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Published 20 hours ago • verified publisher icon NBISweden

Stuck on 'Check8: check exons'

Open sanderthierens opened this issue 2 years ago • 1 comments

We use AGAT version: v0.8.0 as a preprocessing step in one of our pipelines. During testing, a GFF with the correct amount of columns, but with a bad syntax, caused the AGAT script agat_convert_sp_gxf2gxf.pl to be stuck on check 8 (check exons) for hours. No errors were thrown and the problems was only discovered on closer examination of the GFF file. A time out functionality would help us a lot to handle this type of scenario. Nithil2_GeneCatalog_genes_20201125.gff.gz

sanderthierens avatar Jul 12 '22 12:07 sanderthierens

Some users experienced the same problem. It occurred for particular GFF formatted files. It has been resolved in more recent version of AGAT. Please update AGAT.

Juke34 avatar Jul 12 '22 14:07 Juke34