Question: findGenomeMotif.pl in Homer couldn't work properly
0
gravatar for xuenjun1
24 months ago by
xuenjun10
xuenjun10 wrote:
./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...
chip-seq homer • 1.6k views
ADD COMMENTlink modified 23 months ago by toniford1250 • written 24 months ago by xuenjun10

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

ADD REPLYlink written 24 months ago by xuenjun10

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.....

ADD REPLYlink written 23 months ago by toniford1250
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