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EDTA crahed after no SINE found

Open CongLiu37 opened this issue 5 months ago • 5 comments

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

CongLiu37 avatar Feb 02 '24 04:02 CongLiu37