A new error for LTR

[SC-Duan]

Hi, when I test EDTA in conda EDTA environment with "EDTA.pl --genome genome.fa --cds genome.cds.fa --curatedlib ../database/rice6.9.5.liban --exclude genome.exclude.bed --overwrite 1 --sensitive 1 --anno 1 --evaluate 1 --threads 10", I got an error:

Sat May 27 15:36:22 CST 2023 Dependency checking: All passed!

    A custom library ../database/rice6.9.5.liban is provided via --curatedlib. Please make sure this is a manually curated library but not machine generated.

    A CDS file genome.cds.fa is provided via --cds. Please make sure this is the DNA sequence of coding regions only.

    A BED file is provided via --exclude. Regions specified by this file will be excluded from TE annotation and masking.

Sat May 27 15:36:30 CST 2023 Obtain raw TE libraries using various structure-based programs: Sat May 27 15:36:30 CST 2023 EDTA_raw: Check dependencies, prepare working directories.

Sat May 27 15:36:33 CST 2023 Start to find LTR candidates.

Sat May 27 15:36:33 CST 2023 Identify LTR retrotransposon candidates from scratch.

Invalid value for shared scalar at ~/soft/anaconda3/envs/edta/share/LTR_retriever/bin/LTR.identifier.pl line 114, line 11. cp: cannot stat 'genome.fa.mod.retriever.scn.adj': No such file or directory awk: fatal: cannot open file `genome.fa.mod.pass.list' for reading (No such file or directory) Warning: LOC list - is empty.

Error: Error while loading sequence perl filter_gff3.pl file.gff3 file.list > new.gff3

Sat May 27 15:37:02 CST 2023 Warning: The LTR result file has 0 bp!

Sat May 27 15:37:02 CST 2023 Start to find TIR candidates.

Sat May 27 15:37:02 CST 2023 Identify TIR candidates from scratch.

Species: others Sat May 27 15:38:39 CST 2023 Finish finding TIR candidates.

Sat May 27 15:38:39 CST 2023 Start to find Helitron candidates.

Sat May 27 15:38:39 CST 2023 Identify Helitron candidates from scratch.

Sat May 27 15:40:09 CST 2023 Finish finding Helitron candidates.

Sat May 27 15:40:09 CST 2023 Execution of EDTA_raw.pl is finished!

ERROR: Raw LTR results not found in genome.fa.mod.EDTA.raw/genome.fa.mod.LTR.raw.fa If you believe the program is working properly, this may be caused by the lack of intact LTRs in your genome. Consider to use the -- force 1 parameter to overwrite this check

I install the EDTA by Conda. How should I check the problem? Thank you!

[SC-Duan]

Same as https://github.com/oushujun/LTR_retriever/issues/153

[SC-Duan]

Well, the version of LTR_retriever is 2.9.x under automatic conda installation. Downgrading to 2.8.x and it woks.

[oushujun]

Thank you for catching the bug. I will look into the recent LTR_retriever update and see what's going on.

Shujun

On Sat, May 27, 2023 at 4:28 AM SC-Duan @.***> wrote:

Well, the version of LTR_retriever is 2.9.x under automatic conda installation. Downgrading to 2.8.x and it woks.

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