gff3 loading error

[Wes Barris]

Hi,

I just updated bioperl-live on our system.  Now, I can no longer load
a .gff3 file using bp_seqfeature_load.pl.  When I try, I get these
errors:

wes@biodata> bp_seqfeature_load.pl -d rachel -f -c junk.gff3 *-*.gff3
DBD::mysql::db do failed: BLOB/TEXT column 'tag' used in key specification without a key length at /usr/lib/perl5/site_perl/5.8.5/Bio/DB/SeqFeature/Store/DBI/mysql.pm line 450.

-------------------- EXCEPTION --------------------
MSG: BLOB/TEXT column 'tag' used in key specification without a key length
STACK Bio::DB::SeqFeature::Store::DBI::mysql::_create_table /usr/lib/perl5/site_perl/5.8.5/Bio/DB/SeqFeature/Store/DBI/mysql.pm:450
STACK Bio::DB::SeqFeature::Store::DBI::mysql::_init_database /usr/lib/perl5/site_perl/5.8.5/Bio/DB/SeqFeature/Store/DBI/mysql.pm:425
STACK Bio::DB::SeqFeature::Store::init_database /usr/lib/perl5/site_perl/5.8.5/Bio/DB/SeqFeature/Store.pm:407
STACK Bio::DB::SeqFeature::Store::DBI::mysql::init /usr/lib/perl5/site_perl/5.8.5/Bio/DB/SeqFeature/Store/DBI/mysql.pm:223
STACK Bio::DB::SeqFeature::Store::new /usr/lib/perl5/site_perl/5.8.5/Bio/DB/SeqFeature/Store.pm:370
STACK toplevel /usr/bin/bp_seqfeature_load.pl:85
-------------------------------------------

I know that this may really be a bioperl question, but I wanted to
post here to see if perhaps I should not be using bioperl-live with
gbrowse.
--
Wes Barris <wes.barris@...>

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[Matthew Conte-2]

Hi Wes,

Were you (or anyone else) able to track down this problem?  I'm running into this error when running bp_seqfeature_load.pl after upgrading to bioperl 1.6 from 1.5.  I can point to my 1.5 install to get bp_seqfeature_load.pl to run, but I figured I'd mention you're not the only one seeing this.

-Matt 

On Sun, Oct 4, 2009 at 11:47 PM, Wes Barris <wes.barris@...> wrote:

Hi,

I just updated bioperl-live on our system.  Now, I can no longer load
a .gff3 file using bp_seqfeature_load.pl.  When I try, I get these
errors:

wes@biodata> bp_seqfeature_load.pl -d rachel -f -c junk.gff3 *-*.gff3
DBD::mysql::db do failed: BLOB/TEXT column 'tag' used in key specification without a key length at /usr/lib/perl5/site_perl/5.8.5/Bio/DB/SeqFeature/Store/DBI/mysql.pm line 450.

-------------------- EXCEPTION --------------------
MSG: BLOB/TEXT column 'tag' used in key specification without a key length
STACK Bio::DB::SeqFeature::Store::DBI::mysql::_create_table /usr/lib/perl5/site_perl/5.8.5/Bio/DB/SeqFeature/Store/DBI/mysql.pm:450
STACK Bio::DB::SeqFeature::Store::DBI::mysql::_init_database /usr/lib/perl5/site_perl/5.8.5/Bio/DB/SeqFeature/Store/DBI/mysql.pm:425
STACK Bio::DB::SeqFeature::Store::init_database /usr/lib/perl5/site_perl/5.8.5/Bio/DB/SeqFeature/Store.pm:407
STACK Bio::DB::SeqFeature::Store::DBI::mysql::init /usr/lib/perl5/site_perl/5.8.5/Bio/DB/SeqFeature/Store/DBI/mysql.pm:223
STACK Bio::DB::SeqFeature::Store::new /usr/lib/perl5/site_perl/5.8.5/Bio/DB/SeqFeature/Store.pm:370
STACK toplevel /usr/bin/bp_seqfeature_load.pl:85
-------------------------------------------

I know that this may really be a bioperl question, but I wanted to
post here to see if perhaps I should not be using bioperl-live with
gbrowse.
--
Wes Barris <wes.barris@...>

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[Keiran Raine]

Hi all,

Was your GFF3 file created from a GTF file using the gtf2gff3 script?

I discovered some errors in this (and the supplied config file) when using the resulting files as an in memory database.

One of the problems was that the config file causes the Name attribute tag to be written in all upper case which is incorrect.  The other issue relates to the same attribute column.  The final attribute of each record was being written with a  trailing '; '.  I think this may be your problem below.

You can check this by loading your gff3 file (or part of it) into this:

http://dev.wormbase.org/db/validate_gff3/validate_gff3_online

I've attached a corrected version of this and the config file.

-- The Wellcome Trust Sanger Institute is operated by Genome Research Limited, a charity registered in England with number 1021457 and a compa ny registered in England with number 2742969, whose registered office is 2 15 Euston Road, London, NW1 2BE.

I tried to report this to the author in the readme file but the email address is no longer valid.

Hope this helps.

Regards,

Keiran Raine

Senior Computer Biologist

The Cancer Genome Project

Ext: 2100

kr2@...

The Wellcome Trust Sanger Institute is operated by Genome Research 
Limited, a charity registered in England with number 1021457 and a 
company registered in England with number 2742969, whose registered 
office is 215 Euston Road, London, NW1 2BE. 

On 20 Nov 2009, at 22:51, Matthew Conte wrote:

Hi Wes,

Were you (or anyone else) able to track down this problem?  I'm running into this error when running bp_seqfeature_load.pl after upgrading to bioperl 1.6 from 1.5.  I can point to my 1.5 install to get bp_seqfeature_load.pl to run, but I figured I'd mention you're not the only one seeing this.

-Matt 

On Sun, Oct 4, 2009 at 11:47 PM, Wes Barris <wes.barris@...> wrote:

Hi,

I just updated bioperl-live on our system.  Now, I can no longer load
a .gff3 file using bp_seqfeature_load.pl.  When I try, I get these
errors:

wes@biodata> bp_seqfeature_load.pl -d rachel -f -c junk.gff3 *-*.gff3
DBD::mysql::db do failed: BLOB/TEXT column 'tag' used in key specification without a key length at /usr/lib/perl5/site_perl/5.8.5/Bio/DB/SeqFeature/Store/DBI/mysql.pm line 450.

-------------------- EXCEPTION --------------------
MSG: BLOB/TEXT column 'tag' used in key specification without a key length
STACK Bio::DB::SeqFeature::Store::DBI::mysql::_create_table /usr/lib/perl5/site_perl/5.8.5/Bio/DB/SeqFeature/Store/DBI/mysql.pm:450
STACK Bio::DB::SeqFeature::Store::DBI::mysql::_init_database /usr/lib/perl5/site_perl/5.8.5/Bio/DB/SeqFeature/Store/DBI/mysql.pm:425
STACK Bio::DB::SeqFeature::Store::init_database /usr/lib/perl5/site_perl/5.8.5/Bio/DB/SeqFeature/Store.pm:407
STACK Bio::DB::SeqFeature::Store::DBI::mysql::init /usr/lib/perl5/site_perl/5.8.5/Bio/DB/SeqFeature/Store/DBI/mysql.pm:223
STACK Bio::DB::SeqFeature::Store::new /usr/lib/perl5/site_perl/5.8.5/Bio/DB/SeqFeature/Store.pm:370
STACK toplevel /usr/bin/bp_seqfeature_load.pl:85
-------------------------------------------

I know that this may really be a bioperl question, but I wanted to
post here to see if perhaps I should not be using bioperl-live with
gbrowse.
--
Wes Barris <wes.barris@...>

------------------------------------------------------------------------------
Come build with us! The BlackBerry&reg; Developer Conference in SF, CA
is the only developer event you need to attend this year. Jumpstart your
developing skills, take BlackBerry mobile applications to market and stay
ahead of the curve. Join us from November 9&#45;12, 2009. Register now&#33;
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[Wes Barris]

Matthew Conte wrote:
> Hi Wes,
>
> Were you (or anyone else) able to track down this problem?  I'm running
> into this error when running bp_seqfeature_load.pl
> <http://bp_seqfeature_load.pl> after upgrading to bioperl 1.6 from 1.5.
>  I can point to my 1.5 install to get bp_seqfeature_load.pl
> <http://bp_seqfeature_load.pl> to run, but I figured I'd mention you're
> not the only one seeing this.

Hi Matt,

I was never able to solve that problem.  In my case, I had to back down
from bioperl-live and reinstall bioperl-1.6 which works fine for me.

Sorry.

> -Matt
>
> On Sun, Oct 4, 2009 at 11:47 PM, Wes Barris <wes.barris@...> wrote:
>
>     Hi,
>
>     I just updated bioperl-live on our system.  Now, I can no longer load
>     a .gff3 file using bp_seqfeature_load.pl
>     <http://bp_seqfeature_load.pl>.  When I try, I get these
>     errors:
>
>     wes@biodata> bp_seqfeature_load.pl <http://bp_seqfeature_load.pl> -d
>     rachel -f -c junk.gff3 *-*.gff3
>     DBD::mysql::db do failed: BLOB/TEXT column 'tag' used in key
>     specification without a key length at
>     /usr/lib/perl5/site_perl/5.8.5/Bio/DB/SeqFeature/Store/DBI/mysql.pm
>     <http://mysql.pm> line 450.
>
>     -------------------- EXCEPTION --------------------
>     MSG: BLOB/TEXT column 'tag' used in key specification without a key
>     length
>     STACK Bio::DB::SeqFeature::Store::DBI::mysql::_create_table
>     /usr/lib/perl5/site_perl/5.8.5/Bio/DB/SeqFeature/Store/DBI/mysql.pm:450
>     <http://mysql.pm:450>
>     STACK Bio::DB::SeqFeature::Store::DBI::mysql::_init_database
>     /usr/lib/perl5/site_perl/5.8.5/Bio/DB/SeqFeature/Store/DBI/mysql.pm:425
>     <http://mysql.pm:425>
>     STACK Bio::DB::SeqFeature::Store::init_database
>     /usr/lib/perl5/site_perl/5.8.5/Bio/DB/SeqFeature/Store.pm:407
>     STACK Bio::DB::SeqFeature::Store::DBI::mysql::init
>     /usr/lib/perl5/site_perl/5.8.5/Bio/DB/SeqFeature/Store/DBI/mysql.pm:223
>     <http://mysql.pm:223>
>     STACK Bio::DB::SeqFeature::Store::new
>     /usr/lib/perl5/site_perl/5.8.5/Bio/DB/SeqFeature/Store.pm:370
>     STACK toplevel /usr/bin/bp_seqfeature_load.pl:85
>     <http://bp_seqfeature_load.pl:85>
>     -------------------------------------------
>
>     I know that this may really be a bioperl question, but I wanted to
>     post here to see if perhaps I should not be using bioperl-live with
>     gbrowse.
>     --
>     Wes Barris <wes.barris@...>
>
>     ------------------------------------------------------------------------------
>     Come build with us! The BlackBerry® Developer Conference in SF, CA
>     is the only developer event you need to attend this year. Jumpstart your
>     developing skills, take BlackBerry mobile applications to market and
>     stay
>     ahead of the curve. Join us from November 9-12, 2009. Register
>     now!
>     http://p.sf.net/sfu/devconf
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>     Gmod-gbrowse mailing list
>     Gmod-gbrowse@...
>     <mailto:Gmod-gbrowse@...>
>     https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse
>
>

--
Wes Barris <wes.barris@...>

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[Matthew Conte-2]

Keiran,

I was using a GFF3 file that had trailing a trailing ';' at the end of each attribute (created by Maker, not the gtf2gff3 script though).  However, I still get the error with or without the trailing ';' using Bioperl 1.6.  Using Bioperl 1.5 bp_seqfeature_load.pl loads the file fine, with or without the trailing ';'.

-Matt

On Sun, Nov 22, 2009 at 11:39 AM, Keiran Raine <kr2@...> wrote:

Hi all,

Was your GFF3 file created from a GTF file using the gtf2gff3 script?

I discovered some errors in this (and the supplied config file) when using the resulting files as an in memory database.

One of the problems was that the config file causes the Name attribute tag to be written in all upper case which is incorrect.  The other issue relates to the same attribute column.  The final attribute of each record was being written with a  trailing '; '.  I think this may be your problem below.

You can check this by loading your gff3 file (or part of it) into this:

http://dev.wormbase.org/db/validate_gff3/validate_gff3_online

I've attached a corrected version of this and the config file.

-- The Wellcome Trust Sanger Institute is operated by Genome Research Limited, a charity registered in England with number 1021457 and a compa ny registered in England with number 2742969, whose registered office is 2 15 Euston Road, London, NW1 2BE.

I tried to report this to the author in the readme file but the email address is no longer valid.

Hope this helps.

Regards,

Keiran Raine

Senior Computer Biologist

The Cancer Genome Project

Ext: 2100

kr2@...

The Wellcome Trust Sanger Institute is operated by Genome Research 
Limited, a charity registered in England with number 1021457 and a 
company registered in England with number 2742969, whose registered 
office is 215 Euston Road, London, NW1 2BE. 

On 20 Nov 2009, at 22:51, Matthew Conte wrote:

Hi Wes,

Were you (or anyone else) able to track down this problem?  I'm running into this error when running bp_seqfeature_load.pl after upgrading to bioperl 1.6 from 1.5.  I can point to my 1.5 install to get bp_seqfeature_load.pl to run, but I figured I'd mention you're not the only one seeing this.

-Matt 

On Sun, Oct 4, 2009 at 11:47 PM, Wes Barris <wes.barris@...> wrote:

Hi,

I just updated bioperl-live on our system.  Now, I can no longer load
a .gff3 file using bp_seqfeature_load.pl.  When I try, I get these
errors:

wes@biodata> bp_seqfeature_load.pl -d rachel -f -c junk.gff3 *-*.gff3
DBD::mysql::db do failed: BLOB/TEXT column 'tag' used in key specification without a key length at /usr/lib/perl5/site_perl/5.8.5/Bio/DB/SeqFeature/Store/DBI/mysql.pm line 450.

-------------------- EXCEPTION --------------------
MSG: BLOB/TEXT column 'tag' used in key specification without a key length
STACK Bio::DB::SeqFeature::Store::DBI::mysql::_create_table /usr/lib/perl5/site_perl/5.8.5/Bio/DB/SeqFeature/Store/DBI/mysql.pm:450
STACK Bio::DB::SeqFeature::Store::DBI::mysql::_init_database /usr/lib/perl5/site_perl/5.8.5/Bio/DB/SeqFeature/Store/DBI/mysql.pm:425
STACK Bio::DB::SeqFeature::Store::init_database /usr/lib/perl5/site_perl/5.8.5/Bio/DB/SeqFeature/Store.pm:407
STACK Bio::DB::SeqFeature::Store::DBI::mysql::init /usr/lib/perl5/site_perl/5.8.5/Bio/DB/SeqFeature/Store/DBI/mysql.pm:223
STACK Bio::DB::SeqFeature::Store::new /usr/lib/perl5/site_perl/5.8.5/Bio/DB/SeqFeature/Store.pm:370
STACK toplevel /usr/bin/bp_seqfeature_load.pl:85
-------------------------------------------

I know that this may really be a bioperl question, but I wanted to
post here to see if perhaps I should not be using bioperl-live with
gbrowse.
--
Wes Barris <wes.barris@...>

------------------------------------------------------------------------------
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developing skills, take BlackBerry mobile applications to market and stay
ahead of the curve. Join us from November 9&#45;12, 2009. Register now&#33;
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