EDTA crashing after not finding any SINE candidates

[cohen-r]

Hello and thanks for the great tool!

I have been trying to run EDTA on a plant genome that I assembled, but have been running into issues. I installed EDTA using conda + cloning the github repo. I successfully ran EDTA on my genome 2 weeks ago, but recently adjusted my scaffolding and am trying to re-run the masking and repeat ID process. Now, every time I try to run EDTA, I get the following error and it crashes:

cp: cannot stat 'genome.fa.mod.SINE.raw.fa': No such file or directory
Error: SINE results not found!

ERROR: Raw SINE results not found in genome.fa.mod.EDTA.raw/genome.fa.mod.SINE.raw.fa
If you believe the program is working properly, this may be caused by the lack of SINEs in your genome.

I don't have any expectation that there wouldn't be SINEs in this genome. When I try running the command with --force 1, it gets past the SINE identification stage but fails to properly repeat mask the genome.

When a colleague runs EDTA with the same genome using his installation, it runs properly.

Do you have any idea what could be going on?

Here is the command and exact error:
perl EDTA/EDTA.pl --genome ../Assembly/hifiasm_hic_2/Pgroen.Genome02.fa --overwrite 1 --sensitive 1 --anno 1 --threads 8

#########################################################

Extensive de-novo TE Annotator (EDTA) v2.2.1

Shujun Ou ([email protected])

#########################################################

Parameters: --genome ../Assembly/hifiasm_hic_2/Pgroen.Genome02.fa --overwrite 1 --sensitive 1 --anno 1 --threads 8

Tue Apr 29 05:53:17 PM UTC 2025 Dependency checking:
All passed!

Tue Apr 29 05:53:52 PM UTC 2025 Obtain raw TE libraries using various structure-based programs:
Tue Apr 29 05:53:52 PM UTC 2025 EDTA_raw: Check dependencies, prepare working directories.

Tue Apr 29 05:53:54 PM UTC 2025 Start to find LTR candidates.

Tue Apr 29 05:53:54 PM UTC 2025 Identify LTR retrotransposon candidates from scratch.

Wed Apr 30 09:29:32 AM UTC 2025 Finish finding LTR candidates.

Wed Apr 30 09:29:32 AM UTC 2025 Start to find SINE candidates.

cp: cannot stat 'Pgroen.Genome02.fa.mod.SINE.raw.fa': No such file or directory
Error: SINE results not found!

ERROR: Raw SINE results not found in Pgroen.Genome02.fa.mod.EDTA.raw/Pgroen.Genome02.fa.mod.SINE.raw.fa
If you believe the program is working properly, this may be caused by the lack of SINEs in your genome.