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Old 10-10-2018, 08:12 AM   #1
lu_Ste
Junior Member
 
Location: Cambridge

Join Date: Oct 2018
Posts: 3
Unhappy 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...
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