HOMER: ./findMotifsGenome.pl
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Entering edit mode
12 months ago
radicav06 • 0

Hello all!

I want find motifs FOXA1 in the complete human genome. I have a file with peaks 10_FOXA1.bed. Format file: chr1 629136 629408 peak1 73.27334

chr1 629818 630074 peak2 43.09303

chr1 632321 632823 peak3 60.18918

chr1 633893 634164 peak4 76.32769

chr1 1006509 1006749 peak5 5.47672

chr1 1013066 1013303 peak6 7.29493

chr1 1153892 1154186 peak7 26.75187

chr1 1400839 1401123 peak8 39.31495

chr1 1429716 1429986 peak9 10.08591

chr1 1768631 1768890 peak10 18.00644

...

I use Homer command: ./findMotifsGenome.pl 10_FOXA1.bed hg38 10_FOXA1_MotifOutput -mask

But in the end I get the following message: " Position file = 10_FOXA1.bed Genome = hg38 Output Directory = 10_FOXA1_MotifOutput Found mset for "human", will check against vertebrates motifs Peak/BED file conversion summary: BED/Header formatted lines: 26173 peakfile formatted lines: 0

Peak File Statistics:
    Total Peaks: 26173
    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.

!!!! Might have something wrong with preparsed files !!!! Rerun and add "-preparse" to the command line to force recreation of the files !!! HOMER not configured properly!!!! !!! Could not open �L�� !!!

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/vladimir/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: 10_FOXA1_MotifOutput/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
440 motifs loaded
Cache length = 11180
Using binomial scoring
Checking enrichment of 440 motif(s)
|0%                                    50%                                  100%|
=================================================================================

Illegal division by zero at /home/vladimir/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/vladimir/Homer/bin/compareMotifs.pl line 1394. !!! Filtered out all motifs!!! Job finished - if results look good, please send beer to ..

Cleaning up tmp files... "

Are there those who encountered this error? What causes it? And how can this be fixed?

ChIP-Seq Homer • 794 views
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