runHomer

[Brawni]

Hi Fang,

Thanks for this great package! I'm stuck at the runHomer function as i need to pass the argument '-preparsedDir' from the findMotifsGenome.pl function but it doesnt seem to work when i add it in the runHomer function (as 'preparseDir'). How do I pass this argument?

Thanks!

[ninal88]

Hi! I have the same issue. I assume because you are using Homer that is pre-installed on a cluster as opposed to your own home directory. I haven't figured out how to pass the -preparsedDir function to findGenomeMotif.py. How did you do it?

[Brawni]

Hi, your assumption is correct :), i didn't...I exported the genomic regions and run homer from the command line.

[ninal88]

Thanks for the quick reply!

So it still didn't work even doing it separately? That was my next thing to try..

[Brawni]

By doing separately i meant to run homer from the command line and yes it works

[QianhuiXu]

@Brawni @ninal88 @r3fang Hi, thanks for a great package! I am having some issues when trying to perform runHomer for motif discovery across my clusters. This is my code:

motifs = runHomer(

• x.sp[,idy,"pmat"],
• mat = "pmat",
• path.to.homer = "/home/qianhui/anaconda3/envs/chipseq/share/homer/bin/findMotifsGenome.pl",
• result.dir = "./homer/DoubleNegativeTcell",
• num.cores=5,
• genome = 'hg19',
• motif.length = 10,
• scan.size = 300,
• optimize.count = 2,
• background = 'automatic',
• local.background = FALSE,
• only.known = TRUE,
• only.denovo = FALSE,
• fdr.num = 5,
• cache = 100,
• overwrite = TRUE,
• keep.minimal = FALSE
• );

Here is the error: Position file = ./homer/DoubleNegativeTcell/target_7d9156c7a25 Genome = hg19 Output Directory = ./homer/DoubleNegativeTcell Motif length set at 10, Fragment size set to 300 Will optimize 2 putative motifs Using 5 CPUs Using 100 MB for statistics cache Will randomize and repeat motif finding 5 times to estimate FDR Will not run homer for de novo motifs 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/qianhui/anaconda3/envs/chipseq/share/homer/.//data/genomes/hg19//preparsed//hg19.*.cgbins': No such file or directory Could not find background files for 300 bp fragments Below are the sizes that are already available prepared. HOMER will now create background files for 300 bp fragments To CANCEL and rerun with a differet "-size <#>", hit <CTRL+C> now! 5 4 3 2 1 Preparsing genome for 300 bp fragments...(will probably take 1-5 min) sh: 1: preparseGenome.pl: not found wc: /home/qianhui/anaconda3/envs/chipseq/share/homer/.//data/genomes/hg19//preparsed//hg19.300.gcbins: No such file or directory Use of uninitialized value $lineCount in numeric lt (<) at /home/qianhui/anaconda3/envs/chipseq/share/homer/bin/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/qianhui/anaconda3/envs/chipseq/share/homer/.//data/genomes/hg19//preparsed//hg19.300.gcbins: No such file or directory cat: /home/qianhui/anaconda3/envs/chipseq/share/homer/.//data/genomes/hg19//preparsed//hg19.300.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 Skipping... Job finished - if results look good, please send beer to ..

Cleaning up tmp files...

Error in file(file, "rt") : cannot open the connection In addition: Warning message: In file(file, "rt") : cannot open file './homer/DoubleNegativeTcell/knownResults.txt': No such file or directory I've made sure to add the path to homer in my bash_profile. Please let me know the solution of the problem. Thank you very much!