A colleague of mine who's a molecular biologist too and doesn't know bioinformatics at all has been trying to run findmotifs.pl as explained on this page without any success.
Following the syntx:
findMotifsGenome.pl <peak/BED file> <genome> <output directory> -size # [options]
She is submitting the following command:
/software/homer/bin/findMotifs.pl /project/homer/LPep.txt mouse-p /project/homer/LPEP/ -rna -len 5
The job terminates because apparently, Homer can’t find the mouse-p promoter file.
!!! mouse-o not found in /projects/p30120/software/homer/.//config.txt Try typing "perl /projects/p30120/software/homer/.//configureHomer.pl -list" to see available promoter sets If avaliable, type "perl /projects/p30120/software/homer/.//configureHomer.pl -install mouse-o" to install
I tried to do what was suggested in the log file :
perl /projects/p30120/software/homer/.//configureHomer.pl -install mouse-p
following which I checked by
perl /projects/p30120/software/homer/.//configureHomer.pl -list
Although it shows that the promoter set is present, she gets the exact same error every time.
I’ve also tried replacing mouse-p directly with Mus_musculus.GRCm38.75.dna.primary_assembly.fa but I get the exact same error. Anyone here knows what's going on?