Homer findmotifs.pl keeps failing because it can't find the promoter set which is installed

Question

[sandKings]

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?

[Benn]

Why mouse-p instead of mouse-o?

[sandKings]

None of the options work at all. We've tried mm10, mm9, mouse-p, mouse-o but they all generate the same error stating that the component isn't available. We've even tried to export path to all the folders within Homer but that didn't help either.

export PATH=$PATH:/projects/p30120/software/homer/
export PATH=$PATH:/projects/p30120/software/homer/data
export PATH=$PATH:/projects/p30120/software/homer/data/accession/
export PATH=$PATH:/projects/p30120/software/homer/data/promoters/
export PATH=$PATH:/projects/p30120/software/homer/data/genomes/
export PATH=$PATH:/projects/p30120/software/homer/data/GO/
export PATH=$PATH:/projects/p30120/software/homer/data/knownTFs/

[Benn]

Did you try?:

/software/homer/bin/findMotifs.pl  /project/homer/LPep.txt mouse /project/homer/LPEP/ -rna -len 5

[sandKings]

I tried it just now and I got a different error:

Selected Options:
    Input file = /projects/b1042/SKlab/MSC_TPA_project/homer/LPep.txt
    Promoter Set = mouse
    Output Directory = /projects/b1042/SKlab/MSC_TPA_project/homer/LPEP/
    Modifying analysis for RNA analysis
    Motif length set at 5, 
    Found mset for "mouse", will check against vertebrates motifs

    Progress: Step1 - Convert input file to refseq IDs
could not find ID file for organism = mouse (/software/homer/4.10/.//data/accession//mouse2gene.tsv does not exist)
    Percentage of IDs converted into refseq: 0.0% (0 out of 4894)
!!!! Homer converted less than 5% of the rows in your file.
!!!! Check to be sure the input file has valid gene identifiers
!!!! Check to be sure the input file has valid gene identifiers

I checked and found that /software/homer/4.10/.//data/accession//mouse2gene.tsv does exist.

[clayluo]

Hi, sandKings your input ID in "LPep.txt" must be wrong, Please convert ID to Gene_ID by using relative tools, such as “ http://asia.ensembl.org/biomart/martview”