[maker-devel] RV: Problem training agustus

[djerroud samia]

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

cds: accession, protein product, protein sequence, start, end , locus_tag,
gene, .....
My problem is I don't know the pipeline I should follow to get all this
informaitions

thank you, Samia

Le mar. 21 mai 2019 à 07:25, p sz <seoanezonjic at hotmail.com> a écrit :

> Hi Xavier
> I've changed from zff2genbank.pl to zff2augustus_gbk.pl  and the the
> problem is fixed. I used zff2genbank.pl  because it is packaged into the
> maker suite. I think that MAKER authors should include zff2augustus_gbk.pl
> into the main suite, I didn't know about this genome-scripts repository.
> By the way, I would like to show you my training steps with augustus, in
> order to know if they are correct:
>
> zff2augustus_gbk.pl export.ann export.dna > final_genes.gb
> randomSplit.pl final_genes.gb 500
> new_species.pl --species=Demo
> etraining --species=Demo final_genes.gb
> optimize_augustus.pl --species=Demo --onlytrain=final_genes.gb.train
> final_genes.gb.test
> etraining --species=Demo final_genes.gb
>
> I have taken the training parameters (excepting the 500 parameter) from
> the train_augustus.pl script included in MAKER suite.
> Thank you in advance
> Pedro Seoane
> ------------------------------
> *De:* Xabier Vázquez-Campos <xvazquezc at gmail.com>
> *Enviado:* jueves, 16 de mayo de 2019 4:42
> *Para:* p sz
> *Cc:* maker-devel at yandell-lab.org
> *Asunto:* Re: [maker-devel] RV: Problem training agustus
>
> Hi Pedro,
> 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.
> You need to use zff2augustus_gbk.pl not zff2genbank.pl. I don't remember
> the differences but I know that zff2augustus_gbk.pl works for sure.
>
> Link:
> https://github.com/hyphaltip/genome-scripts/blob/master/gene_prediction/zff2augustus_gbk.pl
> Cheers,
> Xabi
>
> On Tue, 14 May 2019 at 18:12, p sz <seoanezonjic at hotmail.com> wrote:
>
> Hi Maker author
> 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
> train_augustus.pl script as follows:
>
> zff2genbank.pl export.ann export.dna > final_genes.gb
> train_augustus.pl final_genes.gb MyOrg
>
> For each of my gene models the error is the following:
>
> 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
> GBProcessor::getGeneList(): GBFeature constructor:Format error when
> reading genbank format.
> Encountered error after reading 0 annotations.
>
> 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:
> (export.ann file)
> >MODEL236
> Eterm   23624   23647   MODEL236
> Exon    23354   23549   MODEL236
> Exon    23004   23249   MODEL236
> Exon    20923   21067   MODEL236
> Exon    20389   20558   MODEL236
> Exon    18821   18898   MODEL236
> Exon    18471   18637   MODEL236
> Exon    14945   14971   MODEL236
> Exon    13511   13598   MODEL236
> Exon    11920   13315   MODEL236
> Exon    10459   10467   MODEL236
> Exon    8873    9050    MODEL236
> Exon    8628    8775    MODEL236
> Exon    8374    8485    MODEL236
> Exon    7880    7993    MODEL236
> Exon    7689    7791    MODEL236
> Exon    1917    2051    MODEL236
> Einit   1001    1006    MODEL236
>
> (genbankfile)
> LOCUS       MODEL236               24647 bp    dna     linear   UNK
> ACCESSION   unknown
> FEATURES             Location/Qualifiers
>      source          1..24647
>      CDS             complement(join(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))
>
> 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?
> Thank you in advance
> Pedro Seoane
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>
>
>
> --
> Xabier Vázquez-Campos, *PhD*
> *Research Associate*
> NSW Systems Biology Initiative
> School of Biotechnology and Biomolecular Sciences
> The University of New South Wales
> Sydney NSW 2052 AUSTRALIA
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