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[其他] chip-seq findMotifsGenome.pl出问题了

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发表于 2017-8-28 21:54:43 | 显示全部楼层 |阅读模式
[mw_shl_code=applescript,true]xuenjundeMacBook-Pro:CHIP-seq xuenjun$ ./Homer/bin/findMotifsGenome.pl myc1_vs_input1.txt tair10 motif_based_on_myc1_vs_input1_cleaned_peaks/ -size given

        Position file = myc1_vs_input1.txt
        Genome = tair10
        Output Directory = motif_based_on_myc1_vs_input1_cleaned_peaks/
        Using actual sizes of regions (-size given)
        Fragment size set to given
        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 fragment size set to 138 (avg size of targets)
        Background files for 138 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...[/mw_shl_code]


试过各种长度的motif finding可是都不好使,到底是哪里有问题呢,非常感谢
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 楼主| 发表于 2017-8-30 13:46:13 | 显示全部楼层
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