Have you succeeded in running this analysis? I'm just attempting to run it with the demo dataset, but I have a problem at step 3, where I get the following:

step 3: calculate opn... mkdir: Enrichment: File exists

Position file = region.bed
Genome = mm9
Output Directory = ./.
Using actual sizes of regions (-size given)
Fragment size set to given
Will use repeat masked sequences
Will not run homer for de novo motifs
Will search for known motifs in file: ../../../Data/all_motif_rmdup
Found mset for "mouse", will check against vertebrates motifs
Peak/BED file conversion summary:
    BED/Header formatted lines: 0
    peakfile formatted lines: 0

Peak File Statistics:
    Total Peaks: 0
    Redundant Peak IDs: 0
    Peaks lacking information: 0 (need at least 5 columns per peak)
    Peaks with misformatted coordinates: 0 (should be integer)
    Peaks with misformatted strand: 0 (should be either +/- or 0/1)

Only 0 peaks found! If many more expected, maybe the file format is for Macs only
Try running the command: changeNewLine.pl "././target.clean..pos"

Background fragment size set to 0 (avg size of targets)
ls: ../../../Homer//mm9r.*.cgbins: No such file or directory