[maker-devel] MAKER output has different genes with same name

[Matt Simenc]

Hi, I figured out the problem. I needed to use map_forward=1. With that
set, no duplicates.

Matt

On Sat, Jul 16, 2016 at 10:40 PM, Matt Simenc <mcsimenc at gmail.com> wrote:

> I have been using MAKER to iteratively update previous run's annotations
> by running ab initios with fresh training and feeding the previous run's
> GFF using the maker_gff option like this:
>
> maker_gff=previous_run.gff
>
> est_pass=1
>
> altest_pass=1
>
> protein_pass=1
>
> rm_pass=1
>
> model_pass=1
>
> pred_pass=1
>
> other_pass=0
>
>
> Along the way it seems that non-identical features with the same name,
> some covering the same region and some not, accumulate. When I use
> fasta_merge -d ...index.log I get sequences for the duplicates. Am I using
> the control file options incorrectly? Any suggestions how to select final
> models? Or should I redo the runs if I had some settings wrong?
>
>
> Here is a snippet of the gff produced by gff3_merge -d ...index.log
> showing duplicate models:
>
> -------------------------------------
>
> *Sacu_v1_s0077 maker gene 136647 138568 . - .
> ID=snap_masked-Sacu_v1_s0077-abinit-gene-1.20;Name=snap_masked-Sacu_v1_s0077-abinit-gene-1.20;score=70.704*
>
> *Sacu_v1_s0077 maker mRNA 136647 138568 . - .
> ID=snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1;Parent=snap_masked-Sacu_v1_s0077-abinit-gene-1.20;Name=snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1;_AED=1.00;_eAED=1.00;_QI=0|0|0|0|1|1|5|0|158;score=70.704*
>
> Sacu_v1_s0077 maker exon 138512 138568 . - .
> ID=snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1:exon:2329;Parent=snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1
>
> Sacu_v1_s0077 maker exon 138297 138361 . - .
> ID=snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1:exon:2328;Parent=snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1
>
> Sacu_v1_s0077 maker exon 137723 137786 . - .
> ID=snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1:exon:2327;Parent=snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1
>
> Sacu_v1_s0077 maker exon 137578 137643 . - .
> ID=snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1:exon:2326;Parent=snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1
>
> Sacu_v1_s0077 maker exon 136647 136871 . - .
> ID=snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1:exon:2325;Parent=snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1
>
> Sacu_v1_s0077 maker CDS 138512 138568 . - 0
> ID=snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1:cds;Parent=snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1
>
> Sacu_v1_s0077 maker CDS 138297 138361 . - 0
> ID=snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1:cds;Parent=snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1
>
> Sacu_v1_s0077 maker CDS 137723 137786 . - 1
> ID=snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1:cds;Parent=snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1
>
> Sacu_v1_s0077 maker CDS 137578 137643 . - 0
> ID=snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1:cds;Parent=snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1
>
> Sacu_v1_s0077 maker CDS 136647 136871 . - 0
> ID=snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1:cds;Parent=snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1
>
> *Sacu_v1_s0077 maker gene 98236 98541 . - .
> ID=snap_masked-Sacu_v1_s0077-abinit-gene-1.20;Name=snap_masked-Sacu_v1_s0077-abinit-gene-1.20;score=18.18,18.18,18.18*
>
> *Sacu_v1_s0077 maker mRNA 98236 98541 . - .
> ID=snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1;Parent=snap_masked-Sacu_v1_s0077-abinit-gene-1.20;Name=snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1;_AED=1.00;_eAED=1.00;_QI=0|-1|0|0|-1|1|1|0|101;score=18.18,18.18,18.18*
>
>
>
>
> *Sacu_v1_s0004 maker gene 4775142 4775554 . + .
> ID=snap_masked-Sacu_v1_s0004-abinit-gene-47.3;Name=snap_masked-Sacu_v1_s0004-abinit-gene-47.3;score=14.976*
>
> *Sacu_v1_s0004 maker mRNA 4775142 4775554 . + .
> ID=snap_masked-Sacu_v1_s0004-abinit-gene-47.3-mRNA-1;Parent=snap_masked-Sacu_v1_s0004-abinit-gene-47.3;Name=snap_masked-Sacu_v1_s0004-abinit-gene-47.3-mRNA-1;_AED=1.00;_eAED=1.00;_QI=0|0|0|0|1|1|2|0|129;score=14.976*
>
> Sacu_v1_s0004 maker exon 4775142 4775330 . + .
> ID=snap_masked-Sacu_v1_s0004-abinit-gene-47.3-mRNA-1:exon:204;Parent=snap_masked-Sacu_v1_s0004-abinit-gene-47.3-mRNA-1
>
> Sacu_v1_s0004 maker exon 4775354 4775554 . + .
> ID=snap_masked-Sacu_v1_s0004-abinit-gene-47.3-mRNA-1:exon:205;Parent=snap_masked-Sacu_v1_s0004-abinit-gene-47.3-mRNA-1
>
> Sacu_v1_s0004 maker CDS 4775142 4775330 . + 0
> ID=snap_masked-Sacu_v1_s0004-abinit-gene-47.3-mRNA-1:cds;Parent=snap_masked-Sacu_v1_s0004-abinit-gene-47.3-mRNA-1
>
> Sacu_v1_s0004 maker CDS 4775354 4775554 . + 0
> ID=snap_masked-Sacu_v1_s0004-abinit-gene-47.3-mRNA-1:cds;Parent=snap_masked-Sacu_v1_s0004-abinit-gene-47.3-mRNA-1
>
> *Sacu_v1_s0004 maker gene 4767976 4768158 . - .
> ID=snap_masked-Sacu_v1_s0004-abinit-gene-47.3;Name=snap_masked-Sacu_v1_s0004-abinit-gene-47.3;score=-0.624,-0.624,-0.624*
>
> *Sacu_v1_s0004 maker mRNA 4767976 4768158 . - .
> ID=snap_masked-Sacu_v1_s0004-abinit-gene-47.3-mRNA-1;Parent=snap_masked-Sacu_v1_s0004-abinit-gene-47.3;Name=snap_masked-Sacu_v1_s0004-abinit-gene-47.3-mRNA-1;_AED=1.00;_eAED=1.00;_QI=0|-1|0|0|-1|1|1|0|60;score=-0.624,-0.624,-0.624*
>
> Sacu_v1_s0004 maker exon 4767976 4768158 . - .
> ID=snap_masked-Sacu_v1_s0004-abinit-gene-47.3-mRNA-1:exon:211;Parent=snap_masked-Sacu_v1_s0004-abinit-gene-47.3-mRNA-1
>
> Sacu_v1_s0004 maker CDS 4767976 4768158 . - 0
> ID=snap_masked-Sacu_v1_s0004-abinit-gene-47.3-mRNA-1:cds;Parent=snap_masked-Sacu_v1_s0004-abinit-gene-47.3-mRNA-1
>
> Sacu_v1_s0004 snap_masked match 4775142 4775554 14.976 + .
> ID=Sacu_v1_s0004:hit:181:4.5.0.47;Name=snap_masked-Sacu_v1_s0004-abinit-gene-47.3-mRNA-1;score=14.976
>
>
> Here the models' headers from the maker.proteins.fasta:
>
> -------------------------------------
>
> >snap_masked-Sacu_v1_s0004-abinit-gene-47.3-mRNA-1 protein AED:1.00
> eAED:1.00 QI:0|0|0|0|1|1|2|0|129
>
> >snap_masked-Sacu_v1_s0004-abinit-gene-47.3-mRNA-1 protein AED:1.00
> eAED:1.00 QI:0|-1|0|0|-1|1|1|0|60
>
> >snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1 protein AED:1.00
> eAED:1.00 QI:0|0|0|0|1|1|5|0|158
>
> >snap_masked-Sacu_v1_s0077-abinit-gene-1.20-mRNA-1 protein AED:1.00
> eAED:1.00 QI:0|-1|0|0|-1|1|1|0|101
>
>
>
> Thanks!
>
> Matt
>
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