Question

在我发布之前，我阅读了之前的帖子并检查了床上的chr表示法。

HOMER de novo motif discovery cannot open hg19 fasta files

我决定使用HOMER来查找文件中的已知图案。我的文件是BED格式。由于我有BED文件和.pos文件，我决定使用findMotifGenome.pl，我在手册中调用它。我得到了这个输出，我有空输出文件。在我检查了可能的问题后;即使bed2pos.pl，checkPeakFile.pl cleanUpPeak.pl等位于bin文件中，它们也无法找到，因此我收到了此错误。给出BED / .pos文件我得到了相同的结果。你能帮我解决这个问题吗？在下面我分享了该程序的输出。

    Tuncs-MacBook-Pro:final_overlap morova$ perl ~/homer/bin/findMotifsGenome.pl deneme.pos hg19 motif/ -size 200 -len 8 

    Position file = deneme.pos
    Genome = hg19
    Output Directory = motif/
    Fragment size set to 200
    Motif length set at 8,
    Found mset for "human", will check against vertebrates motifs
sh: bed2pos.pl: command not found
sh: checkPeakFile.pl: command not found
sh: cleanUpPeakFile.pl: command not found
ls: /Users/morova/homer/.//data/genomes/hg19//preparsed//hg19.*.cgbins: No such file or directory
    Could not find background files for 200 bp fragments
    Below are the sizes that are already available prepared.
    HOMER will now create background files for 200 bp fragments
    To CANCEL and rerun with a differet "-size <#>", hit <CTRL+C> now!
        5
        4
        3
        2
        1
    Preparsing genome for 200 bp fragments...(will probably take 1-5 min)
sh: preparseGenome.pl: command not found
wc: /Users/morova/homer/.//data/genomes/hg19//preparsed//hg19.200.gcbins: open: No such file or directory
Use of uninitialized value $lineCount in numeric lt (<) at /Users/morova/homer/bin/findMotifsGenome.pl line 640.
!!!! Might have something wrong with preparsed files
!!!! Rerun and add "-preparse" to the command line to force recreation of the files
sh: resizePosFile.pl: command not found
sh: homerTools: command not found
sh: cleanUpSequences.pl: command not found
sh: removePoorSeq.pl: command not found

    Not removing redundant sequences

sh: homerTools: command not found
sh: freq2group.pl: command not found

    Total sequences set to 50000

    Choosing background that matches in CpG/GC Content...
wc: /Users/morova/homer/.//data/genomes/hg19//preparsed//hg19.200.gcbins: open: No such file or directory
cat: /Users/morova/homer/.//data/genomes/hg19//preparsed//hg19.200.gcbins: No such file or directory
sh: makeBinaryFile.pl: command not found
sh: randRemoveBackground.pl: command not found
sh: assignGeneWeights.pl: command not found
    Assembling sequence file...
sh: filterListBy.pl: command not found
    Normalizing lower order oligos using homer2
sh: homer2: command not found
    Finished preparing sequence/group files

    ----------------------------------------------------------
    Known motif enrichment
sh: findKnownMotifs.pl: command not found
    ----------------------------------------------------------
    De novo motif finding (HOMER)
sh: homer2: command not found
cat: motif//homerMotifs.motifs*: No such file or directory

 sh: compareMotifs.pl: command not found    Job finished - if results
 look good, please send beer to ..

    Cleaning up tmp files...

如果它们位于bin文件夹中，我检查了那些perl脚本。是的，他们确实位于那个特定的地方。有办法绕行吗？

Answer 1

您必须将HOMER可执行文件的位置添加到bashrc文件的PATH变量中：PATH = $ PATH：/ XXX / XXXX / HOMER / bin

Answer 2

为避免此错误，请将homer / bin目录添加到可执行路径（〜/ .bash_profile文件）中。两步：（1）vim〜/ .bash_profile（添加一行）（2）来源〜/ .bash_profile

您可以在以下官方网址中查看安装说明：http://homer.ucsd.edu/homer/introduction/install.html [安装基本HOMER软件]

HOMER findMotifsGenome.pl找不到它的sub.pl文件

2 个答案: