homer findMotifsGenome.pl

Question

[biology_inform]

Hi all,

I have an ATAC-seq data and from differential expressed peaks I would like to find any motif that can be useful for me. This is my bed file (first 5 row);

chr1 816940 818102 Interval_1 0 +
chr1 826720 828040 Interval_2 0 +
chr1 858479 858908 Interval_3 0 +
chr1 869659 870152 Interval_4 0 +
chr1 875146 875666 Interval_5 0 +

this is my command for running findMotifsGenome.pl;

findMotifsGenome.pl ./DE_bed.bed hg38 ./170124/ -size given -preparsedDir ./170124_preparsed

I downloaded my genome data using following command;

perl /path-to-homer/configureHomer.pl -install hg38

When I run the findMotifsGenome.pl, I get this error;

 !!! Something is wrong... are you sure you chose the right length for motif finding?
    !!! i.e. also check your sequence file!!!

    -blen automatically set to 2
    Scanning input files...

I couldn't find the solution of this. If you can help me I will be happy. Thanks

[Trivas]

Not a solution, but I don't see the flag for -preparsedDir in the manual. What happens if you remove that?