Penelope elements missing from *.tbl and repeat landscapes

[TobyBaril]

Using RepeatMasker with a library generated by RepeatModeler, PLEs are missing from final RepeatMasker quantifications. In the consensus library, RepeatClassifier classifies these elements as family#PLE/subclass. I think this is due to RepBase PLEs having the headers as family#LINE/Penelope, so the inconsistency leads to PLEs not being quantified in the final summaries.

Reproduction steps

RepeatMasker with a library from RepeatModeler in which PLEs are named by RepeatClassifier as: family#PLE/subclass. (E.G family#PLE/Chlamys

• Which version of RepeatMasker do you have?

4.1.4

• Have you installed RepBase RepeatMasker Edition, or the full Dfam database?

Full Dfam 3.7

• Operating system and version.

Ubuntu LTS 22.04

[rmhubley]

This is a timely question. This is an update that is scheduled for the next update of RepeatMasker which should be out in the next week.

[rmhubley]

This has been fixed in RepeatMasker 4.1.5 released today.