Open PatrickKratsch opened 6 years ago
Indeed, the fact that the gene and transcript features have the same ID caused the problem there (gene_id is taken as the ID for the gene feature). Thanks FlyBase for generating malformed GTF files once again.. :). The GFF3 version of this file would have exposed the problem even more glaringly (the same ID cannot be used for different features).
Anyway, I was just adjusting a few more things in/around GFF/GTF parsing, again.. I think I fixed this special case too. Please get the pre-release version 1.3.4a (that means: "alpha") and give it a whirl.. (fetch it from: http://ccb.jhu.edu/software/stringtie/#install ) This version should no longer stumble while parsing that GTF, but please let me know if you encounter any other problems.
Thanks a lot for your quick reply, I will give 1.3.4alpha a go soon and let you know how it went. :) Again, really appreciate the quick response and help!
Works! Using the 1.3.4 version fixed this issue. Thanks!
Hi there,
I read over the last thread from 2016 that dealt with this issue already, but I am using Stringtie 1.3.3b (which has an updated GFF parser since the bug from back then), and get the following error:
GFF Error: overlapping duplicate transcript feature (ID=FBgn0013687)
My command:
$STRINGTIE -p $CPUS -G $GTF -o $BASEDIR/assembled/$b.gtf $BASEDIR/BAM/$b
($b is a loop variable, which is the name of a BAM file)I am not running --merge, I am getting this error for assembly.
grep 'FBgn0013687' 'Drosophila_melanogaster.BDGP6.91.gtf'
returns:It seems that gene, exon, and transcript all overlap. Is this a known issue, and do you have an idea about how to solve it?
Thanks a lot in advance.
Best,
Patrick