repeatmasker analysis results not loading into chado

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repeatmasker analysis results not loading into chado

claudia

Hi,

 I am getting errors when trying to load repeatmasker results into chado, I have attached a sample gff3 that generates this error, and this has occurred with every gff3, from various projects,  I have tried to load. I am specifying model organism GLYCINE in the maker_opts.ctl file for repeat masking. It seems I don't have this problem with repeatrunner resuls.

EXCEPTION: Bio::Root::Exception -------------
MSG: The value in the Target string, species:A-rich genus:Low_complexity 1 64 +, does not conform to the GFF3 specification
STACK: Error::throw
STACK: Bio::Root::Root::throw /usr/share/perl5/Bio/Root/Root.pm:368
STACK: Bio::FeatureIO::gff::_handle_feature /usr/share/perl5/Bio/FeatureIO/gff.pm:685
STACK: Bio::FeatureIO::gff::next_feature /usr/share/perl5/Bio/FeatureIO/gff.pm:172
STACK: /usr/local/bin/gmod_bulk_load_gff3.pl:777


Any advice on how to fix this is appreciated.
Thanks,
Claudia


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repeatmasker.gff (71K) Download Attachment
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Re: [Gmod-schema] repeatmasker analysis results not loading into chado

Scott Cain
Hi Claudia,

The GFF is fine, the problem is that BioPerl is parsing it
incorrectly, unescaping %20 URI codes in the strings that should be
left in place.  I was made aware of this behavior a few months ago and
fixed it in BioPerl, and that fix should be present in the most recent
release, version 1.6.901.  You should try upgrading to that.

Scott



On Thu, May 19, 2011 at 3:17 PM, Dinatale C <[hidden email]> wrote:

> Hi,
>
>  I am getting errors when trying to load repeatmasker results into chado, I
> have attached a sample gff3 that generates this error, and this has occurred
> with every gff3, from various projects,  I have tried to load. I am
> specifying model organism GLYCINE in the maker_opts.ctl file for repeat
> masking. It seems I don't have this problem with repeatrunner resuls.
>
> EXCEPTION: Bio::Root::Exception -------------
> MSG: The value in the Target string, species:A-rich genus:Low_complexity 1
> 64 +, does not conform to the GFF3 specification
> STACK: Error::throw
> STACK: Bio::Root::Root::throw /usr/share/perl5/Bio/Root/Root.pm:368
> STACK: Bio::FeatureIO::gff::_handle_feature
> /usr/share/perl5/Bio/FeatureIO/gff.pm:685
> STACK: Bio::FeatureIO::gff::next_feature
> /usr/share/perl5/Bio/FeatureIO/gff.pm:172
> STACK: /usr/local/bin/gmod_bulk_load_gff3.pl:777
>
> Any advice on how to fix this is appreciated.
> Thanks,
> Claudia
>
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--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research

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