HOMER find motifs from BED data

Question

[morovatunc]

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

[morovatunc]

I apologize for the text formats...

[Giovanni M Dall'Olio]

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

[morovatunc]

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??

[Sam]

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

[morovatunc]

$perl /Users/morova/homer/configureHomer.pl -install

Thank you all for helping me.

[Fidel]

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

Answer 1

[keryruo]

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]