problem with HOMER findMotifsGenome.pl

Question

[ste.lu]

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:

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...

[Lucy]

Hi,

I am having the same problem. Did you ever work out what the problem was?

Many thanks,

Lucy

[o.mikh90]

Hi, any luck solving this? I'm having the same issue.. Thanks!

[shangguandong1996]

Maybe you should set the strand info with "." instead of "*"

[radicav06]

I have a similar problem. Tell me, have you solved this?

Answer 1

[Shannon]

I also had this problem and solved it.

Firstly , maybe the chrosome name in your bed file and genome file are different , or not "chr blabla"/"chr1 blabla" format.

Secondly , check if your command was killed,like this,

Choosing background that matches in CpG/GC content... sh: line 1: 23241 Killed randRemoveBackground.pl "./0.54176262726924.2.tmp" "676904" "./0.54176262726924.tmp" > "./0.54176262726924.3.tmp"

Finaly, make sure your output dir is not "/" ended, it should be "output_dir" not "output_dir/"

wrong message:

Autonormalization: 3-mers (64 total) Normalization weights can be found in file: ./output_dir//seq.autonorm.tsv

Hope it could be useful for you.

Answer 2

[Chava]

the chr name sould be: chr2 and not just 2

Answer 3

[kaaz]

I also ran into this issue, but it was solved by removing the quotes in my .bed file.