Question: SNAP error in MAKER exon:out_of_bounds
0
gravatar for preethibagopi5
11 months ago by
preethibagopi50 wrote:

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.

maker2 snap annotation genome • 386 views
ADD COMMENTlink modified 5 months ago by cheapshoppinggifts0 • written 11 months ago by preethibagopi50

Are you sure you're using the same genome assembly fasta with the same gffs? This looks like you have exons with coordinates longer than your assembly contigs/chromosomes, which normally only happens if it's the wrong one

ADD REPLYlink written 11 months ago by Philipp Bayer6.6k

Yes I am using the same GFF file from same genome assembly file..... A part of my GFF file:

Scaffold_94%3BHRSCAF%3D190 . contig 1 59085 . . .
Scaffold_94%3BHRSCAF%3D190 maker exon 4576 4872 . - .
Scaffold_94%3BHRSCAF%3D190 maker exon 4576 4938 . - .
Scaffold_94%3BHRSCAF%3D190 maker exon 4576 5007 . - .
Scaffold_94%3BHRSCAF%3D190 maker exon 4519 4552 . - .
Scaffold_94%3BHRSCAF%3D190 maker exon 4628 4938 . - .
Scaffold_94%3BHRSCAF%3D190 maker exon 4501 4516 . - .
Scaffold_94%3BHRSCAF%3D190 maker exon 4604 4938 . - .
Scaffold_94%3BHRSCAF%3D190 maker exon 4501 4515 . - .
Scaffold_94%3BHRSCAF%3D190 maker exon 4591 4938 . - .
Scaffold_94%3BHRSCAF%3D190 maker exon 4479 4549 . - .
Scaffold_94%3BHRSCAF%3D190 maker exon 4635 4938 . - .
Scaffold_94%3BHRSCAF%3D190 maker exon 4519 4573 . - .

ADD REPLYlink modified 11 months ago • written 11 months ago by preethibagopi50

out of curiosity: what are the %-signs doing in the GFF file?

ADD REPLYlink written 11 months ago by lieven.sterck7.8k

Name of the scaffold is having the % symbol in it. Is that will be the problem.....?

ADD REPLYlink written 11 months ago by preethibagopi50

Not sure but I have personally never encountered that before

ADD REPLYlink written 11 months ago by lieven.sterck7.8k
2
gravatar for s.kyungyong64
5 months ago by
Berkeley, USA
s.kyungyong6430 wrote:

Did you solve this problem? I have not encountered any problems when training SNAP with MAKER outputs. But when training SNAP for other matters, the out_of_bounds issue occurred to me when the the fasta headers are not listed in the same order in both genome.ann and genome.dna.

less genome.ann | grep ">"
>chrUn_random
>chr01
>chr02
>chr03
>chr04
>chr05
>chr06
>chr07
>chr08
>chr09
>chr10
>chr11


 less genome.dna | grep ">"
   >chr01
   >chr02
   >chr03
   >chr04
   >chr05
   >chr06
   >chr07
   >chr08
   >chr09
   >chr10
   >chr11
   >mito1
   >mito2
   >mito3
   >mito4
   >mito5
   >mito6
   >mito7
   >mito8
   >mito9
   >mito10
   >mito11
   >mito12
   >chrUn_random

It looked like SNAP was trying to get the coordinates in ChrUn_random in genome.ann from chr01 in genome.dna. I reordered genome.ann to match the order in genome.dna, and the error was gone. I hope this works!

ADD COMMENTlink written 5 months ago by s.kyungyong6430
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