[maker-devel] Duplicated exons

Michael Nuhn

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May 10, 2013, 8:10:35 AM5/10/13

to maker...@yandell-lab.org

Hello Carson!

I have been trying to get to the bottom of an error message when
(re)training snap. Snap, or more precisely fathom, was giving me unclear
error messages about misordered and overlapping exons.

I have looked into the gff files from which these exons originate and
noticed that a lot of exons in that file were duplicated. For example I
have found these:

LSalAtl2s75 maker exon 186317 186936 . + .
ID=maker-LSalAtl2s75-snap-gene-2.15-mRNA-1:exon:3;Parent=maker-LSalAtl2s75-snap-gene-2.15-mRNA-1
LSalAtl2s75 maker exon 187007 191531 . + .
ID=maker-LSalAtl2s75-snap-gene-2.15-mRNA-1:exon:4;Parent=maker-LSalAtl2s75-snap-gene-2.15-mRNA-1

and then about four hundred lines later there are these:

LSalAtl2s75 maker exon 186317 186936 . + .
ID=maker-LSalAtl2s75-snap-gene-2.15-mRNA-1:exon:1;Parent=maker-LSalAtl2s75-snap-gene-2.15-mRNA-1
LSalAtl2s75 maker exon 187007 191531 . + .
ID=maker-LSalAtl2s75-snap-gene-2.15-mRNA-1:exon:2;Parent=maker-LSalAtl2s75-snap-gene-2.15-mRNA-1

which are identical except for the order number after "exon:".

This seems to have happened to a lot of features in that file.

How can I avoid this? Or if this is just a rare problem, can I have
maker recompute the gff file without redoing all the computations again?

Cheers,
Michael.

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Carson Holt

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May 10, 2013, 12:25:17 PM5/10/13

to Michael Nuhn, maker...@yandell-lab.org

Very odd. Which version of MAEKR are you using. Are you using GFF3
passthrough in the run that generates the duplication?

Thanks,
Carson

Michael Nuhn

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May 10, 2013, 1:35:37 PM5/10/13

to Carson Holt, maker...@yandell-lab.org

On 05/10/2013 05:25 PM, Carson Holt wrote:
> Very odd. Which version of MAEKR are you using. Are you using GFF3
> passthrough in the run that generates the duplication?

I am using version 2.27 of maker. I am not using the passthrough option.

Cheers,
Michael.

Michael Nuhn

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May 10, 2013, 8:29:10 PM5/10/13

to Carson Holt, maker...@yandell-lab.org

On 05/10/2013 07:08 PM, Carson Holt wrote:
> 2.27 from the website download or the SVN devel version?

SVN. I checked it out on 19/03/2013.

> Thanks,
> Carson

Daniel Hughes

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May 10, 2013, 8:20:42 PM5/10/13

to Michael Nuhn, maker...@yandell-lab.org

That is odd. i've run that version of maker 30-40x at ebi lately and never seen it. Is it just one scaffold? While i'd be surprised if it's the cause but have you been playing with the file locking options Carson mentioned a while back? I'd definitely be inclined to re-process it if it's just the one scaffold.

Dan

Carson Holt

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May 13, 2013, 10:01:58 AM5/13/13

to Michael Nuhn, maker...@yandell-lab.org

Could you send me your maker opts files, the contig that fails, and the
evidence files you use for that contig.

Thanks,
Carson

Michael Nuhn

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May 13, 2013, 12:30:36 PM5/13/13

to Carson Holt, maker...@yandell-lab.org

Hello Carson!

On 05/13/2013 03:01 PM, Carson Holt wrote:
> Could you send me your maker opts files, the contig that fails, and the
> evidence files you use for that contig.

Thanks for offering your help.

I worked around the problem this morning by removing all exons from the
training set for which I was getting the error. Now I'm rerunning maker
and I can't find any gff files at the moment with this problem.

If the problem reappears, I'll send you the files.

Carson Holt

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May 13, 2013, 12:07:13 PM5/13/13

to Michael Nuhn, maker...@yandell-lab.org

Ok.

Thanks,
Carson

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