problem with motif length meme-chip

[Nicolas Descostes]

Dear all,

I am trying to find only motifs between 30 and 45 bp using meme-chip (v 4.11.1) in command line:

meme-chip -o /ifs/home/****/markov1/ -db /ifs/home/****/JASPAR/JASPAR_CORE_2016_vertebrates.meme -dna -order 1 -norand -ccut 0 -group-thresh 0.05 -filter-thresh 0.05 -desc meme-chip -meme-minw 30 -meme-maxw 45 -meme-nmotifs 10 -meme-minsites 2 -meme-maxsites 50 -meme-p 20 -meme-maxsize 606 -dreme-e 0.05 -dreme-m 10 -centrimo-local -centrimo-score 5 -centrimo-maxreg 300 -centrimo-ethresh 10 -centrimo-flip /ifs/home/***/***.fa

I get motifs between 6 and 9 bp in the results.

I cannot find where my error is.

any idea?

Thanks

[CharlesEGrant]

Hmm. You've set the -meme-minw and -meme-maxw options appropriately. Are the motifs identified by MEME or by DREME?

Could you attach the messages.txt file from the MEME-ChIP output directory and the meme.html file from the meme_out directory under the MEME-ChIP output directory? That would help us troubleshoot the problem.