runHomer
Brawni opened this issue · comments
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!
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?
Hi, your assumption is correct :), i didn't...I exported the genomic regions and run homer from the command line.
Thanks for the quick reply!
So it still didn't work even doing it separately? That was my next thing to try..
By doing separately i meant to run homer from the command line and yes it works
@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!