Question: HOMER load genomes not working
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gravatar for c78483
3 months ago by
c784830
c784830 wrote:

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.

ADD COMMENTlink modified 3 months ago by genomax91k • written 3 months ago by c784830

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.

ADD REPLYlink modified 3 months ago • written 3 months ago by genomax91k

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!

ADD REPLYlink modified 3 months ago by genomax91k • written 3 months ago by c784830

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.

ADD REPLYlink written 3 months ago by genomax91k

That worked, thanks for your help!

ADD REPLYlink written 3 months ago by c784830
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