Question: SNAP error in MAKER exon:out_of_bounds
0
5 weeks ago
preethibagopi5 • 0

Hi, I am running a genome annotation in MAKER2 in which I completed the evidence round of maker and got a GFF3 file as output. I used the GFF3 file from the first maker run to train the SNAP in which it is showing me the error as this.

MODEL20592 1 1 3 + errors(3): exon-1:out_of_bounds exon-2:out_of_bounds exon-3:out_of_bounds
MODEL20593 1 1 3 - errors(3): exon-3:out_of_bounds exon-2:out_of_bounds exon-1:out_of_bounds
MODEL20594 1 1 3 - errors(3): exon-3:out_of_bounds exon-2:out_of_bounds exon-1:out_of_bounds
MODEL58264 1 1 5 + errors(5): exon-1:out_of_bounds exon-2:out_of_bounds exon-3:out_of_bounds exon-4:out_of_bounds exon-5:out_of_bounds
MODEL58265 1 1 3 - errors(3): exon-3:out_of_bounds exon-2:out_of_bounds exon-1:out_of_bounds
MODEL58266 1 1 2 - errors(2): exon-2:out_of_bounds exon-1:out_of_bounds
MODEL58267 1 1 4 - errors(4): exon-4:out_of_bounds exon-3:out_of_bounds exon-2:out_of_bounds exon-1:out_of_bounds
MODEL58268 1 1 4 - errors(4): exon-4:out_of_bounds exon-3:out_of_bounds exon-2:out_of_bounds exon-1:out_of_bounds
MODEL58269 1 1 1 - errors(1): exon-1:out_of_bounds
MODEL39568 1 1 1 - errors(1): exon-1:out_of_bounds
***10652 genes, 0 OK, 0 warnings, 10652 errors***

All the gene models are showing errors. I checked with NCBI provided GFF3 file also to train SNAP but I ended up in same error telling that all gene models as error.

**Command Used*****

maker2zff genome.all.gff
fathom -validate geneome.ann genome.dna > snap_validate.output.txt

Can anyone please help me to solve this problem... I don't know whether this is the right place to ask? But I rised my question in maker forum also i didn't get any solution Thanks in advance.

ADD COMMENTlink 5 weeks ago preethibagopi5 • 0 • updated 5 weeks ago h.mon 25k

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