AME "--control" option not consistent

[guipe...@gmail.com]

I have a question about AME usage. I use the newest release of MEME(meme_4.10.0_4.tar.gz). I found that the newest version of AME doesn't accept the "--control" option while the online version does. The info at http://meme.nbcr.net/meme/doc/ame.html is not consistent with the help message of ame tool. How can I configure the parameters to use a collection of control sequences? 

The job details from MEME server is as below.  

"Status Messages 

.     Parsing arguments 

.     Arguments ok 

.     Starting fasta-dinucleotide-shuffle 

fasta-dinucleotide-shuffle -f tag1R.bed.fa -t -dinuc 

.     fasta-dinucleotide-shuffle ran successfully in 158.63 seconds 

.     Starting ame 

ame --verbose 1 --oc . --control shuffled_tag1R.bed.fa --bgformat 1 --scoring avg --method ranksum --pvalue-report-threshold 0.05 tag1R.bed.fa motifs.meme

 .     ame ran successfully in 11.4 seconds 

"

[James Johnson]

Hmmm, it should work. The ame used online is built from the same source!

The old way of using ame was to concatenate the two source files together with the normal set followed by the control and set the "--fix-partition" parameter to the size of the normal set so you could try that?

If possible I'd recommend using CentriMo, AME is a bit quirky and we don't have the original author around to help us work out what various features were meant to do.