option -p is not working MEME

[j.blan...@gmail.com]

Hello,
I use MEME like this :

meme seq.fa -mod anr -dna -nmotifs 5 -maxsize 10000000 -p 7

And it leads to the meme help. But without the -p option, it runs correctly.
What's wrong?
Thanks

[CharlesEGrant]

That would indicate that you don't have MPI installed on you system. Using the parallel version of MEME requires that you've installed a compatible MPI library. Check the section "Parallel MEME" in the MEME Suite installation guide for more information. Once you've installed a compatible MPI library you'll need to rebuild and reinstall the MEME Suite. 

[James Johnson]

Are you running version 4.10.0?

By "leads to the meme help" do you mean it prints something like:

error at: -p
 USAGE:
    meme    <dataset> [optional arguments]

    <dataset>         file containing sequences in FASTA format
    [-h]            print this message
    [-o <output dir>]    name of directory for output files

Or it prints something like:

 -p <np> given but Parallel MEME not configured. Refer to doc/install.html.

 
So far I get the second error if I don't configure MPI properly.

[CharlesEGrant]

I just noticed that your job has '-maxsize 10000000'.  I'm not sure if you actually want to run MEME on a file that big, or if you just chose a large round number, but be aware that running MEME on a 10Mb sequence file would probably take a couple of years, even with 7 processors. You may find this post helpful: MEME: Dataset size and run time issues. If you sequence file is highly redundant, like ChIP-Seq data, you may want to use MEME-ChIP instead.