Question: HOMER find motifs from BED data
0
gravatar for morovatunc
4.4 years ago by
morovatunc450
Turkey
morovatunc450 wrote:

Hi,

I decided to use HOMER in order to find known motifs in a file. My file is in BED format. Since I have BED files and .pos files, I decided to use findMotifGenome.pl and I call it as it is in the manual. I got this output where I have empty output file. After I checked the possible problems; even though bed2pos.pl, checkPeakFile.pl cleanUpPeak.pl etc are located in the bin file, they cannot be located thus I got this error. I got the same results with giving either BED/.pos file. Could you help me out with this?

 

Best regards,

I wish you all a good new year.

Tunc

$~/homer/bin/findMotifsGenome.pl GSM1358399_DF_1373_normal_peaks.pos hg19 motif/ 


$Tuncs-MacBook-Pro:final_overlap morova$ ~/homer/bin/findMotifsGenome.pl GSM1358399_DF_1373_normal_peaks.pos hg19 motif/ 


    Position file = GSM1358399_DF_1373_normal_peaks.pos

    Genome = hg19

    Output Directory = motif/

    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

sh: homer2: command not found

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...




I also installed the hg19


homer.package.zip                100%[=========================================================>]   1.37G  1.32MB/s   in 14m 24ss


2015-12-30 11:43:52 (1.62 MB/s) - 'homer.package.zip' saved [1467473855/1467473855]


        Unzipping...


/Users/morova/homer/data/genomes/hg19/chr22.fa:  write error (disk full?).  Continue? (y/n/^C) y

 bad CRC 7b0a4859  (should be 6bd2f572)

y

y

        Finished Installing hg19

 

chip-seq homer • 4.3k views
ADD COMMENTlink modified 22 months ago by keryruo10 • written 4.4 years ago by morovatunc450

I apologize for the text formats...

ADD REPLYlink written 4.4 years ago by morovatunc450

It seems you didn't install HOMER correctly, as there are many "command not found" errors.

ADD REPLYlink written 4.4 years ago by Giovanni M Dall'Olio27k

well I followed the instructions as it is written in the guide. http://homer.salk.edu/homer/introduction/install.html. The instillation is consisted of one line code. Also, I have used one of the functions before and then got the same output with the reinstalled one??

ADD REPLYlink modified 5 months ago by RamRS27k • written 4.4 years ago by morovatunc450

Could you post what code/steps you used to install homer?

ADD REPLYlink written 4.4 years ago by Sam90
$perl /Users/morova/homer/configureHomer.pl -install

Thank you all for helping me.

ADD REPLYlink modified 5 months ago by RamRS27k • written 4.4 years ago by morovatunc450

Why don't you use the MEME suite? This set of tools specialises on motif discovery. You can install it or run it online.

ADD REPLYlink modified 5 months ago by RamRS27k • written 4.3 years ago by Fidel1.9k
1
gravatar for keryruo
22 months ago by
keryruo10
keryruo10 wrote:

To avoid this error, add the homer/bin directory to your executable path(~/.bash_profile file).

two steps:

(1) vim ~/.bash_profile
(add a line)
(2) source ~/.bash_profile

you can check install instruction in official url [Installing the basic HOMER software]

ADD COMMENTlink modified 5 months ago by RamRS27k • written 22 months ago by keryruo10
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