EDTA
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EDTA crahed after no SINE found
Hello,
I am using EDTA v2.2.0 to process my insect genomes. The commands looks like this:
EDTA.pl --genome ${genome.fa} --species others --step all --overwrite 0 --sensitive 1 --anno 1 --threads 30 --cds ${rep.fna}
The program crashed after failure of finding SINE:
Thu 1 Feb 23:29:39 JST 2024 EDTA_raw: Check dependencies, prepare working directories.
Thu 1 Feb 23:29:41 JST 2024 Start to find LTR candidates.
Thu 1 Feb 23:29:41 JST 2024 Identify LTR retrotransposon candidates from scratch.
Fri 2 Feb 00:09:12 JST 2024 Finish finding LTR candidates.
Fri 2 Feb 00:09:12 JST 2024 Start to find SINE candidates.
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.
It might make some sense as RepeatModeler+RepeatMasker estimated low SINE load in my genomes (<5% for most cases, generally 1.5%-3%). So I am wondering if there is any way to finish EDTA pipeline even if no SINE is found in the genome?
Sincerely,
Cong