Stringtie error : discarding overlapping duplicate miRNA feature

Question

[Hojn]

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 :

So here are the corresponding structures of :

Arabidopsis.gtf file:

the result of the stringtie construction:

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!