Hi All,

I did and ATAC-Seq experiment in different cell lines and I was curious to see if they have different motifs in the open chromatin. I was planning to use HOMER for this, but running from linux bash:

Code:

findMotifsGenome.pl ATAC_d001_peaks_called_with_homer.txt hg38 ATACAd001_FIND_MOTIF
I got this message of error (see below), it looks like the problem is in assignGeneWeights.pl line 63. Any tips on how to fix it?
Position file = ATAC_d001_peaks_called_with_homer.txt
Genome = hg38
Output Directory = ATACAd001_FIND_MOTIF
Fragment size set to 400
Found mset for "human", will check against vertebrates motifs
Peak/BED file conversion summary:
BED/Header formatted lines: 0
peakfile formatted lines: 42719
Peak File Statistics:
Total Peaks: 42719
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 400 bp fragments found.
Extracting sequences from file: /home/l..
Looking for peak sequences in a single file (/home/ls760/r...nome.fa)
Not removing redundant sequences
Sequences processed:
0 total
Frequency Bins: 0.2 0.25 0.3 0.35 0.4 0.45 0.5 0.6 0.7 0.8
Freq Bin Count
Total sequences set to 50000
Choosing background that matches in CpG/GC content...
Illegal division by zero at /home..mer/bin/assignGeneWeights.pl line 63.
Assembling sequence file...
Normalizing lower order oligos using homer2
Reading input files...
0 total sequences read
Autonormalization: 1-mers (4 total)
A inf% inf% -nan
C inf% inf% -nan
G inf% inf% -nan
T inf% inf% -nan
Autonormalization: 2-mers (16 total)
AA inf% inf% -nan
CA inf% inf% -nan
GA inf% inf% -nan
TA inf% inf% -nan
AC inf% inf% -nan
CC inf% inf% -nan
GC inf% inf% -nan
TC inf% inf% -nan
AG inf% inf% -nan
CG inf% inf% -nan
GG inf% inf% -nan
TG inf% inf% -nan
AT inf% inf% -nan
CT inf% inf% -nan
GT inf% inf% -nan
TT inf% inf% -nan
Autonormalization: 3-mers (64 total)
Normalization weights can be found in file: ATACAd001_FIND_MOTIF/seq.autonorm.tsv
Converging on autonormalization solution:
...............................................................................
Final normalization: Autonormalization: 1-mers (4 total)
A inf% inf% -nan
C inf% inf% -nan
G inf% inf% -nan
T inf% inf% -nan
Autonormalization: 2-mers (16 total)
AA inf% inf% -nan
CA inf% inf% -nan
GA inf% inf% -nan
TA inf% inf% -nan
AC inf% inf% -nan
CC inf% inf% -nan
GC inf% inf% -nan
TC inf% inf% -nan
AG inf% inf% -nan
CG inf% inf% -nan
GG inf% inf% -nan
TG inf% inf% -nan
AT inf% inf% -nan
CT inf% inf% -nan
GT inf% inf% -nan
TT inf% inf% -nan
Autonormalization: 3-mers (64 total)
Finished preparing sequence/group files
----------------------------------------------------------
Known motif enrichment
Reading input files...
0 total sequences read
414 motifs loaded
Cache length = 11180
Using binomial scoring
Checking enrichment of 414 motif(s)
|0% 50% 100%|
=================================================================================
Illegal division by zero at /home/l...3/homer/bin/findKnownMotifs.pl line 152.
----------------------------------------------------------
De novo motif finding (HOMER)
Scanning input files...
!!! Something is wrong... are you sure you chose the right length for motif finding?
!!! i.e. also check your sequence file!!!
Scanning input files...
!!! Something is wrong... are you sure you chose the right length for motif finding?
!!! i.e. also check your sequence file!!!
-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.../homer/bin/compareMotifs.pl line 1389.
!!! Filtered out all motifs!!!
Job finished - if results look good, please send beer to ..
Cleaning up tmp files...