Entering edit mode
4.0 years ago
danielcgingerich
▴
10
I am trying to do motif analysis on a set of ATAC peaks with findMotifsGenome.pl using HOMER installed on a computer cluster. I submit a simple slurm job:
#!/bin/bash
#SBATCH -J HOMER.test
#SBATCH -o %A_%a.out.txt
#SBATCH -e %A_%a.err.txt
#SBATCH --mem=24G
#SBATCH -n 8
#SBATCH --mail-type=END
#SBATCH --mail-user=xxyyxx@institution.edu
findMotifsGenome.pl homer.peaks.test.txt GRCh38.p13.genome.fa ./homer.test/ -size 200 -mask
and receive the following .err.txt file:
Position file = homer.peaks.test.txt
Genome = GRCh38.p13.genome.fa
Output Directory = ./homer.test/
Fragment size set to 200
Will use repeat masked sequences
Using Custom Genome
!!! Could not open peak/position file homer.peaks.test.txt !!!
I formatted the peak.txt file tab delimited with all the columns specified on the website.
Try using absolute paths for your files to make sure that it's not an issue with using incorrect relative paths.