Good day all,
I have been trying HOMER to identify txn factor motifs enriched in my ATACseq data sets. I have been using the narrow peak files as input, in which HOMER indicates are acceptable. I am using the following command in Ubuntu:
findMotifsGenome.pl /mnt/f/CartilageATACseq_Aug20_21/Atacseq_BEDfiles/Day3_nolysis_R2_peaks.narrowPeak mm10 /mnt/f/CartilageATACseq_Aug20_21\Atacseq_BEDfiles -size 200 -p 7
However, for the mouse genome I am using (mm10) I am receiving the following error:
Position file = /mnt/f/CartilageATACseq_Aug20_21/Atacseq_BEDfiles/Day3_nolysis_R2_peaks.pos Genome = mm10 Output Directory = /mnt/f/CartilageATACseq_Aug20_21Atacseq_BEDfiles Fragment size set to 200 Using 7 CPUs Found mset for "mouse", will check against vertebrates motifs Peak/BED file conversion summary: BED/Header formatted lines: 0 peakfile formatted lines: 195958
Peak File Statistics:
Total Peaks: 195958
Redundant Peak IDs: 0
Peaks lacking information: 0 (need at least 5 columns per peak)
Peaks with misformatted coordinates: 0 (should be integer)
Peaks with misformatted strand: 0 (should be either +/- or 0/1)
Peak file looks good!
Background files for 200 bp fragments found.
Extracting sequences from directory: /home/ceskiw/.//data/genomes/mm10// !!Could not open file for 1 (.fa or .fa.masked) !!Could not open file for 10 (.fa or .fa.masked) !!Could not open file for 11 (.fa or .fa.masked) etc
De novo motif finding (HOMER)
Number of Trial motifs (-T) set to 7 (from 10) to work well with 7 CPUs
Scanning input files...
!!! Something is wrong... are you sure you chose the right length for motif finding? !!! i.e. also check your sequence file!!!
Number of Trial motifs (-T) set to 7 (from 10) to work well with 7 CPUs
Scanning input files...
!!! Something is wrong... are you sure you chose the right length for motif finding? !!! i.e. also check your sequence file!!!
Number of Trial motifs (-T) set to 7 (from 10) to work well with 7 CPUs
-blen automatically set to 2
Scanning input files...
!!! Something is wrong... are you sure you chose the right length for motif finding? !!! i.e. also check your sequence file!!! Use of uninitialized value in numeric gt (>) at /home/ceskiw/bin/compareMotifs.pl line 1394. !!! Filtered out all motifs!!! Job finished - if results look good, please send beer to ..
This results in no output. I have tried to convert my narrow peak files (which are BED) to .pos as suggested by another post but to no avail.
Thanks in advance
