Stringtie error : discarding overlapping duplicate miRNA feature


Hi everyone!

I am following a pipeline to extract new variants for A. thaliana. I have already conducted this part of the process but I am doing it again with a newer annotation.gtf to improve and actualize results.

However, the structure of that new .gtf is slightly different, and I am facing errors while running stringtie.

I don't really have clue about how to "resolve" it, or if that is really an issue?

Here is the command I execute :
$ stringtie --rf -G ../files/Arabidopsis.gtf -o myFolder myfile.bam

Here are the errors I get :
enter image description here

So here are the corresponding structures of :

Arabidopsis.gtf file:
enter image description here

the result of the stringtie construction:
enter image description here

Perhaps I am wrong, but I don't really see any discard of information here?
Hope someone had to face the problem, thanks in advance!






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