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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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Two genomes LTR result file has 0 bp, while the others are not. #437

Open ZhuYongli1212 opened 4 months ago

ZhuYongli1212 commented 4 months ago

Hi Shujun,

I'm annotating the over 50 maize genomes using EDTA. I ran into a weird situation where the LTR annotation results for two genomes showing as 0, while the others are normal. I've checked the input files for these two genomes, and they seem no different from the others. Not sure where things went wrong, so I'm reaching out for your help. Any insights would be greatly appreciated.

I am using the below-presented command: EDTA.pl --genome Zm-S37.chr10.fa --anno 1 --threads 3 --curatedlib NAM..MTEC02052020.clean.fa

Error: Mon Feb 26 14:41:26 CST 2024 Obtain raw TE libraries using various structure-based programs: Mon Feb 26 14:41:26 CST 2024 EDTA_raw: Check dependencies, prepare working directories. Mon Feb 26 14:41:29 CST 2024 Start to find LTR candidates. Mon Feb 26 14:41:29 CST 2024 Identify LTR retrotransposon candidates from scratch. ERROR: No candidate is found in the file(s) you specified. awk: cannot open Zm-S37_chr10.fa.mod.pass.list (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 Mon Feb 26 14:41:42 CST 2024 Warning: The LTR result file has 0 bp!

*scn file contains no additional information.

dc783e5ce4d65f29ec872ae3ce63190 865472b0d517e16fe70c18d840dafd3

Looking forward to your response. Thanks a bunch!

Best, Yongli

oushujun commented 3 months ago

Hi Yongli,

Sorry for the delay. Please check the sequence header of your genomes. Also try to run LTR_FINDER_parallel separately and see if there's any error message.

Best, Shujun

oushujun commented 2 months ago

Any luck?

ZhuYongli1212 commented 2 months ago

Apologies for the delay. I've been occupied with other matters recently, and this issue was temporarily set aside. I'll continue addressing this problem and provide timely updates as soon as there are any results. Thank you for your ongoing patience and interest in this matter.