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Old 04-01-2019, 12:53 PM   #1
yueli
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Location: china

Join Date: May 2013
Posts: 59
Default running findMotifsGenome.pl error

Hello,

I am running findMotifGenome.pl in homer package.

Any help is appreciated!

With Best!

Yue Li


administrator@ACB-Ubuntu:~/homer/bin$ perl findMotifsGenome.pl fox2ClipSeq.hg18.bed hg38 peakAnalysis -size 200 -len 8

Position file = fox2ClipSeq.hg18.bed
Genome = hg38
Output Directory = peakAnalysis
Fragment size set to 200
Motif length set at 8,
Found mset for "human", will check against vertebrates motifs
sh: 1: bed2pos.pl: not found
sh: 1: checkPeakFile.pl: not found
sh: 1: cleanUpPeakFile.pl: not found
ls: cannot access /home/administrator/homer/.//data/genomes/hg38//preparsed//hg38.*.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: 1: preparseGenome.pl: not found
wc: /home/administrator/homer/.//data/genomes/hg38//preparsed//hg38.200.gcbins: No such file or directory
Use of uninitialized value $lineCount in numeric lt (<) at findMotifsGenome.pl line 648.
!!!! Might have something wrong with preparsed files
!!!! Rerun and add "-preparse" to the command line to force recreation of the files
sh: 1: resizePosFile.pl: not found
sh: 1: homerTools: not found
sh: 1: cleanUpSequences.pl: not found
sh: 1: removePoorSeq.pl: not found

Not removing redundant sequences

sh: 1: homerTools: not found
sh: 1: freq2group.pl: not found

Total sequences set to 50000

Choosing background that matches in CpG/GC content...
wc: /home/administrator/homer/.//data/genomes/hg38//preparsed//hg38.200.gcbins: No such file or directory
cat: /home/administrator/homer/.//data/genomes/hg38//preparsed//hg38.200.gcbins: No such file or directory
sh: 1: makeBinaryFile.pl: not found
sh: 1: randRemoveBackground.pl: not found
sh: 1: assignGeneWeights.pl: not found
Assembling sequence file...
sh: 1: filterListBy.pl: not found
Normalizing lower order oligos using homer2
sh: 1: homer2: not found
Finished preparing sequence/group files

----------------------------------------------------------
Known motif enrichment
sh: 1: findKnownMotifs.pl: not found
----------------------------------------------------------
De novo motif finding (HOMER)
sh: 1: homer2: not found
cat: peakAnalysis/homerMotifs.motifs*: No such file or directory
sh: 1: compareMotifs.pl: not found
Job finished - if results look good, please send beer to ..

Cleaning up tmp files...
yueli is offline   Reply With Quote
Old 04-01-2019, 03:17 PM   #2
yueli
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Location: china

Join Date: May 2013
Posts: 59
Default

every time open the terminal

nano ~/.bash_profile

PATH=$PATH:/home/administrator/homer/bin

ctrlX

Y

enter

source ~/.bash_profile

Last edited by yueli; 04-02-2019 at 06:42 AM.
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