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  • HOMER: findMotifsGenome.pl error message

    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...

  • #2
    Hello.

    I have the same. Have you solved this problem?

    Comment


    • #3
      Hi,

      I am running into the same problem... Have any of you solved it already?

      Comment

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