Linux命令使用：

$ perl的/home/chipseq_project/homer/bin/findMotifsGenome.pl /home/chipseq_project/homer/findpeak_output/peaks.txt hg19 /家庭/ chipseq_project /荷馬/ motif_output/- 給定大小

標準輸出文本：

Position file = /home/chipseq_project/homer/findpeak_output/peaks.txt 
    Genome = hg19 
    Output Directory = /home/chipseq_project/homer/motif_output/ 
    Using actual sizes of regions (-size given) 
    Fragment size set to given 
    Found mset for "human", will check against vertebrates motifs 
    Peak/BED file conversion summary: 
      BED/Header formatted lines: 0 
      peakfile formatted lines: 7662 

    Peak File Statistics: 
      Total Peaks: 7662 
      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 81 (avg size of targets) 
    Background files for 81 bp fragments found. 

    Extracting sequences from directory: /home/chipseq_project/homer/.//data/genomes/hg19// 
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    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...

非法除數爲零/home/chipseq_project/homer/bin/assignGeneWeights.pl線63 裝配序列文件... 正火低ORD使用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: /home/chipseq_project/homer/motif_output//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 
    264 motifs loaded 
    Cache length = 11180 
    Using binomial scoring 
    Checking enrichment of 264 motif(s) 
    |0%         50%         100%|

非法司/home/chipseq_project/homer/bin/findKnownMotifs.pl線142 呃寡零------------------ ---------------------------------------- De novo motif finding（HOMER）

Scanning input files...

!!!有什麼不對......你確定你選擇了正確的長度來尋找主題嗎？ !!!即也檢查你的序列文件！

Scanning input files...

！有什麼不對......你確定你選擇了正確的長度來尋找主題嗎？ !!!即也檢查你的序列文件！

-blen automatically set to 2 
    Scanning input files...

！有什麼不對......你確定你選擇了正確的長度來尋找主題嗎？ !!!即也檢查你的序列文件！在/home/chipseq_project/homer/bin/compareMotifs.pl 1289行的數字gt（>）中使用未初始化的值。 !!!過濾掉所有圖案！工作完成 - 如果結果看起來不錯，請發送啤酒..