SNAP error in MAKER exon:out_of_bounds

Question

[preethibagopi5]

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.

[Philipp Bayer]

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

[preethibagopi5]

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 . - .

[lieven.sterck]

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

[preethibagopi5]

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

[lieven.sterck]

Not sure but I have personally never encountered that before

Answer 1

[s.kyungyong64]

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!

[shinasplitzo]

@s.kyungyong64 How did you reorder, please? I have the same problem as @preethibagopi5 . Thank you