HOMER load genomes not working

Question

[c78483]

Hi. I am using HOMER bioinformatics software and I am running into an issue when trying to analyze repeats. I need to load a genome for pombe yeast (ASM294v2.47).

I've attempted to load the genome using this code:

perl pathToHomer/HOMER/bin/loadGenome.pl –name spombe1 –fasta pathToGenome/PombeFullGenome.fa –gtf pathToGTF/Schizosaccharomyces_pombe.ASM294v2.47.gtf –org null

but I get this output:

Current Settings:
                Genome name = 
                FASTA file = 
                GTF file =  
                Organism = 
                Version = custom
        Genome will be stored in directory:
                pathToHomer/HOMER//data/genomes// !! Options -name, -fasta, -gtf, and -org are REQUIRED !!
        Program will prepare a custom genome for use with HOMER
        Usage: loadGenome.pl <Required Parameters ...> [options]
        NOTE: If your genome is available at UCSC, consider using the update scripts
                located in the pathToHomer/HOMER//update directory
        Required Parameters:
                -name <genome name> (i.e. hg19, tair10, etc.)
                -fasta <genome fasta file> (Single genome sequence, preferrabley soft masked, unzipped)
                -gtf <gene annotation file> (Transcript annotation in gtf format, -gff/-gff3 to use them)
                        (Always best to use a gtf file whenever possible, gffs can be organized differently.. .)
                -org <organism name, ok to use 'null'>

        Other options:
                -force (Overwrite any existing genome with the same name)
                -promoters <promoter set name> (Create promoter set with genome and gtf files)
                        -id <idtype> (options: gene, refseq, unigene, ensembl, or custom, default: custom)
                -version <version id> (Assign version, versions starting with 'v' are managed
                        by the configureHomer.pl script and my be overwritten, default: custom)
                -gid (Use gene_id instead of transcript_id to identify the transcripts from GTF files)
                -tid (Use transcript_id instead of gene_id to identify the transcripts from GTF files, default)
                -ensemblRepeats <GFF3 file> (gff3 annotations from ensembl usually have repeat definitions to o)

So I don't think the command is executing properly. I've also tried:

perl pathToHomer/HOMER/configureHomer.pl -install pombe

And it runs but I don't see "pombe" anywhere.

When I try to run analyzeRepeats, it doesn't run.

[GenoMax]

Are you using macOS by any chance and/or copying and pasting the command line from a file? Just to be sure pathTo values are real paths in your real command. Because it appears that the program is not able to parse the inputs you are providing.

[c78483]

I just typed the command in by hand and was able to load the genome. Thanks!

I'm now trying to run analyzeRepeats by typing this:

pathToHomer/HOMER/bin/analyzeRepeats.pl pathToGTF/Schizosaccharomyces_pombe.ASM294v2.47.gtf spombe1 -count cds -d pathToTagsFolder/Pombe.wt.N.noCHX.mRNA.1_tags > pathToDesiredOutput/Pombe.wt.
N.noCHX.mRNA.1_Repeats

But analyzeRepeats still isn't working (even with typing it in by hand rather than copy-pasting from a document). It makes a Pombe.wt.N.noCHX.mRNA.1_Repeats file but the file doesn't contain any data. I also get this output:

   Tag Directories:
            pathToTagsFolder/Pombe.wt.N.noCHX.mRNA.1_tags
    Input file format: gtf sh: parseGTF.pl: command not found sh: parseGTF.pl: command not found
    Filtering based on repeat parameters: kept 0 of 0
    Calculating read coverage for pathToTagsFolder/Pombe.wt.N.noCHX.mRNA.1_tags sh: getPeakTags: command not found
            Normalizing...
    Printing output
            Printed 0 of 0 repeats (expression >= -1e+20)

Do you have any advice on how to fix this? Thanks!

[GenoMax]

Did you properly install the package following directions? Looks like there are more than one .pl scripts and they need to be available in your $PATH. You could find the directory that contains those scripts and then add it to your $PATH by doing export PATH=$PATH:/dir_w_perl_scripts and then try again.

[c78483]

That worked, thanks for your help!