Entering edit mode
3.0 years ago
jeni ▴ 90
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
# 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:
How can I solve this?
Did you end up figuring this out? I ran into the same error
No, I didn't. If you figure it out I would be so grateful to get some information
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.