I have been using the findMotifsGenome.pl to find enriched motifs in bed files containing CUT&RUN peaks called using SEACR, but I keep getting the error below for the known and de novo motif discovery meaning they are missing from the output. I have never had a problem running and installing HOMER on previous computers.

Running the command:

findMotifsGenome.pl relaxed.bed hg38 motif_results/ -size 200

First error:

Known motif enrichment Missing comma after first argument to return at /Users/imb41/HOMER/.//bin/HomerSVGLogo.pm line 163, near ");" Compilation failed in require at /Users/imb41/HOMER/bin/findKnownMotifs.pl line 10. BEGIN failed--compilation aborted at /Users/imb41/HOMER/bin/findKnownMotifs.pl line 10.

Second error:

Missing comma after first argument to return at /Users/imb41/HOMER/.//bin/HomerSVGLogo.pm line 163, near ");" Compilation failed in require at /Users/imb41/HOMER/bin/compareMotifs.pl line 11. BEGIN failed--compilation aborted at /Users/imb41/HOMER/bin/compareMotifs.pl line 11. Job finished - if results look good, please send beer to ..

I tried reconfiguring using perl configureHomer.pl and then removing the HOMER installation, and reinstalling, but still got the same error.

I was wondering if it could be a problem with the latest version of Perl (v5.40.1)? I can't see anything obvious wrong with line 163 of HomerSVGLogo.pm (below), but I am not familiar with working with Perl.

sed -n '163p' ~/HOMER/bin/HomerSVGLogo.pm return $plotXY(\@data,$xlabel,$ylabel,\@seriesLabels,$xlow,$xhigh,$ylow,$yhigh); perl -c ~/HOMER/bin/HomerSVGLogo.pm Missing comma after first argument to return at /Users/imb41/HOMER/bin/HomerSVGLogo.pm line 163, near ");" /Users/imb41/HOMER/bin/HomerSVGLogo.pm had compilation errors.

Thank you in advance for any help!!