I've been running motif analysis on my ATAC dataset using Homer's findMotifsGenome.pl command. I pretty much have just been following the basic command outlined on the salk page:
findMotifsGenome.pl ~/path/file.bed mm9 ~/path/directory/ -size 200
This worked fine up until yesterday when I started getting long strings of errors. The error message essentially just reads "GPL Ghostscript 9.20: Unrecoverable error, exit code 1" and tries to open up ghostscripts in xcode. I haven't changed how I run the command aside from using different paths and files(and have replicated the error with multiple files of different origins), so I'm not entirely sure what has gone wrong here. Anyway, if I just let it run itself out, the script will actually be completed and I'll have useable results, except the images of motifs are all broken.
Has anyone else encountered this error? If so, how did you resolve it?
Sounds like a problem with the Ghostscript dependency. I suggest re-installing it. Follow the instructions on the HOMER installation page.