.repeatmasker.org) on your sequences before running MEME.

[zhou...@googlemail.com]

Hi James and Charles,

Sorry for the delay. There is a mistake in the phrase, the MEME output was from completemotif, a webserver with MEME installed. As you two pointed out, the problem was the old version of MEME didn't match the new FIMO. I used MEME and FIMO at NCBR then it was fine.

Charles, thanks for the Repeatmasker, I will try it and see.

Best regards,
Qifeng