```
./Homer/bin/findMotifsGenome.pl myc1_vs_input1.txt tair10 motif_based_on_myc1_vs_input1_cleaned_peaks/ -size 200 -mask
Position file = myc1_vs_input1.txt
Genome = tair10
Output Directory = motif_based_on_myc1_vs_input1_cleaned_peaks/
Fragment size set to 200
Will use repeat masked sequences
Found mset for "arabidopsis", will check against plants motifs
Peak/BED file conversion summary:
BED/Header formatted lines: 0
peakfile formatted lines: 4467
Peak File Statistics:
Total Peaks: 4467
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 file: /Users/xuenjun/Documents/CHIP-seq/Homer/.//data/genomes/tair10///genome.fa
Looking for peak sequences in a single file (/Users/xuenjun/Documents/CHIP-seq/Homer/.//data/genomes/tair10///genome.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 /Users/xuenjun/Documents/CHIP-seq/Homer/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: motif_based_on_myc1_vs_input1_cleaned_peaks//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
502 motifs loaded
Cache length = 11180
Using binomial scoring
Checking enrichment of 502 motif(s)
|0% 50% 100%|
=================================================================================
```

Illegal division by zero at /Users/xuenjun/Documents/CHIP-seq/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 /Users/xuenjun/Documents/CHIP-seq/Homer/bin/compareMotifs.pl line 1381. !!! Filtered out all motifs!!! Job finished - if results look good, please send beer to ..

```
Cleaning up tmp files...
```

This once happened to me because my input files had the chromosome column in the "1","2,"3"... format, whereas HOMER's genomes have the "chr1","chr2","chr3"... format. Thus, adding "chr" to my chromosome columns solved the problem.

Hi, I encountered the same error message. However, I made the chromosome column names are consistent with my bed file chromosome names. Was wondering if you know some other reason I might get this error message

Good day,

Do you have a quick command for adding this? Greatly appreciated.

Cheers, Chris

`mutate(Chrom = paste('chr', Chrom, sep =''))`

Where Chrom is the name of your column with the chromosome numberGood day,

Not sure if this is relevant to many now, but to solve this problem I had to change the chromosomes from, for example '1' to 'chr1'.

I did this in Excel using the concatenate function. Please let me know if you want the gory details on how I did this. More brute force and ignorance than skill....

what would be the reason to cause this, I checked the peaks file, and no zero value was observed.

Hi! Have solved the problem? I ran into the same problem as you. I have checked all the possible problems and I am now very frustrated and confused.....

Hi,

Did you ever solve this? I have the same problem.

Many thanks,

Lucy