Problem with HOMER -find <motif file>
I am trying to search for specific motifs in my set of promoters. It should be possible with the option -find *.motif
I know that there are for sure some occurrences because I have found them with search function in Notepad. However HOMER does not give me anything. It did not even created output file (it only created motifFindingParameters.txt). There is no error message. Does anyone no what can be the problem. I will be grateful for any suggestion.
Here is my command:
findMotifsGenome.pl promoters.bed genome.fa results -find motifsA_B.motif > output.txt
And here is the motif file:
TTWCCATATW 1-TTWCCATATW,BestGuess:SVP(MADS)/col-SVP-DAP-Seq(GSE60143)/Homer(0.831) 8.149215 -312.349827 0 T:1342.0(53.94%),B:12610.0(29.97%),P:1e-135
0.105 0.038 0.001 0.856
0.001 0.001 0.001 0.997
0.387 0.127 0.001 0.485
0.074 0.924 0.001 0.001
0.001 0.997 0.001 0.001
0.577 0.124 0.001 0.298
0.412 0.001 0.001 0.586
0.550 0.118 0.001 0.331
0.321 0.001 0.001 0.677
0.398 0.001 0.146 0.455CCAWAAATGG 2-CCAWAAATGG,BestGuess:MF0008.1_MADS_class/Jaspar(0.932) 6.759706 -198.265402 0 T:1069.0(42.97%),B:10443.6(24.82%),P:1e-86
0.096 0.715 0.080 0.109
0.073 0.688 0.022 0.217
0.710 0.033 0.084 0.173
0.364 0.063 0.127 0.446
0.900 0.017 0.035 0.048
0.821 0.030 0.015 0.134
0.740 0.017 0.041 0.202
0.203 0.051 0.061 0.685
0.352 0.020 0.616 0.012
0.094 0.101 0.721 0.084
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