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?
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