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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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Annotation issue still there in v2.1.3 #372

Closed sahoo-rk closed 7 months ago

sahoo-rk commented 11 months ago

Hi Shujun, With the EDTA v2.1.3, TE identification and annotation completed. But with an empty .sum file, along with the following messages. I guess, I can safely ignore the first two warnings. However, the last one seems the problem for an empty .sum file (previously discussed here #171 ,#219 , #229 ).

  1. polinton/NA not found in the TE_SO database, it will not be used to rename sequences in the final annotation.
  2. Warning: TIR/Sola1 not found in the TE_SO database, will use the general term 'repeat_region SO:0000657' to replace it.
  3. Use of uninitialized value $type in concatenation (.) or string at /home/sahoork/EDTA/util/gff2bed.pl line 110, line 2069.

How to fix this? The temporary solution discussed at #219 doesn't meet the exact line number in current gff2bed.pl file. Please suggest.

Best, -sahoo

oushujun commented 10 months ago

Hi Sahoo,

Sorry, somehow I missed this thread. Please replace the following two files in /EDTA/util/ and try again. gff2bed.txt (rename txt to pl) TE_Sequence_Ontology.txt

Let me know how it goes, thanks!

Shujun

sahoo-rk commented 7 months ago

It works fine now. Thanks.