I have installed the MEME suite locally (bioconda, MEME 5.1.1, python=2.7) because I want to search for motifs in a number of sets of sequences automatically instead of uploading each manually to the website. When I run them though the output does not contain any motifs. When I compare the same set of sequences through the online tool it does result in a list of motifs. I'm using the same command line code locally as is given at the end of the (successfull) online file. (dreme -verbosity 1 -oc . -dna -p cluster1_filtered.txt -t 18000 -e 0.05).
Does anyone have a suggestion what could be going on?