HOMER hg19 not found in config.txt
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16 months ago
jeni ▴ 50

Hi!

I am trying to run findMotif.pl from HOMER, in order to detect some regulatory motifs in a set of fasta sequences. When I type:

findMotifs.pl sequences.fasta hg19 .

I get the following error:

!!! hg19 not found in /mnt/lustre/scratch/home/programs/HOMER/.//config.txt
        Try typing "perl /mnt/lustre/scratch/home/programs/HOMER//.//configureHomer.pl -list" to see available promoter sets
        If avaliable, type "perl /mnt/lustre/scratch/home/programs/HOMER//.//configureHomer.pl -install hg19" to install

I have executed those commands and now this is my config.txt file:

# Homer Configuration File (automatically generated)
#
# This file is updated from the Homer website and contains information about data available for
# use with the program.
#
# Each section has the same format, which is <tab> separated values specifying:
# package name <tab> version <tab> description <tab> url <tab> optional parameters (, separated)
#
SOFTWARE
homer   v4.11.1 Code/Executables, ontologies, motifs for HOMER  http://homer.ucsd.edu/homer/data/software/homer.v4.11.1.zip     ./
ORGANISMS
human   v6.3    Homo sapiens (human) accession and ontology information http://homer.ucsd.edu/homer/data/organisms/human.v6.3.zip       data/accession/ 9606,NCBI Gene
PROMOTERS
GENOMES
hg19    v6.4    human genome and annotation for UCSC hg19       http://homer.ucsd.edu/homer/data/genomes/hg19.v6.4.zip  data/genomes/hg19/      human,default
SETTINGS

So, actually hg19 does exist in my config.txt file.

Additionally, I have checked HOMER data directory and it has all neccessary files:

/mnt/lustre/scratch/home/programs/HOMER/data/genomes/hg19

How can I solve this?

HOMER motif finding • 909 views
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Did you end up figuring this out? I ran into the same error

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No, I didn't. If you figure it out I would be so grateful to get some information

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I don't know if this will still help anyone or if you figured out a way by now. For me (working with fly data) it helped to just type 'fly' instead of any other identifier (not fly-p, not dm6) that was previously used to install the packages. So in your case 'human' might work.

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