Annotation issue still there in v2.1.3

[sahoo-rk]

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]

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]

It works fine now. Thanks.