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oushujun / EDTA

Extensive de-novo TE Annotator
https://genomebiology.biomedcentral.com/articles/10.1186/s13059-019-1905-y
GNU General Public License v3.0
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LTR retriever fails #420

Closed foriin closed 5 months ago

foriin commented 5 months ago

Hello, I get this error from EDTA when running on this assembly:

2024-01-17T15:01:18 CET Identify LTR retrotransposon candidates from scratch.
Invalid value for shared scalar at /home/foriin/anaconda3/envs/te/share/LTR_retriever/bin/LTR.identifier.pl line 114, <ANNO> line 3939.

The last file generated is .rawLTR.scn

oushujun commented 5 months ago

Can you please indicate what versions of LTR_retriever and edta you are using?

Shujun

On Thu, Jan 18, 2024 at 3:24 AM Artem Ilin @.***> wrote:

Hello, I get this error from EDTA when running on this assembly https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/013/340/165/GCF_013340165.1_LBDM_Dsuz_2.1.pri/GCF_013340165.1_LBDM_Dsuz_2.1.pri_genomic.fna.gz :

2024-01-17T15:01:18 CET Identify LTR retrotransposon candidates from scratch. Invalid value for shared scalar at /home/foriin/anaconda3/envs/te/share/LTR_retriever/bin/LTR.identifier.pl line 114, line 3939.

The last file generated is .rawLTR.scn

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foriin commented 5 months ago

EDTA v 2.2.0, LTR_retriever v 2.9.4

foriin commented 5 months ago

I've update retriever to 2.9.9, now trying to run EDTA again. Is there a way to set up the maximum length of LTR when running it?

oushujun commented 5 months ago

Yes this is a known bug for LTR_retriever v2.9.4 https://github.com/oushujun/LTR_retriever/issues/153, and has been fixed since v2.9.5. Setting max length for the LTR region is not enabled in LTR_retriever, you may manually filter them using the pass.list file.

foriin commented 5 months ago

Yes, thanks, Shujun, EDTA got to the end after the update.