Finding transposable elements using RepeatMasker I'm using RepeatMasker to detect, classify the Transposable elements. My Input is a eukaryotic non-reference genome.
I made a run via RepeatMasker many times to Mask the TEs, but return 0 Annotation tables.
Further, I used a different -species option each time, but Annotation results contain only short and simple repeats.

Do I have to create a unique library to detect them?

The command I used:

./RepeatMasker -no_is -noint - species mammal Genome.fna


Results:

sequences:         32573
total length: 2004063690 bp  (1981588036 bp excl N/X-runs)
GC level:         41.28 %
bases masked:   33282890 bp ( 1.66 %)
==================================================
               number of      length   percentage
               elements*    occupied  of sequence
--------------------------------------------------
SINEs:                0            0 bp    0.00 %
      ALUs            0            0 bp    0.00 %
      MIRs            0            0 bp    0.00 %

LINEs:                0            0 bp    0.00 %
      LINE1           0            0 bp    0.00 %
      LINE2           0            0 bp    0.00 %
      L3/CR1          0            0 bp    0.00 %

LTR elements:         0            0 bp    0.00 %
      ERVL            0            0 bp    0.00 %
      ERVL-MaLRs      0            0 bp    0.00 %
      ERV_classI      0            0 bp    0.00 %
      ERV_classII     0            0 bp    0.00 %

DNA elements:         0            0 bp    0.00 %
     hAT-Charlie      0            0 bp    0.00 %
     TcMar-Tigger     0            0 bp    0.00 %

Unclassified:         0            0 bp    0.00 %

Total interspersed repeats:        0 bp    0.00 %


Small RNA:            0            0 bp    0.00 %

Satellites:           1          267 bp    0.00 %
Simple repeats:  663679     27953718 bp    1.39 %
Low complexity:  123705      6154714 bp    0.31 %
==================================================
You need to model the repeats in your de novo genome.

See:
http://www.repeatmasker.org/RepeatModeler/ and
https://www.biostars.org/p/154290/ (from previous answer)

You first build a database named "name_of_your_database" (insert whatever you want to call it) and run it on the fasta file of your genome (e.g. your_genome.fasta).

Make you find the right paths for the software.

## build the database
BuildDatabase -engine ncbi -name name_of_your_database your_genome.fasta

## run the modeler (in this case using ncbi)
RepeatModeler -database name_of_your_database -engine ncbi