<div dir="ltr">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:<div><br></div><div>
<p class="">maker_gff=previous_run.gff</p>
<p class="">est_pass=1</p><p class="">altest_pass=1</p>
<p class="">protein_pass=1</p>
<p class="">rm_pass=1</p>
<p class="">model_pass=1</p>
<p class="">pred_pass=1</p>
<p class="">other_pass=0</p><p class=""><br></p><p class="">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?</p><p class=""><br></p><p class="">Here is a snippet of the gff produced by gff3_merge -d ...index.log showing duplicate models:</p><p class="">-------------------------------------<br></p><p class=""><b>Sacu_v1_s0077<span class=""> </span>maker<span class=""> </span>gene<span class=""> </span>136647<span class=""> </span>138568<span class=""> </span>.<span class=""> </span>-<span class=""> </span>.<span class=""> </span>ID=snap_masked-Sacu_v1_s0077-abinit-gene-1.20;Name=snap_masked-Sacu_v1_s0077-abinit-gene-1.20;score=70.704</b></p><p class=""><b>Sacu_v1_s0077<span class=""> </span>maker<span class=""> </span>mRNA<span class=""> </span>136647<span class=""> </span>138568<span class=""> </span>.<span class=""> </span>-<span class=""> </span>.<span class=""> </span>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</b></p><p class="">Sacu_v1_s0077<span class=""> </span>maker<span class=""> </span>exon<span class=""> </span>138512<span class=""> </span>138568<span class=""> </span>.<span class=""> </span>-<span class=""> </span>.<span class=""> </span>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</p><p class="">Sacu_v1_s0077<span class=""> </span>maker<span class=""> </span>exon<span class=""> </span>138297<span class=""> </span>138361<span class=""> </span>.<span class=""> </span>-<span class=""> </span>.<span class=""> </span>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</p><p class="">Sacu_v1_s0077<span class=""> </span>maker<span class=""> </span>exon<span class=""> </span>137723<span class=""> </span>137786<span class=""> </span>.<span class=""> </span>-<span class=""> </span>.<span class=""> </span>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</p><p class="">Sacu_v1_s0077<span class=""> </span>maker<span class=""> </span>exon<span class=""> </span>137578<span class=""> </span>137643<span class=""> </span>.<span class=""> </span>-<span class=""> </span>.<span class=""> </span>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</p><p class="">Sacu_v1_s0077<span class=""> </span>maker<span class=""> </span>exon<span class=""> </span>136647<span class=""> </span>136871<span class=""> </span>.<span class=""> </span>-<span class=""> </span>.<span class=""> </span>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</p><p class="">Sacu_v1_s0077<span class=""> </span>maker<span class=""> </span>CDS<span class=""> </span>138512<span class=""> </span>138568<span class=""> </span>.<span class=""> </span>-<span class=""> </span>0<span class=""> </span>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</p><p class="">Sacu_v1_s0077<span class=""> </span>maker<span class=""> </span>CDS<span class=""> </span>138297<span class=""> </span>138361<span class=""> </span>.<span class=""> </span>-<span class=""> </span>0<span class=""> </span>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</p><p class="">Sacu_v1_s0077<span class=""> </span>maker<span class=""> </span>CDS<span class=""> </span>137723<span class=""> </span>137786<span class=""> </span>.<span class=""> </span>-<span class=""> </span>1<span class=""> </span>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</p><p class="">Sacu_v1_s0077<span class=""> </span>maker<span class=""> </span>CDS<span class=""> </span>137578<span class=""> </span>137643<span class=""> </span>.<span class=""> </span>-<span class=""> </span>0<span class=""> </span>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</p><p class="">Sacu_v1_s0077<span class=""> </span>maker<span class=""> </span>CDS<span class=""> </span>136647<span class=""> </span>136871<span class=""> </span>.<span class=""> </span>-<span class=""> </span>0<span class=""> </span>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</p><p class=""><b>Sacu_v1_s0077<span class=""> </span>maker<span class=""> </span>gene<span class=""> </span>98236<span class=""> </span>98541<span class=""> </span>.<span class=""> </span>-<span class=""> </span>.<span class=""> </span>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</b></p><p class="">
</p><p class=""><b>Sacu_v1_s0077<span class=""> </span>maker<span class=""> </span>mRNA<span class=""> </span>98236<span class=""> </span>98541<span class=""> </span>.<span class=""> </span>-<span class=""> </span>.<span class=""> </span>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</b></p><p class=""><br></p><p class=""><br></p><p class=""><br></p><p class=""><b>Sacu_v1_s0004<span class=""> </span>maker<span class=""> </span>gene<span class=""> </span>4775142<span class=""> </span>4775554<span class=""> </span>.<span class=""> </span>+<span class=""> </span>.<span class=""> </span>ID=snap_masked-Sacu_v1_s0004-abinit-gene-47.3;Name=snap_masked-Sacu_v1_s0004-abinit-gene-47.3;score=14.976</b></p><p class=""><b>Sacu_v1_s0004<span class=""> </span>maker<span class=""> </span>mRNA<span class=""> </span>4775142<span class=""> </span>4775554<span class=""> </span>.<span class=""> </span>+<span class=""> </span>.<span class=""> </span>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</b></p><p class="">Sacu_v1_s0004<span class=""> </span>maker<span class=""> </span>exon<span class=""> </span>4775142<span class=""> </span>4775330<span class=""> </span>.<span class=""> </span>+<span class=""> </span>.<span class=""> </span>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</p><p class="">Sacu_v1_s0004<span class=""> </span>maker<span class=""> </span>exon<span class=""> </span>4775354<span class=""> </span>4775554<span class=""> </span>.<span class=""> </span>+<span class=""> </span>.<span class=""> </span>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</p><p class="">Sacu_v1_s0004<span class=""> </span>maker<span class=""> </span>CDS<span class=""> </span>4775142<span class=""> </span>4775330<span class=""> </span>.<span class=""> </span>+<span class=""> </span>0<span class=""> </span>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</p><p class="">Sacu_v1_s0004<span class=""> </span>maker<span class=""> </span>CDS<span class=""> </span>4775354<span class=""> </span>4775554<span class=""> </span>.<span class=""> </span>+<span class=""> </span>0<span class=""> </span>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</p><p class=""><b>Sacu_v1_s0004<span class=""> </span>maker<span class=""> </span>gene<span class=""> </span>4767976<span class=""> </span>4768158<span class=""> </span>.<span class=""> </span>-<span class=""> </span>.<span class=""> </span>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</b></p><p class=""><b>Sacu_v1_s0004<span class=""> </span>maker<span class=""> </span>mRNA<span class=""> </span>4767976<span class=""> </span>4768158<span class=""> </span>.<span class=""> </span>-<span class=""> </span>.<span class=""> </span>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</b></p><p class="">Sacu_v1_s0004<span class=""> </span>maker<span class=""> </span>exon<span class=""> </span>4767976<span class=""> </span>4768158<span class=""> </span>.<span class=""> </span>-<span class=""> </span>.<span class=""> </span>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</p><p class="">Sacu_v1_s0004<span class=""> </span>maker<span class=""> </span>CDS<span class=""> </span>4767976<span class=""> </span>4768158<span class=""> </span>.<span class=""> </span>-<span class=""> </span>0<span class=""> </span>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</p><p class="">
</p><p class="">Sacu_v1_s0004<span class=""> </span>snap_masked<span class=""> </span>match<span class=""> </span>4775142<span class=""> </span>4775554<span class=""> </span>14.976<span class=""> </span>+<span class=""> </span>.<span class=""> </span>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</p><p class=""><br></p><p class="">Here the models' headers from the maker.proteins.fasta:</p><p class="">-------------------------------------<br></p><p class="">>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</p><p class="">
</p><p class="">>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</p><p class="">>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</p><p class="">
</p><p class="">>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</p><p class=""><br></p><p class=""><br></p><p class="">Thanks!</p><p class="">Matt</p>
</div></div>