<html><head><meta http-equiv="Content-Type" content="text/html; charset=utf-8"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;" class="">If you are looking to submit to Genebank, tools like GAL are good (<a href="https://github.com/The-Sequence-Ontology/GAL" class="">https://github.com/The-Sequence-Ontology/GAL</a>).<div class=""><br class=""></div><div class="">Things like accession which you listed below only exist inside of GeneBank (i.e. after you submit). They are not produced by pipelines or format converters.</div><div class=""><br class=""></div><div class="">—Carson<br class=""><div><br class=""></div><div><br class=""></div><div><br class=""><blockquote type="cite" class=""><div class="">On May 21, 2019, at 6:11 AM, djerroud samia <<a href="mailto:djerroudsamia@gmail.com" class="">djerroudsamia@gmail.com</a>> wrote:</div><br class="Apple-interchange-newline"><div class=""><div dir="ltr" class="">Hello, thank your for the share, like I said the genbank format is quite important for me. What I really need is to get all this different informations <div class=""><br class=""></div><div class="">cds: accession, protein product, protein sequence, start, end , locus_tag, gene, .....</div><div class="">My problem is I don't know the pipeline I should follow to get all this informaitions</div><div class=""><br class=""></div><div class="">thank you, Samia</div></div><br class=""><div class="gmail_quote"><div dir="ltr" class="gmail_attr">Le mar. 21 mai 2019 à 07:25, p sz <<a href="mailto:seoanezonjic@hotmail.com" target="_blank" class="">seoanezonjic@hotmail.com</a>> a écrit :<br class=""></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" class="">
<div style="font-family: Calibri, Helvetica, sans-serif; font-size: 12pt;" class="">
Hi Xavier<br class="">
I've changed from <a href="http://zff2genbank.pl/" rel="noopener noreferrer" target="_blank" class="">
zff2genbank.pl</a> to <a href="http://zff2augustus_gbk.pl/" rel="noopener noreferrer" target="_blank" class="">
zff2augustus_gbk.pl</a> and the the problem is fixed. I used <a href="http://zff2genbank.pl/" rel="noopener noreferrer" target="_blank" class="">
zff2genbank.pl</a> because it is packaged into the maker suite. I think that MAKER authors should include
<a href="http://zff2augustus_gbk.pl/" rel="noopener noreferrer" target="_blank" class="">zff2augustus_gbk.pl</a> into the main suite, I didn't know about this genome-scripts repository.
<br class="">
By the way, I would like to show you my training steps with augustus, in order to know if they are correct:<br class="">
<span class=""><br class="">
<a href="http://zff2augustus_gbk.pl/" target="_blank" class="">zff2augustus_gbk.pl</a> export.ann export.dna > <a href="http://final_genes.gb/" target="_blank" class="">final_genes.gb</a><br class="">
</span>
<div class="">randomSplit.pl <a href="http://final_genes.gb/" target="_blank" class="">final_genes.gb</a> 500<br class="">
</div>
<div class=""><a href="http://new_species.pl/" target="_blank" class="">new_species.pl</a> --species=Demo<br class="">
</div>
etraining --species=Demo <a href="http://final_genes.gb/" target="_blank" class="">final_genes.gb</a><br class="">
<span class=""><a href="http://optimize_augustus.pl/" target="_blank" class="">optimize_augustus.pl</a> --species=Demo --onlytrain=final_genes.gb.train final_genes.gb.test<br class="">
</span>
<div class="">etraining --species=Demo <a href="http://final_genes.gb/" target="_blank" class="">final_genes.gb</a><br class="">
</div>
<span class=""></span><br class="">
I have taken the training parameters (excepting the 500 parameter) from the <a href="http://train_augustus.pl/" target="_blank" class="">train_augustus.pl</a> script included in MAKER suite.<br class="">
Thank you in advance<br class="">
Pedro Seoane<br class="">
</div>
<div id="gmail-m_1953182863190140628gmail-m_3953440890217211073appendonsend" class=""></div>
<hr style="display:inline-block;width:98%" class="">
<div id="gmail-m_1953182863190140628gmail-m_3953440890217211073divRplyFwdMsg" dir="ltr" class=""><font face="Calibri, sans-serif" style="font-size:11pt" class=""><b class="">De:</b> Xabier Vázquez-Campos <<a href="mailto:xvazquezc@gmail.com" target="_blank" class="">xvazquezc@gmail.com</a>><br class="">
<b class="">Enviado:</b> jueves, 16 de mayo de 2019 4:42<br class="">
<b class="">Para:</b> p sz<br class="">
<b class="">Cc:</b> <a href="mailto:maker-devel@yandell-lab.org" target="_blank" class="">maker-devel@yandell-lab.org</a><br class="">
<b class="">Asunto:</b> Re: [maker-devel] RV: Problem training agustus</font>
<div class=""> </div>
</div>
<div class="">
<div dir="ltr" class="">
<div dir="ltr" class="">
<div class="">Hi Pedro,</div>
<div class="">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 class="">You need to use <a href="http://zff2augustus_gbk.pl/" target="_blank" class="">zff2augustus_gbk.pl</a> not
<a href="http://zff2genbank.pl/" target="_blank" class="">zff2genbank.pl</a>. I don't remember the differences but I know that
<a href="http://zff2augustus_gbk.pl/" target="_blank" class="">zff2augustus_gbk.pl</a> works for sure.</div>
<div class=""><br class="">
</div>
<div class="">Link: <a href="https://github.com/hyphaltip/genome-scripts/blob/master/gene_prediction/zff2augustus_gbk.pl" target="_blank" class="">
https://github.com/hyphaltip/genome-scripts/blob/master/gene_prediction/zff2augustus_gbk.pl</a><br class="">
</div>
<div class="">Cheers,</div>
<div class="">Xabi<br class="">
</div>
</div>
</div>
<br class="">
<div class="gmail-m_1953182863190140628gmail-m_3953440890217211073x_gmail_quote">
<div dir="ltr" class="gmail-m_1953182863190140628gmail-m_3953440890217211073x_gmail_attr">On Tue, 14 May 2019 at 18:12, p sz <<a href="mailto:seoanezonjic@hotmail.com" target="_blank" class="">seoanezonjic@hotmail.com</a>> wrote:<br class="">
</div>
<blockquote class="gmail-m_1953182863190140628gmail-m_3953440890217211073x_gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">
<div dir="ltr" class="">
<div class="">Hi Maker author<br class="">
<div class="">
<div style="font-family: Calibri, Helvetica, sans-serif; font-size: 12pt;" class="">
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" class="">train_augustus.pl</a> script as follows:<br class="">
<br class="">
<a href="http://zff2genbank.pl/" target="_blank" class="">zff2genbank.pl</a> export.ann export.dna >
<a href="http://final_genes.gb/" target="_blank" class="">final_genes.gb</a><br class="">
<a href="http://train_augustus.pl/" target="_blank" class="">train_augustus.pl</a> <a href="http://final_genes.gb/" target="_blank" class="">
final_genes.gb</a> MyOrg<br class="">
<br class="">
For each of my gene models the error is the following:<br class="">
<br class="">
<span class="">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 class="">
</span>
<div class="">GBProcessor::getGeneList(): GBFeature constructor:Format error when reading genbank format.<br class="">
</div>
<span class="">Encountered error after reading 0 annotations.</span><br class="">
<br class="">
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 class="">
(export.ann file)<br class="">
<span class="">>MODEL236<br class="">
</span>
<div class="">Eterm 23624 23647 MODEL236<br class="">
</div>
<div class="">Exon 23354 23549 MODEL236<br class="">
</div>
<div class="">Exon 23004 23249 MODEL236<br class="">
</div>
<div class="">Exon 20923 21067 MODEL236<br class="">
</div>
<div class="">Exon 20389 20558 MODEL236<br class="">
</div>
<div class="">Exon 18821 18898 MODEL236<br class="">
</div>
<div class="">Exon 18471 18637 MODEL236<br class="">
</div>
<div class="">Exon 14945 14971 MODEL236<br class="">
</div>
<div class="">Exon 13511 13598 MODEL236<br class="">
</div>
<div class="">Exon 11920 13315 MODEL236<br class="">
</div>
<div class="">Exon 10459 10467 MODEL236<br class="">
</div>
<div class="">Exon 8873 9050 MODEL236<br class="">
</div>
<div class="">Exon 8628 8775 MODEL236<br class="">
</div>
<div class="">Exon 8374 8485 MODEL236<br class="">
</div>
<div class="">Exon 7880 7993 MODEL236<br class="">
</div>
<div class="">Exon 7689 7791 MODEL236<br class="">
</div>
<div class="">Exon 1917 2051 MODEL236<br class="">
</div>
<span class="">Einit 1001 1006 MODEL236<br class="">
<br class="">
</span>(genbankfile)<br class="">
<span class="">LOCUS MODEL236 24647 bp dna linear UNK<br class="">
</span>
<div class="">ACCESSION unknown<br class="">
</div>
<div class="">FEATURES Location/Qualifiers<br class="">
</div>
<div class=""> source 1..24647<br class="">
</div>
<div class=""> CDS complement(join(1006..1001,2051..1917,7791..7689,<br class="">
</div>
<div class=""> 7993..7880,8485..8374,8775..8628,9050..8873,10467..10459,<br class="">
</div>
<div class=""> 13315..11920,13598..13511,14971..14945,18637..18471,<br class="">
</div>
<div class=""> 18898..18821,20558..20389,21067..20923,23249..23004,<br class="">
</div>
<div class=""> 23549..23354,23647..23624))<br class="">
<br class="">
</div>
<span class=""></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 class="">
Thank you in advance<br class="">
Pedro Seoane<br class="">
</div>
</div>
</div>
</div>
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<div class="">Xabier Vázquez-Campos, <i class="">PhD</i><br class="">
<i class="">Research Associate</i><br class="">
NSW Systems Biology Initiative<br class="">
School of Biotechnology and Biomolecular Sciences<br class="">
The University of New South Wales<br class="">
Sydney NSW 2052 AUSTRALIA<br class="">
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