Hello everyone,

I just ran RepeatModeler and RepeatMasker to identify repeats in a fungal genome and mask them but I see that the RepeatMasker output doesn't look like I expected. I see that there are no elements corresponding to DNA transposons, satellites and SINEs. Am I doing something wrong? In other species of the same fungal, elements that are not shown in my fungal are present.

The script I executed was the following:

# Run RepeatModeler
BuildDatabase -name fungal_T9 fungal_T9_kmer.fasta

RepeatModeler -database fungal_T9 -threads 8 -LTRStruct

# Run RepeatMasker
RepeatMasker fungal_T9_kmer.fasta -lib consensi.fa.classified -xsmall -gff -pa 8 -s -dir RepeatMasker_consensi/

The output of RepeatMasker::

fungal_T9_kmer.fasta.cat.gz  
fungal_T9_kmer.fasta.out      
fungal_T9_kmer.fasta.tbl
fungal_T9_kmer.fasta.masked  
fungal_T9_kmer.fasta.out.gff

My fungal_T9_kmer.fasta.tbl file:

==================================================
file name: fungal_T9_kmer.fasta
sequences:           142
total length:   39853892 bp  (39853892 bp excl N/X-runs)
GC level:         48.24 %
bases masked:    2066966 bp ( 5.19 %)
==================================================
               number of      length   percentage
               elements*    occupied  of sequence
--------------------------------------------------
Retroelements          530      1139611 bp    2.86 %
   SINEs:                0            0 bp    0.00 %
   Penelope:             0            0 bp    0.00 %
   LINEs:               92       180401 bp    0.45 %
    CRE/SLACS            0            0 bp    0.00 %
     L2/CR1/Rex          0            0 bp    0.00 %
     R1/LOA/Jockey       0            0 bp    0.00 %
     R2/R4/NeSL          0            0 bp    0.00 %
     RTE/Bov-B           0            0 bp    0.00 %
     L1/CIN4             0            0 bp    0.00 %
   LTR elements:       438       959210 bp    2.41 %
     BEL/Pao             0            0 bp    0.00 %
     Ty1/Copia           0            0 bp    0.00 %
     Gypsy/DIRS1       342       812490 bp    2.04 %
       Retroviral       96       146720 bp    0.37 %

DNA transposons          0            0 bp    0.00 %
   hobo-Activator        0            0 bp    0.00 %
   Tc1-IS630-Pogo        0            0 bp    0.00 %
   En-Spm                0            0 bp    0.00 %
   MULE-MuDR             0            0 bp    0.00 %
   PiggyBac              0            0 bp    0.00 %
   Tourist/Harbinger     0            0 bp    0.00 %
   Other (Mirage,        0            0 bp    0.00 %
    P-element, Transib)

Rolling-circles          0            0 bp    0.00 %

Unclassified:         1549       496138 bp    1.24 %

Total interspersed repeats:     1635749 bp    4.10 %


Small RNA:               0            0 bp    0.00 %

Satellites:              0            0 bp    0.00 %
Simple repeats:       8560       360341 bp    0.90 %
Low complexity:       1434        70876 bp    0.18 %
==================================================

* most repeats fragmented by insertions or deletions
  have been counted as one element


RepeatMasker version 4.1.5 , sensitive mode

run with rmblastn version 2.14.1+
The query was compared to classified sequences in ".../consensi.fa.classified"
FamDB: