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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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The LTR result file has 0 bp! #408

Closed bvs closed 5 months ago

bvs commented 6 months ago

Dear @oushujun,

I am using EDTA v2.0.1 to annotate TEs/repeats in highly fragmented de novo genome assemblies (50K - 100K scaffolds/assembly). I am annotating several assemblies using the divide-and-conquer strategy, but I am only getting the error below for a few assemblies. This error generates empty files for LTRs.

I am using the below-presented command: $EDTA_raw.pl --genome $genome --type ltr --repeatmasker $repeatmasker -t 5 --convert_seq_name 0

Error:

Thu 30 Nov 18:15:46 CET 2023 EDTA_raw: Check dependencies, prepare working directories. Thu 30 Nov 18:16:00 CET 2023 Start to find LTR candidates. Thu 30 Nov 18:16:00 CET 2023 Identify LTR retrotransposon candidates from scratch. awk: fatal: cannot open file `GCA_029582405.1_S15_genomic.fna2.pass.list' for reading (No such file or directory) Warning: LOC list - is empty. perl rename_LTR_skim.pl target_sequence.fa LTR_retriever.defalse Error: Error while loading sequence perl filter_gff3.pl file.gff3 file.list > new.gff3 Fri 1 Dec 06:57:53 CET 2023 Warning: The LTR result file has 0 bp! Fri 1 Dec 06:57:53 CET 2023 Execution of EDTA_raw.pl is finished!

Please look into this error and let me know a possible solution.

Best, Suresh

linshengnan09 commented 6 months ago

hi, I encountered a similar error. Is your problem solved? The command: EDTA.pl --genome $ref --anno 1 --force 1 --debug 1 -sensitive 1 -t $thread --rmout ${ref}.out --repeatmasker ~/02biosoft/RepeatMasker/RepeatMasker

The log information： Wed Dec 6 12:03:24 CST 2023 EDTA_raw: Check dependencies, prepare working directories.

Wed Dec 6 12:04:25 CST 2023 Start to find LTR candidates.

Wed Dec 6 12:04:25 CST 2023 Identify LTR retrotransposon candidates from scratch.

Invalid value for shared scalar at $home/micromamba/envs/EDTA/share/LTR_retriever/bin/LTR.identifier.pl line 114, line 79176. cp: cannot stat 'Aa_225.fa.mod.retriever.scn.adj': No such file or directory awk: fatal: cannot open file `Aa_225.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

Wed Dec 6 14:09:30 CST 2023 Warning: The LTR result file has 0 bp!

Wed Dec 6 14:09:30 CST 2023 Start to find TIR candidates.

Wed Dec 6 14:09:30 CST 2023 Identify TIR candidates from scratch.

Thank you!

jacquelinemattos commented 6 months ago

Hi, I'm also finding the same error. Any solutions from anyone?

Thanks!

oushujun commented 5 months ago

Please update your LTR_retriever. https://github.com/oushujun/LTR_retriever/issues/153