Hi All,
I did and ATAC-Seq experiment in different cell lines and I was curious to see if they have different motifs in the open chromatin. I was planning to use HOMER for this, but running from linux bash:
I did and ATAC-Seq experiment in different cell lines and I was curious to see if they have different motifs in the open chromatin. I was planning to use HOMER for this, but running from linux bash:
Code:
findMotifsGenome.pl ATAC_d001_peaks_called_with_homer.txt hg38 ATACAd001_FIND_MOTIF I got this message of error (see below), it looks like the problem is in assignGeneWeights.pl line 63. Any tips on how to fix it? Position file = ATAC_d001_peaks_called_with_homer.txt Genome = hg38 Output Directory = ATACAd001_FIND_MOTIF Fragment size set to 400 Found mset for "human", will check against vertebrates motifs Peak/BED file conversion summary: BED/Header formatted lines: 0 peakfile formatted lines: 42719 Peak File Statistics: Total Peaks: 42719 Redundant Peak IDs: 0 Peaks lacking information: 0 (need at least 5 columns per peak) Peaks with misformatted coordinates: 0 (should be integer) Peaks with misformatted strand: 0 (should be either +/- or 0/1) Peak file looks good! Background files for 400 bp fragments found. Extracting sequences from file: /home/l.. Looking for peak sequences in a single file (/home/ls760/r...nome.fa) Not removing redundant sequences Sequences processed: 0 total Frequency Bins: 0.2 0.25 0.3 0.35 0.4 0.45 0.5 0.6 0.7 0.8 Freq Bin Count Total sequences set to 50000 Choosing background that matches in CpG/GC content... Illegal division by zero at /home..mer/bin/assignGeneWeights.pl line 63. Assembling sequence file... Normalizing lower order oligos using homer2 Reading input files... 0 total sequences read Autonormalization: 1-mers (4 total) A inf% inf% -nan C inf% inf% -nan G inf% inf% -nan T inf% inf% -nan Autonormalization: 2-mers (16 total) AA inf% inf% -nan CA inf% inf% -nan GA inf% inf% -nan TA inf% inf% -nan AC inf% inf% -nan CC inf% inf% -nan GC inf% inf% -nan TC inf% inf% -nan AG inf% inf% -nan CG inf% inf% -nan GG inf% inf% -nan TG inf% inf% -nan AT inf% inf% -nan CT inf% inf% -nan GT inf% inf% -nan TT inf% inf% -nan Autonormalization: 3-mers (64 total) Normalization weights can be found in file: ATACAd001_FIND_MOTIF/seq.autonorm.tsv Converging on autonormalization solution: ............................................................................... Final normalization: Autonormalization: 1-mers (4 total) A inf% inf% -nan C inf% inf% -nan G inf% inf% -nan T inf% inf% -nan Autonormalization: 2-mers (16 total) AA inf% inf% -nan CA inf% inf% -nan GA inf% inf% -nan TA inf% inf% -nan AC inf% inf% -nan CC inf% inf% -nan GC inf% inf% -nan TC inf% inf% -nan AG inf% inf% -nan CG inf% inf% -nan GG inf% inf% -nan TG inf% inf% -nan AT inf% inf% -nan CT inf% inf% -nan GT inf% inf% -nan TT inf% inf% -nan Autonormalization: 3-mers (64 total) Finished preparing sequence/group files ---------------------------------------------------------- Known motif enrichment Reading input files... 0 total sequences read 414 motifs loaded Cache length = 11180 Using binomial scoring Checking enrichment of 414 motif(s) |0% 50% 100%| ================================================================================= Illegal division by zero at /home/l...3/homer/bin/findKnownMotifs.pl line 152. ---------------------------------------------------------- De novo motif finding (HOMER) Scanning input files... !!! Something is wrong... are you sure you chose the right length for motif finding? !!! i.e. also check your sequence file!!! Scanning input files... !!! Something is wrong... are you sure you chose the right length for motif finding? !!! i.e. also check your sequence file!!! -blen automatically set to 2 Scanning input files... !!! Something is wrong... are you sure you chose the right length for motif finding? !!! i.e. also check your sequence file!!! Use of uninitialized value in numeric gt (>) at /home.../homer/bin/compareMotifs.pl line 1389. !!! Filtered out all motifs!!! Job finished - if results look good, please send beer to .. Cleaning up tmp files...
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