Why is this command stopping after finding 1 motif?

[Robert Leach]

I'm somewhat baffled as to why meme is stopping after finding only 1 motif in my data.  What is it in this command that is telling it to stop after finding 1 motif?:

meme 65F.with_weights.fa -oc out4 -mod anr -minw 3 -maxw 20 -V -bfile 65B.fa.freq -dna

The message I get under the 1 motif reported is:

Stopped because requested number of motifs (1) found.

I can't figure out how it is I inadvertently requested to find only 1 motif.  What am I missing?  How do I make it search for more motifs?

I'm sure I must be doing something dumb here.  What did I do wrong?

Thanks,

Rob

[cegrant]

You need to specify the number of motifs you want MEME to find, using the '-nmotifs' option. 

Keep in mind that there are essentially an infinite number of candidate motifs in even a small set of sequences. MEME uses a greedy algorithm, so there is no guarantee that it will report motifs in order of their statistical significance. The heuristics MEME uses to guess starting points generally find good motifs pretty quickly, but it's not an guarantee. Depending on how big you input sequence data is you may want to set '-nmotifs 10' or even '-nmotifs 20' in your initial runs. You should see that the statistical significance of the reported motifs drops off pretty quickly.