failing to run busco support_protocol3 probably because agat does not like GFF files

[JoseLopezArcondo]

I am trying to run support protocol3 of the busco pipeline here (https://currentprotocols.onlinelibrary.wiley.com/doi/full/10.1002/cpz1.323), which is working well with the example and some files, but does not work with some other GFF / genomes files. We guess the problem should be in the GFF which I get from GeneMarkEP+ (this one attached does not work, .txt so I can upload here)

would you have any clue what the issue could be here?

GCA_001579715.1.gff.txt)

GCA_001579715.1.fna.txt

[Juke34]

Hi, what AGAT version are you using?

[JoseLopezArcondo]

HI, thanks: agat=0.6.2

[Juke34]

I guess in that publication they use v0.8.0. I advise you to use the most recent version.

[JoseLopezArcondo]

ok. But the example they provide works fine. It's also embedded in a Snakemake pipeline, so I really don't know how could I change this. Do you think the version would be involved in what kind of files could manage?

[Juke34]

You do not have the AGAT log or the error message? You can change the AGAT version used by the snake pipeline for one more recent.

[Juke34]

I have try AGAT V0.6.2 with your file (agat_convert_sp_gxf2gxf.pl) I do not see any problem.