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

[huaixiaolu]

Hello, thank you for providing such a useful tool. I installed EDTA using conda, and when running the test data, I encountered the following ERROR:

mamba create -n EDTA conda activate EDTA mamba install -c conda-forge -c bioconda edta cd ~/anaconda3/envs/mamba/envs/EDTA/share/EDTA/test 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 --threads 10

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

Extensive de-novo TE Annotator (EDTA) v2.1.0

Shujun Ou ([email protected])

######################################################## Fri Sep 20 17:25:07 CST 2024 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. Fri Sep 20 17:25:09 CST 2024 Obtain raw TE libraries using various structure-based programs: Fri Sep 20 17:25:09 CST 2024 EDTA_raw: Check dependencies, prepare working directories. Fri Sep 20 17:25:10 CST 2024 Start to find LTR candidates. Fri Sep 20 17:25:10 CST 2024 Identify LTR retrotransposon candidates from scratch. Invalid value for shared scalar at /home/DataDisk/zl_data/anaconda3/envs/mamba/envs/EDTA/share/LTR_retriever/bin/LTR.identifier.pl line 114, <ANNO> 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 Fri Sep 20 17:25:19 CST 2024 Warning: The LTR result file has 0 bp! Fri Sep 20 17:25:19 CST 2024 Start to find TIR candidates. Fri Sep 20 17:25:19 CST 2024 Identify TIR candidates from scratch. Species: others Fri Sep 20 17:25:29 CST 2024 Finish finding TIR candidates. Fri Sep 20 17:25:29 CST 2024 Start to find Helitron candidates. Fri Sep 20 17:25:29 CST 2024 Identify Helitron candidates from scratch. Fri Sep 20 17:25:59 CST 2024 Finish finding Helitron candidates. Fri Sep 20 17:25:59 CST 2024 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

After running the software, no results were generated. I found that adding the parameter --force 1 still resulted in the ERROR, but it did produce some results.

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 --threads 10 --force 1

I don't know how to resolve this issue, but I feel that it is affecting the results. How can I solve it?

[oushujun]

It’s a known issue and resolved. Please search on other issues. Reinstall LTR_retriever will work.

Shujun

On Fri, Sep 20, 2024 at 6:36 AM huaixiaolu @.***> wrote:

Hello, thank you for providing such a useful tool. I installed EDTA using conda, and when running the test data, I encountered the following ERROR:

mamba create -n EDTA conda activate EDTA mamba install -c conda-forge -c bioconda edta cd ~/anaconda3/envs/mamba/envs/EDTA/share/EDTA/test 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 --threads 10

######################################################## Extensive de-novo TE Annotator (EDTA) v2.1.0 Shujun Ou ( @.***)

######################################################## Fri Sep 20 17:25:07 CST 2024 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. Fri Sep 20 17:25:09 CST 2024 Obtain raw TE libraries using various structure-based programs: Fri Sep 20 17:25:09 CST 2024 EDTA_raw: Check dependencies, prepare working directories. Fri Sep 20 17:25:10 CST 2024 Start to find LTR candidates. Fri Sep 20 17:25:10 CST 2024 Identify LTR retrotransposon candidates from scratch. Invalid value for shared scalar at /home/DataDisk/zl_data/anaconda3/envs/mamba/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 Fri Sep 20 17:25:19 CST 2024 Warning: The LTR result file has 0 bp! Fri Sep 20 17:25:19 CST 2024 Start to find TIR candidates. Fri Sep 20 17:25:19 CST 2024 Identify TIR candidates from scratch. Species: others Fri Sep 20 17:25:29 CST 2024 Finish finding TIR candidates. Fri Sep 20 17:25:29 CST 2024 Start to find Helitron candidates. Fri Sep 20 17:25:29 CST 2024 Identify Helitron candidates from scratch. Fri Sep 20 17:25:59 CST 2024 Finish finding Helitron candidates. Fri Sep 20 17:25:59 CST 2024 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

After running the software, no results were generated. I found that adding the parameter --force 1 still resulted in the ERROR, but it did produce some results.

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 --threads 10 --force 1

image.png (view on web) https://github.com/user-attachments/assets/b1d5aec9-cb6d-4ba9-9cc6-1800f894b31a

I don't know how to resolve this issue, but I feel that it is affecting the results. How can I solve it?

— Reply to this email directly, view it on GitHub https://github.com/oushujun/EDTA/issues/506, or unsubscribe https://github.com/notifications/unsubscribe-auth/ABNX4NDBKRNXO2JODUCIM7TZXP3CVAVCNFSM6AAAAABORYE6U2VHI2DSMVQWIX3LMV43ASLTON2WKOZSGUZTQNBXGYYTINQ . You are receiving this because you are subscribed to this thread.Message ID: @.***>