<div dir="ltr"><div dir="ltr"><div>Hi Pedro,</div><div>I checked some of my files and there is no issue with a model in the inverse order. And the gb files generated look fine.</div><div>You need to use <a href="http://zff2augustus_gbk.pl" target="_blank">zff2augustus_gbk.pl</a> not <a href="http://zff2genbank.pl" target="_blank">zff2genbank.pl</a>. I don't remember the differences but I know that <a href="http://zff2augustus_gbk.pl" target="_blank">zff2augustus_gbk.pl</a> works for sure.</div><div><br></div><div>Link: <a href="https://github.com/hyphaltip/genome-scripts/blob/master/gene_prediction/zff2augustus_gbk.pl">https://github.com/hyphaltip/genome-scripts/blob/master/gene_prediction/zff2augustus_gbk.pl</a><br></div><div>Cheers,</div><div>Xabi<br></div></div></div><br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">On Tue, 14 May 2019 at 18:12, p sz <<a href="mailto:seoanezonjic@hotmail.com" target="_blank">seoanezonjic@hotmail.com</a>> wrote:<br></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">
<div dir="ltr">
<div>Hi Maker author<br>
<div>
<div style="font-family:Calibri,Helvetica,sans-serif;font-size:12pt;color:rgb(0,0,0)">
I have been using Maker for long years and recently, I've tried to train agustus using the snap training files. To do this, I have used the <a href="http://train_augustus.pl" target="_blank">train_augustus.pl</a> script as follows:<br>
<br>
<a href="http://zff2genbank.pl" target="_blank">zff2genbank.pl</a> export.ann export.dna > <a href="http://final_genes.gb" target="_blank">final_genes.gb</a><br>
<a href="http://train_augustus.pl" target="_blank">train_augustus.pl</a> <a href="http://final_genes.gb" target="_blank">final_genes.gb</a> MyOrg<br>
<br>
For each of my gene models the error is the following:<br>
<br>
<span>Constructing GenBank feature: Feature begins after it ends: 1006..1001,2051..1917,7791..7689,7993..7880,8485..8374,8775..8628,9050..8873,10467..10459,13315..11920,13598..13511,14971..14945,18637..18471,18898..18821,20558..20389,21067..20923,23249..23004,23549..23354,23647..23624<br>
</span>
<div>GBProcessor::getGeneList(): GBFeature constructor:Format error when reading genbank format.<br>
</div>
<span>Encountered error after reading 0 annotations.</span><br>
<br>
The export files are generated with SNAP as described by your reference guides (two maker rounds). The issue seems related with the sense of the gene model that can be inspected here:<br>
(export.ann file)<br>
<span>>MODEL236<br>
</span>
<div>Eterm 23624 23647 MODEL236<br>
</div>
<div>Exon 23354 23549 MODEL236<br>
</div>
<div>Exon 23004 23249 MODEL236<br>
</div>
<div>Exon 20923 21067 MODEL236<br>
</div>
<div>Exon 20389 20558 MODEL236<br>
</div>
<div>Exon 18821 18898 MODEL236<br>
</div>
<div>Exon 18471 18637 MODEL236<br>
</div>
<div>Exon 14945 14971 MODEL236<br>
</div>
<div>Exon 13511 13598 MODEL236<br>
</div>
<div>Exon 11920 13315 MODEL236<br>
</div>
<div>Exon 10459 10467 MODEL236<br>
</div>
<div>Exon 8873 9050 MODEL236<br>
</div>
<div>Exon 8628 8775 MODEL236<br>
</div>
<div>Exon 8374 8485 MODEL236<br>
</div>
<div>Exon 7880 7993 MODEL236<br>
</div>
<div>Exon 7689 7791 MODEL236<br>
</div>
<div>Exon 1917 2051 MODEL236<br>
</div>
<span>Einit 1001 1006 MODEL236<br>
<br>
</span>(genbankfile)<br>
<span>LOCUS MODEL236 24647 bp dna linear UNK<br>
</span>
<div>ACCESSION unknown<br>
</div>
<div>FEATURES Location/Qualifiers<br>
</div>
<div> source 1..24647<br>
</div>
<div> CDS complement(join(1006..1001,2051..1917,7791..7689,<br>
</div>
<div> 7993..7880,8485..8374,8775..8628,9050..8873,10467..10459,<br>
</div>
<div> 13315..11920,13598..13511,14971..14945,18637..18471,<br>
</div>
<div> 18898..18821,20558..20389,21067..20923,23249..23004,<br>
</div>
<div> 23549..23354,23647..23624))<br>
<br>
</div>
<span></span>It seems that augustus needs the direct sense description of the gene model in order to read the gb file and perform the training. How could I fix the problem?<br>
Thank you in advance<br>
Pedro Seoane<br>
</div>
</div>
</div>
</div>
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</blockquote></div><br clear="all"><br>-- <br><div dir="ltr" class="gmail-m_2186290813376944215gmail-m_8068224295018127423gmail_signature"><div dir="ltr"><div><div dir="ltr"><div><div dir="ltr"><div><div dir="ltr"><div><div dir="ltr"><div>Xabier Vázquez-Campos, <i>PhD</i><br><i>Research Associate</i><br>NSW Systems Biology Initiative<br>School of Biotechnology and Biomolecular Sciences<br>
The University of New South Wales<br>Sydney NSW 2052 AUSTRALIA<br></div></div></div></div></div></div></div></div></div></div></div>