I am trying to analyze repeat elements in a new draft genome of a non-model organism. I used RepeatModeler to build a de novo repeat library, and then used RepeatMasker (rmblastn version 2.2.27+) to mask the genome. In the .tbl output, I see that no simple repeats or low complexity regions were annotated and many of the subfamilies of SINEs and LINEs are 0%.
An image of the output can be see here: https://ibb.co/djErSF
The commands I used were:
> BuildDatabase -name Reference -engine ncbi ref.fa > RepeatModeler -engine ncbi -database Reference > RepeatMasker -s -lib ~/consensi.fa.classified -dir ~/my_RM_output_dir_Aug11 -e ncbi ~/database/LS_genome.fa
If this is useful in anyway, the query species was assumed to be fly and the analysis used the RepeatMasker Combined Database: Dfam_Consensus-20170127, RepBase-20170127.
What could be the reason that many of the results are coming back as 0%?
Thank you very much!