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

[Matt Simenc]

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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