problems loading data using gmod_bulk_load_gff3.pl

classic Classic list List threaded Threaded
21 messages Options
12
Reply | Threaded
Open this post in threaded view
|

problems loading data using gmod_bulk_load_gff3.pl

anja
CONTENTS DELETED
The author has deleted this message.
Reply | Threaded
Open this post in threaded view
|

Re: problems loading data using gmod_bulk_load_gff3.pl

Scott Cain
Hi Anja,

In order to refer to a reference sequence in the first column, the
first thing you must do is to provide a GFF line that identifies that
sequence.  For example, I'm guessing whatever "1" is, it has a length
of 2000 (because you have a sequence-region directive in the file).
So, you would need a gff line something like this:

1     .      contig    1     2000    .     .    .    ID=1;Name=1

Of course, the remaining lines in your GFF file aren't valid either,
because they have "NTR" as a reference sequence, but there is not a
line defining the feature called "NTR" in this file (well, it's not
valid assuming there is not already a feature call "NTR" in your
database; if that were the case it would be fine).

Scott


On Wed, Sep 22, 2010 at 12:33 PM, Anja Friedrich
<[hidden email]> wrote:

> Hi all,
>
> I got an error message I can't interpret by using gmod_bulk_load_gff3.pl
>
> anou@anou-laptop:~$ gmod_bulk_load_gff3.pl --organism taro --gfffile
> taro.gff
> Preparing data for inserting into the chado database
> (This may take a while ...)
> Unable to find srcfeature 1 in the database.
> Perhaps you need to rerun your data load with the '--recreate_cache' option.
> at /usr/local/share/perl/5.10.1/Bio/GMOD/DB/Adapter.pm line 4555
>
> Bio::GMOD::DB::Adapter::src_second_chance('Bio::GMOD::DB::Adapter=HASH(0x994b7d0)',
> 'Bio::SeqFeature::Annotated=HASH(0x9b74258)') called at
> /usr/local/bin/gmod_bulk_load_gff3.pl line 841
>
> Abnormal termination, trying to clean up...
>
> Attempting to clean up the loader temp table (so that --recreate_cache
> won't be needed)...
> Trying to remove the run lock (so that --remove_lock won't be needed)...
> Exiting...
>
> Anyone an idea? I attached the file
>
> Cheers,
> Anja
>
> ------------------------------------------------------------------------------
> Start uncovering the many advantages of virtual appliances
> and start using them to simplify application deployment and
> accelerate your shift to cloud computing.
> http://p.sf.net/sfu/novell-sfdev2dev
> _______________________________________________
> Gmod-schema mailing list
> [hidden email]
> https://lists.sourceforge.net/lists/listinfo/gmod-schema
>
>



--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research

------------------------------------------------------------------------------
Start uncovering the many advantages of virtual appliances
and start using them to simplify application deployment and
accelerate your shift to cloud computing.
http://p.sf.net/sfu/novell-sfdev2dev
_______________________________________________
Gmod-schema mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-schema
Reply | Threaded
Open this post in threaded view
|

FW: problems loading data using gmod_bulk_load_gff3.pl

anja
CONTENTS DELETED
The author has deleted this message.
Reply | Threaded
Open this post in threaded view
|

Re: FW: problems loading data using gmod_bulk_load_gff3.pl

Scott Cain
Hi Anja,

I saw the email on that list but didn't look closely at what Mitch
did.  What Mitch wrote is very close to what would be acceptable.  The
only change that would be need would be the addition of the GFF line
for "1".  The sequence-region directive is fine for display, but is
not OK for Chado, where every feature needs to be typed, like
"chromosome" or "contig".

Scott


On Wed, Sep 22, 2010 at 12:57 PM, Anja Friedrich
<[hidden email]> wrote:

>
>
> ________________________________
> From: [hidden email]
> To: [hidden email]
> Subject: RE: [Gmod-schema] problems loading data using
> gmod_bulk_load_gff3.pl
> Date: Wed, 22 Sep 2010 18:56:32 +0200
>
> Hi Scott,
>
> thanks for the explanation. I can give it a try and change it.
> Well I just extended the gff file Mitch Skinner send me don't know if you
> have seen the post),  and he used to display the feature. Thats how he set
> the file up, so I thought its fine.
>
> Anja
>
>> Date: Wed, 22 Sep 2010 12:45:47 -0400
>> Subject: Re: [Gmod-schema] problems loading data using
>> gmod_bulk_load_gff3.pl
>> From: [hidden email]
>> To: [hidden email]
>> CC: [hidden email]
>>
>> Hi Anja,
>>
>> In order to refer to a reference sequence in the first column, the
>> first thing you must do is to provide a GFF line that identifies that
>> sequence. For example, I'm guessing whatever "1" is, it has a length
>> of 2000 (because you have a sequence-region directive in the file).
>> So, you would need a gff line something like this:
>>
>> 1 . contig 1 2000 . . . ID=1;Name=1
>>
>> Of course, the remaining lines in your GFF file aren't valid either,
>> because they have "NTR" as a reference sequence, but there is not a
>> line defining the feature called "NTR" in this file (well, it's not
>> valid assuming there is not already a feature call "NTR" in your
>> database; if that were the case it would be fine).
>>
>> Scott
>>
>>
>> On Wed, Sep 22, 2010 at 12:33 PM, Anja Friedrich
>> <[hidden email]> wrote:
>> > Hi all,
>> >
>> > I got an error message I can't interpret by using gmod_bulk_load_gff3.pl
>> >
>> > anou@anou-laptop:~$ gmod_bulk_load_gff3.pl --organism taro --gfffile
>> > taro.gff
>> > Preparing data for inserting into the chado database
>> > (This may take a while ...)
>> > Unable to find srcfeature 1 in the database.
>> > Perhaps you need to rerun your data load with the '--recreate_cache'
>> > option.
>> > at /usr/local/share/perl/5.10.1/Bio/GMOD/DB/Adapter.pm line 4555
>> >
>> >
>> > Bio::GMOD::DB::Adapter::src_second_chance('Bio::GMOD::DB::Adapter=HASH(0x994b7d0)',
>> > 'Bio::SeqFeature::Annotated=HASH(0x9b74258)') called at
>> > /usr/local/bin/gmod_bulk_load_gff3.pl line 841
>> >
>> > Abnormal termination, trying to clean up...
>> >
>> > Attempting to clean up the loader temp table (so that --recreate_cache
>> > won't be needed)...
>> > Trying to remove the run lock (so that --remove_lock won't be needed)...
>> > Exiting...
>> >
>> > Anyone an idea? I attached the file
>> >
>> > Cheers,
>> > Anja
>> >
>> >
>> > ------------------------------------------------------------------------------
>> > Start uncovering the many advantages of virtual appliances
>> > and start using them to simplify application deployment and
>> > accelerate your shift to cloud computing.
>> > http://p.sf.net/sfu/novell-sfdev2dev
>> > _______________________________________________
>> > Gmod-schema mailing list
>> > [hidden email]
>> > https://lists.sourceforge.net/lists/listinfo/gmod-schema
>> >
>> >
>>
>>
>>
>> --
>> ------------------------------------------------------------------------
>> Scott Cain, Ph. D.                                   scott at scottcain
>> dot net
>> GMOD Coordinator (http://gmod.org/)                     216-392-3087
>> Ontario Institute for Cancer Research
>
> ------------------------------------------------------------------------------
> Start uncovering the many advantages of virtual appliances
> and start using them to simplify application deployment and
> accelerate your shift to cloud computing.
> http://p.sf.net/sfu/novell-sfdev2dev
> _______________________________________________
> Gmod-schema mailing list
> [hidden email]
> https://lists.sourceforge.net/lists/listinfo/gmod-schema
>
>



--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research

------------------------------------------------------------------------------
Start uncovering the many advantages of virtual appliances
and start using them to simplify application deployment and
accelerate your shift to cloud computing.
http://p.sf.net/sfu/novell-sfdev2dev
_______________________________________________
Gmod-schema mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-schema
Reply | Threaded
Open this post in threaded view
|

Re: FW: problems loading data using gmod_bulk_load_gff3.pl

Scott Cain
Right--the terms must be in the Sequence Ontology which must be loaded
into Chado.



On Wed, Sep 22, 2010 at 1:41 PM, Anja Friedrich
<[hidden email]> wrote:

> Hi Scott,
>
> the error message changed. now its saying
>
> MSG: no cvterm for motif_small_b
>
> Anja
>
>> Date: Wed, 22 Sep 2010 13:27:43 -0400
>> Subject: Re: [Gmod-schema] FW: problems loading data using
>> gmod_bulk_load_gff3.pl
>> From: [hidden email]
>> To: [hidden email]
>> CC: [hidden email]
>>
>> Hi Anja,
>>
>> I saw the email on that list but didn't look closely at what Mitch
>> did. What Mitch wrote is very close to what would be acceptable. The
>> only change that would be need would be the addition of the GFF line
>> for "1". The sequence-region directive is fine for display, but is
>> not OK for Chado, where every feature needs to be typed, like
>> "chromosome" or "contig".
>>
>> Scott
>>
>>
>> On Wed, Sep 22, 2010 at 12:57 PM, Anja Friedrich
>> <[hidden email]> wrote:
>> >
>> >
>> > ________________________________
>> > From: [hidden email]
>> > To: [hidden email]
>> > Subject: RE: [Gmod-schema] problems loading data using
>> > gmod_bulk_load_gff3.pl
>> > Date: Wed, 22 Sep 2010 18:56:32 +0200
>> >
>> > Hi Scott,
>> >
>> > thanks for the explanation. I can give it a try and change it.
>> > Well I just extended the gff file Mitch Skinner send me don't know if
>> > you
>> > have seen the post),  and he used to display the feature. Thats how he
>> > set
>> > the file up, so I thought its fine.
>> >
>> > Anja
>> >
>> >> Date: Wed, 22 Sep 2010 12:45:47 -0400
>> >> Subject: Re: [Gmod-schema] problems loading data using
>> >> gmod_bulk_load_gff3.pl
>> >> From: [hidden email]
>> >> To: [hidden email]
>> >> CC: [hidden email]
>> >>
>> >> Hi Anja,
>> >>
>> >> In order to refer to a reference sequence in the first column, the
>> >> first thing you must do is to provide a GFF line that identifies that
>> >> sequence. For example, I'm guessing whatever "1" is, it has a length
>> >> of 2000 (because you have a sequence-region directive in the file).
>> >> So, you would need a gff line something like this:
>> >>
>> >> 1 . contig 1 2000 . . . ID=1;Name=1
>> >>
>> >> Of course, the remaining lines in your GFF file aren't valid either,
>> >> because they have "NTR" as a reference sequence, but there is not a
>> >> line defining the feature called "NTR" in this file (well, it's not
>> >> valid assuming there is not already a feature call "NTR" in your
>> >> database; if that were the case it would be fine).
>> >>
>> >> Scott
>> >>
>> >>
>> >> On Wed, Sep 22, 2010 at 12:33 PM, Anja Friedrich
>> >> <[hidden email]> wrote:
>> >> > Hi all,
>> >> >
>> >> > I got an error message I can't interpret by using
>> >> > gmod_bulk_load_gff3.pl
>> >> >
>> >> > anou@anou-laptop:~$ gmod_bulk_load_gff3.pl --organism taro --gfffile
>> >> > taro.gff
>> >> > Preparing data for inserting into the chado database
>> >> > (This may take a while ...)
>> >> > Unable to find srcfeature 1 in the database.
>> >> > Perhaps you need to rerun your data load with the '--recreate_cache'
>> >> > option.
>> >> > at /usr/local/share/perl/5.10.1/Bio/GMOD/DB/Adapter.pm line 4555
>> >> >
>> >> >
>> >> >
>> >> > Bio::GMOD::DB::Adapter::src_second_chance('Bio::GMOD::DB::Adapter=HASH(0x994b7d0)',
>> >> > 'Bio::SeqFeature::Annotated=HASH(0x9b74258)') called at
>> >> > /usr/local/bin/gmod_bulk_load_gff3.pl line 841
>> >> >
>> >> > Abnormal termination, trying to clean up...
>> >> >
>> >> > Attempting to clean up the loader temp table (so that
>> >> > --recreate_cache
>> >> > won't be needed)...
>> >> > Trying to remove the run lock (so that --remove_lock won't be
>> >> > needed)...
>> >> > Exiting...
>> >> >
>> >> > Anyone an idea? I attached the file
>> >> >
>> >> > Cheers,
>> >> > Anja
>> >> >
>> >> >
>> >> >
>> >> > ------------------------------------------------------------------------------
>> >> > Start uncovering the many advantages of virtual appliances
>> >> > and start using them to simplify application deployment and
>> >> > accelerate your shift to cloud computing.
>> >> > http://p.sf.net/sfu/novell-sfdev2dev
>> >> > _______________________________________________
>> >> > Gmod-schema mailing list
>> >> > [hidden email]
>> >> > https://lists.sourceforge.net/lists/listinfo/gmod-schema
>> >> >
>> >> >
>> >>
>> >>
>> >>
>> >> --
>> >>
>> >> ------------------------------------------------------------------------
>> >> Scott Cain, Ph. D.                                   scott at scottcain
>> >> dot net
>> >> GMOD Coordinator (http://gmod.org/)                     216-392-3087
>> >> Ontario Institute for Cancer Research
>> >
>> >
>> > ------------------------------------------------------------------------------
>> > Start uncovering the many advantages of virtual appliances
>> > and start using them to simplify application deployment and
>> > accelerate your shift to cloud computing.
>> > http://p.sf.net/sfu/novell-sfdev2dev
>> > _______________________________________________
>> > Gmod-schema mailing list
>> > [hidden email]
>> > https://lists.sourceforge.net/lists/listinfo/gmod-schema
>> >
>> >
>>
>>
>>
>> --
>> ------------------------------------------------------------------------
>> Scott Cain, Ph. D.                                   scott at scottcain
>> dot net
>> GMOD Coordinator (http://gmod.org/)                     216-392-3087
>> Ontario Institute for Cancer Research
>



--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research

------------------------------------------------------------------------------
Start uncovering the many advantages of virtual appliances
and start using them to simplify application deployment and
accelerate your shift to cloud computing.
http://p.sf.net/sfu/novell-sfdev2dev
_______________________________________________
Gmod-schema mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-schema
Reply | Threaded
Open this post in threaded view
|

Re: FW: problems loading data using gmod_bulk_load_gff3.pl

Scott Cain
I just checked http://sequenceontology.org/cgi-bin/miso.cgi and the
term motif_small_b is not found.  I seem to remember you asking the SO
people to add terms, is that right?  If so, it doesn't appear to have
happened yet.

Scott


On Wed, Sep 22, 2010 at 2:05 PM, Anja Friedrich
<[hidden email]> wrote:

> I did load the sequence ontology into chado. I will try to restore the
> database
>
>> Date: Wed, 22 Sep 2010 14:00:00 -0400
>> Subject: Re: [Gmod-schema] FW: problems loading data using
>> gmod_bulk_load_gff3.pl
>> From: [hidden email]
>> To: [hidden email]
>> CC: [hidden email]
>>
>> Right--the terms must be in the Sequence Ontology which must be loaded
>> into Chado.
>>
>>
>>
>> On Wed, Sep 22, 2010 at 1:41 PM, Anja Friedrich
>> <[hidden email]> wrote:
>> > Hi Scott,
>> >
>> > the error message changed. now its saying
>> >
>> > MSG: no cvterm for motif_small_b
>> >
>> > Anja
>> >
>> >> Date: Wed, 22 Sep 2010 13:27:43 -0400
>> >> Subject: Re: [Gmod-schema] FW: problems loading data using
>> >> gmod_bulk_load_gff3.pl
>> >> From: [hidden email]
>> >> To: [hidden email]
>> >> CC: [hidden email]
>> >>
>> >> Hi Anja,
>> >>
>> >> I saw the email on that list but didn't look closely at what Mitch
>> >> did. What Mitch wrote is very close to what would be acceptable. The
>> >> only change that would be need would be the addition of the GFF line
>> >> for "1". The sequence-region directive is fine for display, but is
>> >> not OK for Chado, where every feature needs to be typed, like
>> >> "chromosome" or "contig".
>> >>
>> >> Scott
>> >>
>> >>
>> >> On Wed, Sep 22, 2010 at 12:57 PM, Anja Friedrich
>> >> <[hidden email]> wrote:
>> >> >
>> >> >
>> >> > ________________________________
>> >> > From: [hidden email]
>> >> > To: [hidden email]
>> >> > Subject: RE: [Gmod-schema] problems loading data using
>> >> > gmod_bulk_load_gff3.pl
>> >> > Date: Wed, 22 Sep 2010 18:56:32 +0200
>> >> >
>> >> > Hi Scott,
>> >> >
>> >> > thanks for the explanation. I can give it a try and change it.
>> >> > Well I just extended the gff file Mitch Skinner send me don't know if
>> >> > you
>> >> > have seen the post),  and he used to display the feature. Thats how
>> >> > he
>> >> > set
>> >> > the file up, so I thought its fine.
>> >> >
>> >> > Anja
>> >> >
>> >> >> Date: Wed, 22 Sep 2010 12:45:47 -0400
>> >> >> Subject: Re: [Gmod-schema] problems loading data using
>> >> >> gmod_bulk_load_gff3.pl
>> >> >> From: [hidden email]
>> >> >> To: [hidden email]
>> >> >> CC: [hidden email]
>> >> >>
>> >> >> Hi Anja,
>> >> >>
>> >> >> In order to refer to a reference sequence in the first column, the
>> >> >> first thing you must do is to provide a GFF line that identifies
>> >> >> that
>> >> >> sequence. For example, I'm guessing whatever "1" is, it has a length
>> >> >> of 2000 (because you have a sequence-region directive in the file).
>> >> >> So, you would need a gff line something like this:
>> >> >>
>> >> >> 1 . contig 1 2000 . . . ID=1;Name=1
>> >> >>
>> >> >> Of course, the remaining lines in your GFF file aren't valid either,
>> >> >> because they have "NTR" as a reference sequence, but there is not a
>> >> >> line defining the feature called "NTR" in this file (well, it's not
>> >> >> valid assuming there is not already a feature call "NTR" in your
>> >> >> database; if that were the case it would be fine).
>> >> >>
>> >> >> Scott
>> >> >>
>> >> >>
>> >> >> On Wed, Sep 22, 2010 at 12:33 PM, Anja Friedrich
>> >> >> <[hidden email]> wrote:
>> >> >> > Hi all,
>> >> >> >
>> >> >> > I got an error message I can't interpret by using
>> >> >> > gmod_bulk_load_gff3.pl
>> >> >> >
>> >> >> > anou@anou-laptop:~$ gmod_bulk_load_gff3.pl --organism taro
>> >> >> > --gfffile
>> >> >> > taro.gff
>> >> >> > Preparing data for inserting into the chado database
>> >> >> > (This may take a while ...)
>> >> >> > Unable to find srcfeature 1 in the database.
>> >> >> > Perhaps you need to rerun your data load with the
>> >> >> > '--recreate_cache'
>> >> >> > option.
>> >> >> > at /usr/local/share/perl/5.10.1/Bio/GMOD/DB/Adapter.pm line 4555
>> >> >> >
>> >> >> >
>> >> >> >
>> >> >> >
>> >> >> > Bio::GMOD::DB::Adapter::src_second_chance('Bio::GMOD::DB::Adapter=HASH(0x994b7d0)',
>> >> >> > 'Bio::SeqFeature::Annotated=HASH(0x9b74258)') called at
>> >> >> > /usr/local/bin/gmod_bulk_load_gff3.pl line 841
>> >> >> >
>> >> >> > Abnormal termination, trying to clean up...
>> >> >> >
>> >> >> > Attempting to clean up the loader temp table (so that
>> >> >> > --recreate_cache
>> >> >> > won't be needed)...
>> >> >> > Trying to remove the run lock (so that --remove_lock won't be
>> >> >> > needed)...
>> >> >> > Exiting...
>> >> >> >
>> >> >> > Anyone an idea? I attached the file
>> >> >> >
>> >> >> > Cheers,
>> >> >> > Anja
>> >> >> >
>> >> >> >
>> >> >> >
>> >> >> >
>> >> >> > ------------------------------------------------------------------------------
>> >> >> > Start uncovering the many advantages of virtual appliances
>> >> >> > and start using them to simplify application deployment and
>> >> >> > accelerate your shift to cloud computing.
>> >> >> > http://p.sf.net/sfu/novell-sfdev2dev
>> >> >> > _______________________________________________
>> >> >> > Gmod-schema mailing list
>> >> >> > [hidden email]
>> >> >> > https://lists.sourceforge.net/lists/listinfo/gmod-schema
>> >> >> >
>> >> >> >
>> >> >>
>> >> >>
>> >> >>
>> >> >> --
>> >> >>
>> >> >>
>> >> >> ------------------------------------------------------------------------
>> >> >> Scott Cain, Ph. D.                                   scott at
>> >> >> scottcain
>> >> >> dot net
>> >> >> GMOD Coordinator (http://gmod.org/)                     216-392-3087
>> >> >> Ontario Institute for Cancer Research
>> >> >
>> >> >
>> >> >
>> >> > ------------------------------------------------------------------------------
>> >> > Start uncovering the many advantages of virtual appliances
>> >> > and start using them to simplify application deployment and
>> >> > accelerate your shift to cloud computing.
>> >> > http://p.sf.net/sfu/novell-sfdev2dev
>> >> > _______________________________________________
>> >> > Gmod-schema mailing list
>> >> > [hidden email]
>> >> > https://lists.sourceforge.net/lists/listinfo/gmod-schema
>> >> >
>> >> >
>> >>
>> >>
>> >>
>> >> --
>> >>
>> >> ------------------------------------------------------------------------
>> >> Scott Cain, Ph. D.                                   scott at scottcain
>> >> dot net
>> >> GMOD Coordinator (http://gmod.org/)                     216-392-3087
>> >> Ontario Institute for Cancer Research
>> >
>>
>>
>>
>> --
>> ------------------------------------------------------------------------
>> Scott Cain, Ph. D.                                   scott at scottcain
>> dot net
>> GMOD Coordinator (http://gmod.org/)                     216-392-3087
>> Ontario Institute for Cancer Research
>



--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research

------------------------------------------------------------------------------
Start uncovering the many advantages of virtual appliances
and start using them to simplify application deployment and
accelerate your shift to cloud computing.
http://p.sf.net/sfu/novell-sfdev2dev
_______________________________________________
Gmod-schema mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-schema
Reply | Threaded
Open this post in threaded view
|

Re: FW: problems loading data using gmod_bulk_load_gff3.pl

Scott Cain
It's just that Chado is very strict about what it will allow: since it
is intended as a data warehouse where your "important" data goes, it
tries to make sure your data are clean.  Visualization tools like
JBrowse and GBrowse don't care nearly so much, and will let you do
things that aren't technically allowed by the GFF3 specification.

Scott


On Wed, Sep 22, 2010 at 4:25 PM, Anja Friedrich
<[hidden email]> wrote:

> I asked them to add nested_tandem_repeat. I never asked for motif_small_b.
> But Mitch managed to visualise it using this feature. Wondering how. Thank
> for your work and patience Scott.
>
> Anja
>
>> Date: Wed, 22 Sep 2010 14:22:00 -0400
>> Subject: Re: [Gmod-schema] FW: problems loading data using
>> gmod_bulk_load_gff3.pl
>> From: [hidden email]
>> To: [hidden email]
>> CC: [hidden email]
>>
>> I just checked http://sequenceontology.org/cgi-bin/miso.cgi and the
>> term motif_small_b is not found. I seem to remember you asking the SO
>> people to add terms, is that right? If so, it doesn't appear to have
>> happened yet.
>>
>> Scott
>>
>>
>> On Wed, Sep 22, 2010 at 2:05 PM, Anja Friedrich
>> <[hidden email]> wrote:
>> > I did load the sequence ontology into chado. I will try to restore the
>> > database
>> >
>> >> Date: Wed, 22 Sep 2010 14:00:00 -0400
>> >> Subject: Re: [Gmod-schema] FW: problems loading data using
>> >> gmod_bulk_load_gff3.pl
>> >> From: [hidden email]
>> >> To: [hidden email]
>> >> CC: [hidden email]
>> >>
>> >> Right--the terms must be in the Sequence Ontology which must be loaded
>> >> into Chado.
>> >>
>> >>
>> >>
>> >> On Wed, Sep 22, 2010 at 1:41 PM, Anja Friedrich
>> >> <[hidden email]> wrote:
>> >> > Hi Scott,
>> >> >
>> >> > the error message changed. now its saying
>> >> >
>> >> > MSG: no cvterm for motif_small_b
>> >> >
>> >> > Anja
>> >> >
>> >> >> Date: Wed, 22 Sep 2010 13:27:43 -0400
>> >> >> Subject: Re: [Gmod-schema] FW: problems loading data using
>> >> >> gmod_bulk_load_gff3.pl
>> >> >> From: [hidden email]
>> >> >> To: [hidden email]
>> >> >> CC: [hidden email]
>> >> >>
>> >> >> Hi Anja,
>> >> >>
>> >> >> I saw the email on that list but didn't look closely at what Mitch
>> >> >> did. What Mitch wrote is very close to what would be acceptable. The
>> >> >> only change that would be need would be the addition of the GFF line
>> >> >> for "1". The sequence-region directive is fine for display, but is
>> >> >> not OK for Chado, where every feature needs to be typed, like
>> >> >> "chromosome" or "contig".
>> >> >>
>> >> >> Scott
>> >> >>
>> >> >>
>> >> >> On Wed, Sep 22, 2010 at 12:57 PM, Anja Friedrich
>> >> >> <[hidden email]> wrote:
>> >> >> >
>> >> >> >
>> >> >> > ________________________________
>> >> >> > From: [hidden email]
>> >> >> > To: [hidden email]
>> >> >> > Subject: RE: [Gmod-schema] problems loading data using
>> >> >> > gmod_bulk_load_gff3.pl
>> >> >> > Date: Wed, 22 Sep 2010 18:56:32 +0200
>> >> >> >
>> >> >> > Hi Scott,
>> >> >> >
>> >> >> > thanks for the explanation. I can give it a try and change it.
>> >> >> > Well I just extended the gff file Mitch Skinner send me don't know
>> >> >> > if
>> >> >> > you
>> >> >> > have seen the post),  and he used to display the feature. Thats
>> >> >> > how
>> >> >> > he
>> >> >> > set
>> >> >> > the file up, so I thought its fine.
>> >> >> >
>> >> >> > Anja
>> >> >> >
>> >> >> >> Date: Wed, 22 Sep 2010 12:45:47 -0400
>> >> >> >> Subject: Re: [Gmod-schema] problems loading data using
>> >> >> >> gmod_bulk_load_gff3.pl
>> >> >> >> From: [hidden email]
>> >> >> >> To: [hidden email]
>> >> >> >> CC: [hidden email]
>> >> >> >>
>> >> >> >> Hi Anja,
>> >> >> >>
>> >> >> >> In order to refer to a reference sequence in the first column,
>> >> >> >> the
>> >> >> >> first thing you must do is to provide a GFF line that identifies
>> >> >> >> that
>> >> >> >> sequence. For example, I'm guessing whatever "1" is, it has a
>> >> >> >> length
>> >> >> >> of 2000 (because you have a sequence-region directive in the
>> >> >> >> file).
>> >> >> >> So, you would need a gff line something like this:
>> >> >> >>
>> >> >> >> 1 . contig 1 2000 . . . ID=1;Name=1
>> >> >> >>
>> >> >> >> Of course, the remaining lines in your GFF file aren't valid
>> >> >> >> either,
>> >> >> >> because they have "NTR" as a reference sequence, but there is not
>> >> >> >> a
>> >> >> >> line defining the feature called "NTR" in this file (well, it's
>> >> >> >> not
>> >> >> >> valid assuming there is not already a feature call "NTR" in your
>> >> >> >> database; if that were the case it would be fine).
>> >> >> >>
>> >> >> >> Scott
>> >> >> >>
>> >> >> >>
>> >> >> >> On Wed, Sep 22, 2010 at 12:33 PM, Anja Friedrich
>> >> >> >> <[hidden email]> wrote:
>> >> >> >> > Hi all,
>> >> >> >> >
>> >> >> >> > I got an error message I can't interpret by using
>> >> >> >> > gmod_bulk_load_gff3.pl
>> >> >> >> >
>> >> >> >> > anou@anou-laptop:~$ gmod_bulk_load_gff3.pl --organism taro
>> >> >> >> > --gfffile
>> >> >> >> > taro.gff
>> >> >> >> > Preparing data for inserting into the chado database
>> >> >> >> > (This may take a while ...)
>> >> >> >> > Unable to find srcfeature 1 in the database.
>> >> >> >> > Perhaps you need to rerun your data load with the
>> >> >> >> > '--recreate_cache'
>> >> >> >> > option.
>> >> >> >> > at /usr/local/share/perl/5.10.1/Bio/GMOD/DB/Adapter.pm line
>> >> >> >> > 4555
>> >> >> >> >
>> >> >> >> >
>> >> >> >> >
>> >> >> >> >
>> >> >> >> >
>> >> >> >> > Bio::GMOD::DB::Adapter::src_second_chance('Bio::GMOD::DB::Adapter=HASH(0x994b7d0)',
>> >> >> >> > 'Bio::SeqFeature::Annotated=HASH(0x9b74258)') called at
>> >> >> >> > /usr/local/bin/gmod_bulk_load_gff3.pl line 841
>> >> >> >> >
>> >> >> >> > Abnormal termination, trying to clean up...
>> >> >> >> >
>> >> >> >> > Attempting to clean up the loader temp table (so that
>> >> >> >> > --recreate_cache
>> >> >> >> > won't be needed)...
>> >> >> >> > Trying to remove the run lock (so that --remove_lock won't be
>> >> >> >> > needed)...
>> >> >> >> > Exiting...
>> >> >> >> >
>> >> >> >> > Anyone an idea? I attached the file
>> >> >> >> >
>> >> >> >> > Cheers,
>> >> >> >> > Anja
>> >> >> >> >
>> >> >> >> >
>> >> >> >> >
>> >> >> >> >
>> >> >> >> >
>> >> >> >> > ------------------------------------------------------------------------------
>> >> >> >> > Start uncovering the many advantages of virtual appliances
>> >> >> >> > and start using them to simplify application deployment and
>> >> >> >> > accelerate your shift to cloud computing.
>> >> >> >> > http://p.sf.net/sfu/novell-sfdev2dev
>> >> >> >> > _______________________________________________
>> >> >> >> > Gmod-schema mailing list
>> >> >> >> > [hidden email]
>> >> >> >> > https://lists.sourceforge.net/lists/listinfo/gmod-schema
>> >> >> >> >
>> >> >> >> >
>> >> >> >>
>> >> >> >>
>> >> >> >>
>> >> >> >> --
>> >> >> >>
>> >> >> >>
>> >> >> >>
>> >> >> >> ------------------------------------------------------------------------
>> >> >> >> Scott Cain, Ph. D.                                   scott at
>> >> >> >> scottcain
>> >> >> >> dot net
>> >> >> >> GMOD Coordinator (http://gmod.org/)
>> >> >> >> 216-392-3087
>> >> >> >> Ontario Institute for Cancer Research
>> >> >> >
>> >> >> >
>> >> >> >
>> >> >> >
>> >> >> > ------------------------------------------------------------------------------
>> >> >> > Start uncovering the many advantages of virtual appliances
>> >> >> > and start using them to simplify application deployment and
>> >> >> > accelerate your shift to cloud computing.
>> >> >> > http://p.sf.net/sfu/novell-sfdev2dev
>> >> >> > _______________________________________________
>> >> >> > Gmod-schema mailing list
>> >> >> > [hidden email]
>> >> >> > https://lists.sourceforge.net/lists/listinfo/gmod-schema
>> >> >> >
>> >> >> >
>> >> >>
>> >> >>
>> >> >>
>> >> >> --
>> >> >>
>> >> >>
>> >> >> ------------------------------------------------------------------------
>> >> >> Scott Cain, Ph. D.                                   scott at
>> >> >> scottcain
>> >> >> dot net
>> >> >> GMOD Coordinator (http://gmod.org/)                     216-392-3087
>> >> >> Ontario Institute for Cancer Research
>> >> >
>> >>
>> >>
>> >>
>> >> --
>> >>
>> >> ------------------------------------------------------------------------
>> >> Scott Cain, Ph. D.                                   scott at scottcain
>> >> dot net
>> >> GMOD Coordinator (http://gmod.org/)                     216-392-3087
>> >> Ontario Institute for Cancer Research
>> >
>>
>>
>>
>> --
>> ------------------------------------------------------------------------
>> Scott Cain, Ph. D.                                   scott at scottcain
>> dot net
>> GMOD Coordinator (http://gmod.org/)                     216-392-3087
>> Ontario Institute for Cancer Research
>



--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research

------------------------------------------------------------------------------
Start uncovering the many advantages of virtual appliances
and start using them to simplify application deployment and
accelerate your shift to cloud computing.
http://p.sf.net/sfu/novell-sfdev2dev
_______________________________________________
Gmod-schema mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-schema
Reply | Threaded
Open this post in threaded view
|

Re: problems loading data using gmod_bulk_load_gff3.pl

anja
CONTENTS DELETED
The author has deleted this message.
Reply | Threaded
Open this post in threaded view
|

Re: problems loading data using gmod_bulk_load_gff3.pl

Mitch Skinner
Yes, sorry for not elaborating on that earlier.  JBrowse is currently able to make different features visually distinct within a track only if they have different types.  So I set the different motifs to have different types in the GFF I sent.  I didn't use chado; I just used the SeqFeature store memory adapter to get the GFF data into a JBrowse instance.

In the future, we plan to make it possible to make features look different based on other criteria than just type.  But for now, I think you have two options.

If you only want to visualize the features, then you could just take the approach that I did in the taro.json config file I sent, and not use chado.

On the other hand, if it's important to have your data in chado, then I think you can create a local CV for those types?  Scott could tell you for sure.

Sorry for the extra complication,
Mitch

On 09/22/2010 02:00 PM, Anja Friedrich wrote:
Yes I understand that, but that would mean that Mitch did not use chado.
But I can't ask the SO people to add all the motifs to the vocabulary...

Anja


Date: Wed, 22 Sep 2010 13:55:19 -0700
From: [hidden email]
To: [hidden email]
Subject: Re: FW: problems loading data using gmod_bulk_load_gff3.pl

It's just that Chado is very strict about what it will allow: since it
is intended as a data warehouse where your "important" data goes, it
tries to make sure your data are clean.  Visualization tools like
JBrowse and GBrowse don't care nearly so much, and will let you do
things that aren't technically allowed by the GFF3 specification.

Scott


On Wed, Sep 22, 2010 at 4:25 PM, Anja Friedrich
<[hidden email]> wrote:

> I asked them to add nested_tandem_repeat. I never asked for motif_small_b.
> But Mitch managed to visualise it using this feature. Wondering how. Thank
> for your work and patience Scott.
>
> Anja
>
>> Date: Wed, 22 Sep 2010 14:22:00 -0400
>> Subject: Re: [Gmod-schema] FW: problems loading data using
>> gmod_bulk_load_gff3.pl
>> From: [hidden email]
>> To: [hidden email]
>> CC: [hidden email]
>>
>> I just checked http://sequenceontology.org/cgi-bin/miso.cgi and the
>> term motif_small_b is not found. I seem to remember you asking the SO
>> people to add terms, is that right? If so, it doesn't appear to have
>> happened yet.
>>
>> Scott
>>
>>
>> On Wed, Sep 22, 2010 at 2:05 PM, Anja Friedrich
>> <[hidden email]> wrote:
>> > I did load the sequence ontology into chado. I will try to restore the
>> > database
>> >
>> >> Date: Wed, 22 Sep 2010 14:00:00 -0400
>> >> Subject: Re: [Gmod-schema] FW: problems loading data using
>> >> gmod_bulk_load_gff3.pl
>> >> From: [hidden email]
>> >> To: [hidden email]
>> >> CC: [hidden email]
>> >>
>> >> Right--the terms must be in the Sequence Ontology which must be loaded
>> >> into Chado.
>> >>
>> >>
>> >>
>> >> On Wed, Sep 22, 2010 at 1:41 PM, Anja Friedrich
>> >> <[hidden email]> wrote:
>> >> > Hi Scott,
>> >> >
>> >> > the error message changed. now its saying
>> >> >
>> >> > MSG: no cvterm for motif_small_b
>> >> >
>> >> > Anja
>> >> >
>> >> >> Date: Wed, 22 Sep 2010 13:27:43 -0400
>> >> >> Subject: Re: [Gmod-schema] FW: problems loading data using
>> >> >> gmod_bulk_load_gff3.pl
>> >> >> From: [hidden email]
>> >> >> To: [hidden email]
>> >> >> CC: [hidden email]
>> >> >>
>> >> >> Hi Anja,
>> >> >>
>> >> >> I saw the email on that list but didn't look closely at what Mitch
>> >> >> did. What Mitch wrote is very close to what would be acceptable. The
>> >> >> only change that would be need would be the addition of the GFF line
>> >> >> for "1". The sequence-region directive is fine for display, but is
>> >> >> not OK for Chado, where every feature needs to be typed, like
>> >> >> "chromosome" or "contig".
>> >> >>
>> >> >> Scott
>> >> >>
>> >> >>
>> >> >> On Wed, Sep 22, 2010 at 12:57 PM, Anja Friedrich
>> >> >> <[hidden email]> wrote:
>> >> >> >
>> >> >> >
>> >> >> > ________________________________
>> >> >> > From: [hidden email]
>> >> >> > To: [hidden email]
>> >> >> > Subject: RE: [Gmod-schema] problems loading data using
>> >> >> > gmod_bulk_load_gff3.pl
>> >> >> > Date: Wed, 22 Sep 2010 18:56:32 +0200
>> >> >> >
>> >> >> > Hi Scott,
>> >> >> >
>> >> >> > thanks for the explanation. I can give it a try and change it.
>> >> >> > Well I just extended the gff file Mitch Skinner send me don't know
>> >> >> > if
>> >> >> > you
>> >> >> > have seen the post),  and he used to display the feature. Thats
>> >> >> > how
>> >> >> > he
>> >> >> > set
>> >> >> > the file up, so I thought its fine.
>> >> >> >
>> >> >> > Anja
>> >> >> >
>> >> >> >> Date: Wed, 22 Sep 2010 12:45:47 -0400
>> >> >> >> Subject: Re: [Gmod-schema] problems loading data using
>> >> >> >> gmod_bulk_load_gff3.pl
>> >> >> >> From: [hidden email]
>> >> >> >> To: [hidden email]
>> >> >> >> CC: [hidden email]
>> >> >> >>
>> >> >> >> Hi Anja,
>> >> >> >>
>> >> >> >> In order to refer to a reference sequence in the first column,
>> >> >> >> the
>> >> >> >> first thing you must do is to provide a GFF line that identifies
>> >> >> >> that
>> >> >> >> sequence. For example, I'm guessing whatever "1" is, it has a
>> >> >> >> length
>> >> >> >> of 2000 (because you have a sequence-region directive in the
>> >> >> >> file).
>> >> >> >> So, you would need a gff line something like this:
>> >> >> >>
>> >> >> >> 1 . contig 1 2000 . . . ID=1;Name=1
>> >> >> >>
>> >> >> >> Of course, the remaining lines in your GFF file aren't valid
>> >> >> >> either,
>> >> >> >> because they have "NTR" as a reference sequence, but there is not
>> >> >> >> a
>> >> >> >> line defining the feature called "NTR" in this file (well, it's
>> >> >> >> not
>> >> >> >> valid assuming there is not already a feature call "NTR" in your
>> >> >> >> database; if that were the case it would be fine).
>> >> >> >>
>> >> >> >> Scott
>> >> >> >>
>> >> >> >>
>> >> >> >> On Wed, Sep 22, 2010 at 12:33 PM, Anja Friedrich
>> >> >> >> <[hidden email]> wrote:
>> >> >> >> > Hi all,
>> >> >> >> >
>> >> >> >> > I got an error message I can't interpret by using
>> >> >> >> > gmod_bulk_load_gff3.pl
>> >> >> >> >
>> >> >> >> > anou@anou-laptop:~$ gmod_bulk_load_gff3.pl --organism taro
>> >> >> >> > --gfffile
>> >> >> >> > taro.gff
>> >> >> >> > Preparing data for inserting into the chado database
>> >> >> >> > (This may take a while ...)
>> >> >> >> > Unable to find srcfeature 1 in the database.
>> >> >> >> > Perhaps you need to rerun your data load with the
>> >> >> >> > '--recreate_cache'
>> >> >> >> > option.
>> >> >> >> > at /usr/local/share/perl/5.10.1/Bio/GMOD/DB/Adapter.pm line
>> >> >> >> > 4555
>> >> >> >> >
>> >> >> >> >
>> >> >> >> >
>> >> >> >> >
>> >> >> >> >
>> >> >> >> > Bio::GMOD::DB::Adapter::src_second_chance('Bio::GMOD::DB::Adapter=HASH(0x994b7d0)',
>> >> >> >> > 'Bio::SeqFeature::Annotated=HASH(0x9b74258)') called at
>> >> >> >> > /usr/local/bin/gmod_bulk_load_gff3.pl line 841
>> >> >> >> >
>> >> >> >> > Abnormal termination, trying to clean up...
>> >> >> >> >
>> >> >> >> > Attempting to clean up the loader temp table (so that
>> >> >> >> > --recreate_cache
>> >> >> >> > won't be needed)...
>> >> >> >> > Trying to remove the run lock (so that --remove_lock won't be
>> >> >> >> > needed)...
>> >> >> >> > Exiting...
>> >> >> >> >
>> >> >> >> > Anyone an idea? I attached the file
>> >> >> >> >
>> >> >> >> > Cheers,
>> >> >> >> > Anja
>> >> >> >> >
>> >> >> >> >
>> >> >> >> >
>> >> >> >> >
>> >> >> >> >
>> >> >> >> > ------------------------------------------------------------------------------
>> >> >> >> > Start uncovering the many advantages of virtual appliances
>> >> >> >> > and start using them to simplify application deployment and
>> >> >> >> > accelerate your shift to cloud computing.
>> >> >> >> > http://p.sf.net/sfu/novell-sfdev2dev
>> >> >> >> > _______________________________________________
>> >> >> >> > Gmod-schema mailing list
>> >> >> >> > [hidden email]
>> >> >> >> > https://lists.sourceforge.net/lists/listinfo/gmod-schema
>> >> >> >> >
>> >> >> >> >
>> >> >> >>
>> >> >> >>
>> >> >> >>
>> >> >> >> --
>> >> >> >>
>> >> >> >>
>> >> >> >>
>> >> >> >> ------------------------------------------------------------------------
>> >> >> >> Scott Cain, Ph. D.                                   scott at
>> >> >> >> scottcain
>> >> >> >> dot net
>> >> >> >> GMOD Coordinator (http://gmod.org/)
>> >> >> >> 216-392-3087
>> >> >> >> Ontario Institute for Cancer Research
>> >> >> >
>> >> >> >
>> >> >> >
>> >> >> >
>> >> >> > ------------------------------------------------------------------------------
>> >> >> > Start uncovering the many advantages of virtual appliances
>> >> >> > and start using them to simplify application deployment and
>> >> >> > accelerate your shift to cloud computing.
>> >> >> > http://p.sf.net/sfu/novell-sfdev2dev
>> >> >> > _______________________________________________
>> >> >> > Gmod-schema mailing list
>> >> >> > [hidden email]
>> >> >> > https://lists.sourceforge.net/lists/listinfo/gmod-schema
>> >> >> >
>> >> >> >
>> >> >>
>> >> >>
>> >> >>
>> >> >> --
>> >> >>
>> >> >>
>> >> >> ------------------------------------------------------------------------
>> >> >> Scott Cain, Ph. D.                                   scott at
>> >> >> scottcain
>> >> >> dot net
>> >> >> GMOD Coordinator (http://gmod.org/)                     216-392-3087
>> >> >> Ontario Institute for Cancer Research
>> >> >
>> >>
>> >>
>> >>
>> >> --
>> >>
>> >> ------------------------------------------------------------------------
>> >> Scott Cain, Ph. D.                                   scott at scottcain
>> >> dot net
>> >> GMOD Coordinator (http://gmod.org/)                     216-392-3087
>> >> Ontario Institute for Cancer Research
>> >
>>
>>
>>
>> --
>> ------------------------------------------------------------------------
>> Scott Cain, Ph. D.                                   scott at scottcain
>> dot net
>> GMOD Coordinator (http://gmod.org/)                     216-392-3087
>> Ontario Institute for Cancer Research
>



--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research

------------------------------------------------------------------------------
Start uncovering the many advantages of virtual appliances
and start using them to simplify application deployment and
accelerate your shift to cloud computing.
http://p.sf.net/sfu/novell-sfdev2dev
_______________________________________________
Gmod-schema mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-schema




------------------------------------------------------------------------------ Start uncovering the many advantages of virtual appliances and start using them to simplify application deployment and accelerate your shift to cloud computing. http://p.sf.net/sfu/novell-sfdev2dev
_______________________________________________ Gmod-schema mailing list [hidden email] https://lists.sourceforge.net/lists/listinfo/gmod-schema


------------------------------------------------------------------------------
Nokia and AT&T present the 2010 Calling All Innovators-North America contest
Create new apps & games for the Nokia N8 for consumers in  U.S. and Canada
$10 million total in prizes - $4M cash, 500 devices, nearly $6M in marketing
Develop with Nokia Qt SDK, Web Runtime, or Java and Publish to Ovi Store
http://p.sf.net/sfu/nokia-dev2dev
_______________________________________________
Gmod-schema mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-schema
Reply | Threaded
Open this post in threaded view
|

Re: problems loading data using gmod_bulk_load_gff3.pl

anja
CONTENTS DELETED
The author has deleted this message.
Reply | Threaded
Open this post in threaded view
|

Re: problems loading data using gmod_bulk_load_gff3.pl

Scott Cain
Hi Anja,

If all you want is to use a browser with your data, you don't really want chado anyway. Try using Bio::DB::SeqFeature::Store which comes with BioPerl. The loader is called bp_load_seqfeature.pl. It won't mind that your types aren't part of SO and is much faster than chado. 

Scott

--
Scott Cain, Ph. D.
scott at scottcain dot net
Ontario Institute for Cancer Research
216 392 3087 

On Sep 24, 2010, at 4:04 AM, Anja Friedrich <[hidden email]> wrote:

Hi,

I thought it might be better to use a database as I'm storing my data (reference sequence and taro) in it. I tried to find soemthing about the "local cv" you mentioned, but was not successfully yet. I will keep looking or ask someone of the gff people if I can use it in my case.
But anyway, thank you for your help.

Anja



Date: Thu, 23 Sep 2010 15:47:03 -0700
From: [hidden email]
To: [hidden email]
Subject: Re: problems loading data using gmod_bulk_load_gff3.pl

Yes, sorry for not elaborating on that earlier.  JBrowse is currently able to make different features visually distinct within a track only if they have different types.  So I set the different motifs to have different types in the GFF I sent.  I didn't use chado; I just used the SeqFeature store memory adapter to get the GFF data into a JBrowse instance.

In the future, we plan to make it possible to make features look different based on other criteria than just type.  But for now, I think you have two options.

If you only want to visualize the features, then you could just take the approach that I did in the taro.json config file I sent, and not use chado.

On the other hand, if it's important to have your data in chado, then I think you can create a local CV for those types?  Scott could tell you for sure.

Sorry for the extra complication,
Mitch

On 09/22/2010 02:00 PM, Anja Friedrich wrote:
Yes I understand that, but that would mean that Mitch did not use chado.
But I can't ask the SO people to add all the motifs to the vocabulary...

Anja


Date: Wed, 22 Sep 2010 13:55:19 -0700
From: [hidden email]
To: [hidden email]
Subject: Re: FW: problems loading data using gmod_bulk_load_gff3.pl

It's just that Chado is very strict about what it will allow: since it
is intended as a data warehouse where your "important" data goes, it
tries to make sure your data are clean.  Visualization tools like
JBrowse and GBrowse don't care nearly so much, and will let you do
things that aren't technically allowed by the GFF3 specification.

Scott


On Wed, Sep 22, 2010 at 4:25 PM, Anja Friedrich
<[hidden email]> wrote:

> I asked them to add nested_tandem_repeat. I never asked for motif_small_b.
> But Mitch managed to visualise it using this feature. Wondering how. Thank
> for your work and patience Scott.
>
> Anja
>
>> Date: Wed, 22 Sep 2010 14:22:00 -0400
>> Subject: Re: [Gmod-schema] FW: problems loading data using
>> gmod_bulk_load_gff3.pl
>> From: [hidden email]
>> To: [hidden email]
>> CC: [hidden email]
>>
>> I just checked http://sequenceontology.org/cgi-bin/miso.cgi and the
>> term motif_small_b is not found. I seem to remember you asking the SO
>> people to add terms, is that right? If so, it doesn't appear to have
>> happened yet.
>>
>> Scott
>>
>>
>> On Wed, Sep 22, 2010 at 2:05 PM, Anja Friedrich
>> <[hidden email]> wrote:
>> > I did load the sequence ontology into chado. I will try to restore the
>> > database
>> >
>> >> Date: Wed, 22 Sep 2010 14:00:00 -0400
>> >> Subject: Re: [Gmod-schema] FW: problems loading data using
>> >> gmod_bulk_load_gff3.pl
>> >> From: [hidden email]
>> >> To: [hidden email]
>> >> CC: [hidden email]
>> >>
>> >> Right--the terms must be in the Sequence Ontology which must be loaded
>> >> into Chado.
>> >>
>> >>
>> >>
>> >> On Wed, Sep 22, 2010 at 1:41 PM, Anja Friedrich
>> >> <[hidden email]> wrote:
>> >> > Hi Scott,
>> >> >
>> >> > the error message changed. now its saying
>> >> >
>> >> > MSG: no cvterm for motif_small_b
>> >> >
>> >> > Anja
>> >> >
>> >> >> Date: Wed, 22 Sep 2010 13:27:43 -0400
>> >> >> Subject: Re: [Gmod-schema] FW: problems loading data using
>> >> >> gmod_bulk_load_gff3.pl
>> >> >> From: [hidden email]
>> >> >> To: [hidden email]
>> >> >> CC: [hidden email]
>> >> >>
>> >> >> Hi Anja,
>> >> >>
>> >> >> I saw the email on that list but didn't look closely at what Mitch
>> >> >> did. What Mitch wrote is very close to what would be acceptable. The
>> >> >> only change that would be need would be the addition of the GFF line
>> >> >> for "1". The sequence-region directive is fine for display, but is
>> >> >> not OK for Chado, where every feature needs to be typed, like
>> >> >> "chromosome" or "contig".
>> >> >>
>> >> >> Scott
>> >> >>
>> >> >>
>> >> >> On Wed, Sep 22, 2010 at 12:57 PM, Anja Friedrich
>> >> >> <[hidden email]> wrote:
>> >> >> >
>> >> >> >
>> >> >> > ________________________________
>> >> >> > From: [hidden email]
>> >> >> > To: [hidden email]
>> >> >> > Subject: RE: [Gmod-schema] problems loading data using
>> >> >> > gmod_bulk_load_gff3.pl
>> >> >> > Date: Wed, 22 Sep 2010 18:56:32 +0200
>> >> >> >
>> >> >> > Hi Scott,
>> >> >> >
>> >> >> > thanks for the explanation. I can give it a try and change it.
>> >> >> > Well I just extended the gff file Mitch Skinner send me don't know
>> >> >> > if
>> >> >> > you
>> >> >> > have seen the post),  and he used to display the feature. Thats
>> >> >> > how
>> >> >> > he
>> >> >> > set
>> >> >> > the file up, so I thought its fine.
>> >> >> >
>> >> >> > Anja
>> >> >> >
>> >> >> >> Date: Wed, 22 Sep 2010 12:45:47 -0400
>> >> >> >> Subject: Re: [Gmod-schema] problems loading data using
>> >> >> >> gmod_bulk_load_gff3.pl
>> >> >> >> From: [hidden email]
>> >> >> >> To: [hidden email]
>> >> >> >> CC: [hidden email]
>> >> >> >>
>> >> >> >> Hi Anja,
>> >> >> >>
>> >> >> >> In order to refer to a reference sequence in the first column,
>> >> >> >> the
>> >> >> >> first thing you must do is to provide a GFF line that identifies
>> >> >> >> that
>> >> >> >> sequence. For example, I'm guessing whatever "1" is, it has a
>> >> >> >> length
>> >> >> >> of 2000 (because you have a sequence-region directive in the
>> >> >> >> file).
>> >> >> >> So, you would need a gff line something like this:
>> >> >> >>
>> >> >> >> 1 . contig 1 2000 . . . ID=1;Name=1
>> >> >> >>
>> >> >> >> Of course, the remaining lines in your GFF file aren't valid
>> >> >> >> either,
>> >> >> >> because they have "NTR" as a reference sequence, but there is not
>> >> >> >> a
>> >> >> >> line defining the feature called "NTR" in this file (well, it's
>> >> >> >> not
>> >> >> >> valid assuming there is not already a feature call "NTR" in your
>> >> >> >> database; if that were the case it would be fine).
>> >> >> >>
>> >> >> >> Scott
>> >> >> >>
>> >> >> >>
>> >> >> >> On Wed, Sep 22, 2010 at 12:33 PM, Anja Friedrich
>> >> >> >> <[hidden email]> wrote:
>> >> >> >> > Hi all,
>> >> >> >> >
>> >> >> >> > I got an error message I can't interpret by using
>> >> >> >> > gmod_bulk_load_gff3.pl
>> >> >> >> >
>> >> >> >> > anou@anou-laptop:~$ gmod_bulk_load_gff3.pl --organism taro
>> >> >> >> > --gfffile
>> >> >> >> > taro.gff
>> >> >> >> > Preparing data for inserting into the chado database
>> >> >> >> > (This may take a while ...)
>> >> >> >> > Unable to find srcfeature 1 in the database.
>> >> >> >> > Perhaps you need to rerun your data load with the
>> >> >> >> > '--recreate_cache'
>> >> >> >> > option.
>> >> >> >> > at /usr/local/share/perl/5.10.1/Bio/GMOD/DB/Adapter.pm line
>> >> >> >> > 4555
>> >> >> >> >
>> >> >> >> >
>> >> >> >> >
>> >> >> >> >
>> >> >> >> >
>> >> >> >> > Bio::GMOD::DB::Adapter::src_second_chance('Bio::GMOD::DB::Adapter=HASH(0x994b7d0)',
>> >> >> >> > 'Bio::SeqFeature::Annotated=HASH(0x9b74258)') called at
>> >> >> >> > /usr/local/bin/gmod_bulk_load_gff3.pl line 841
>> >> >> >> >
>> >> >> >> > Abnormal termination, trying to clean up...
>> >> >> >> >
>> >> >> >> > Attempting to clean up the loader temp table (so that
>> >> >> >> > --recreate_cache
>> >> >> >> > won't be needed)...
>> >> >> >> > Trying to remove the run lock (so that --remove_lock won't be
>> >> >> >> > needed)...
>> >> >> >> > Exiting...
>> >> >> >> >
>> >> >> >> > Anyone an idea? I attached the file
>> >> >> >> >
>> >> >> >> > Cheers,
>> >> >> >> > Anja
>> >> >> >> >
>> >> >> >> >
>> >> >> >> >
>> >> >> >> >
>> >> >> >> >
>> >> >> >> > ------------------------------------------------------------------------------
>> >> >> >> > Start uncovering the many advantages of virtual appliances
>> >> >> >> > and start using them to simplify application deployment and
>> >> >> >> > accelerate your shift to cloud computing.
>> >> >> >> > http://p.sf.net/sfu/novell-sfdev2dev
>> >> >> >> > _______________________________________________
>> >> >> >> > Gmod-schema mailing list
>> >> >> >> > [hidden email]
>> >> >> >> > https://lists.sourceforge.net/lists/listinfo/gmod-schema
>> >> >> >> >
>> >> >> >> >
>> >> >> >>
>> >> >> >>
>> >> >> >>
>> >> >> >> --
>> >> >> >>
>> >> >> >>
>> >> >> >>
>> >> >> >> ------------------------------------------------------------------------
>> >> >> >> Scott Cain, Ph. D.                                   scott at
>> >> >> >> scottcain
>> >> >> >> dot net
>> >> >> >> GMOD Coordinator (http://gmod.org/)
>> >> >> >> 216-392-3087
>> >> >> >> Ontario Institute for Cancer Research
>> >> >> >
>> >> >> >
>> >> >> >
>> >> >> >
>> >> >> > ------------------------------------------------------------------------------
>> >> >> > Start uncovering the many advantages of virtual appliances
>> >> >> > and start using them to simplify application deployment and
>> >> >> > accelerate your shift to cloud computing.
>> >> >> > http://p.sf.net/sfu/novell-sfdev2dev
>> >> >> > _______________________________________________
>> >> >> > Gmod-schema mailing list
>> >> >> > [hidden email]
>> >> >> > https://lists.sourceforge.net/lists/listinfo/gmod-schema
>> >> >> >
>> >> >> >
>> >> >>
>> >> >>
>> >> >>
>> >> >> --
>> >> >>
>> >> >>
>> >> >> ------------------------------------------------------------------------
>> >> >> Scott Cain, Ph. D.                                   scott at
>> >> >> scottcain
>> >> >> dot net
>> >> >> GMOD Coordinator (http://gmod.org/)                     216-392-3087
>> >> >> Ontario Institute for Cancer Research
>> >> >
>> >>
>> >>
>> >>
>> >> --
>> >>
>> >> ------------------------------------------------------------------------
>> >> Scott Cain, Ph. D.                                   scott at scottcain
>> >> dot net
>> >> GMOD Coordinator (http://gmod.org/)                     216-392-3087
>> >> Ontario Institute for Cancer Research
>> >
>>
>>
>>
>> --
>> ------------------------------------------------------------------------
>> Scott Cain, Ph. D.                                   scott at scottcain
>> dot net
>> GMOD Coordinator (http://gmod.org/)                     216-392-3087
>> Ontario Institute for Cancer Research
>



--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research

------------------------------------------------------------------------------
Start uncovering the many advantages of virtual appliances
and start using them to simplify application deployment and
accelerate your shift to cloud computing.
http://p.sf.net/sfu/novell-sfdev2dev
_______________________________________________
Gmod-schema mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-schema




------------------------------------------------------------------------------ Start uncovering the many advantages of virtual appliances and start using them to simplify application deployment and accelerate your shift to cloud computing. http://p.sf.net/sfu/novell-sfdev2dev
_______________________________________________ Gmod-schema mailing list [hidden email] https://lists.sourceforge.net/lists/listinfo/gmod-schema


------------------------------------------------------------------------------
Nokia and AT&T present the 2010 Calling All Innovators-North America contest
Create new apps & games for the Nokia N8 for consumers in  U.S. and Canada
$10 million total in prizes - $4M cash, 500 devices, nearly $6M in marketing
Develop with Nokia Qt SDK, Web Runtime, or Java and Publish to Ovi Store
http://p.sf.net/sfu/nokia-dev2dev
_______________________________________________
Gmod-schema mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-schema




------------------------------------------------------------------------------
Nokia and AT&T present the 2010 Calling All Innovators-North America contest
Create new apps & games for the Nokia N8 for consumers in  U.S. and Canada
$10 million total in prizes - $4M cash, 500 devices, nearly $6M in marketing
Develop with Nokia Qt SDK, Web Runtime, or Java and Publish to Ovi Store
http://p.sf.net/sfu/nokia-dev2dev
_______________________________________________
Gmod-schema mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-schema

------------------------------------------------------------------------------
Nokia and AT&T present the 2010 Calling All Innovators-North America contest
Create new apps & games for the Nokia N8 for consumers in  U.S. and Canada
$10 million total in prizes - $4M cash, 500 devices, nearly $6M in marketing
Develop with Nokia Qt SDK, Web Runtime, or Java and Publish to Ovi Store
http://p.sf.net/sfu/nokia-dev2dev
_______________________________________________
Gmod-schema mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-schema
Reply | Threaded
Open this post in threaded view
|

Re: problems loading data using gmod_bulk_load_gff3.pl

anja
CONTENTS DELETED
The author has deleted this message.
Reply | Threaded
Open this post in threaded view
|

Re: problems loading data using gmod_bulk_load_gff3.pl

anja
In reply to this post by Scott Cain
CONTENTS DELETED
The author has deleted this message.
Reply | Threaded
Open this post in threaded view
|

Re: problems loading data using gmod_bulk_load_gff3.pl

Scott Cain
Hi Anja,

Getting access denied is a mysql problem; I'm not a mysql person, so I
can't say for sure, but looking at the end of the GBrowse tutorial for
using MySQL.  In particular, make sure you grant all permissions for
your user.

More importantly--you are using a very old version of BioPerl.  At the
very least, you should be using version 1.6.1.

Scott


On Sun, Sep 26, 2010 at 12:47 PM, Anja Friedrich
<[hidden email]> wrote:

> Hi Scott,
> I tried the bp_load_seqfeature.pl as you told me, but I get no access, not
> even with password. Am I doing something wrong?
>
> anou@anou-laptop:~/bioperl-1.5.2_102/scripts/Bio-SeqFeature-Store$ perl
> bp_load_seqfeature.pl -p ****
> DBI connect('test','',...) failed: Access denied for user 'anou'@'localhost'
> (using password: YES) at
> /usr/local/share/perl/5.10.1/Bio/DB/SeqFeature/Store/DBI/mysql.pm line 212
>
> -------------------- EXCEPTION --------------------
> MSG: Access denied for user 'anou'@'localhost' (using password: YES)
> STACK Bio::DB::SeqFeature::Store::DBI::mysql::init
> /usr/local/share/perl/5.10.1/Bio/DB/SeqFeature/Store/DBI/mysql.pm:212
> STACK Bio::DB::SeqFeature::Store::new
> /usr/local/share/perl/5.10.1/Bio/DB/SeqFeature/Store.pm:370
> STACK toplevel bp_load_seqfeature.pl:56
> -------------------------------------------
>
> Anja
> ________________________________
> Date: Fri, 24 Sep 2010 05:38:24 -0700
> From: [hidden email]
> To: [hidden email]
> Subject: Re: problems loading data using gmod_bulk_load_gff3.pl
>
> Hi Anja,
> If all you want is to use a browser with your data, you don't really want
> chado anyway. Try using Bio::DB::SeqFeature::Store which comes with BioPerl.
> The loader is called bp_load_seqfeature.pl. It won't mind that your types
> aren't part of SO and is much faster than chado.
> Scott
>
> --
> Scott Cain, Ph. D.
> scott at scottcain dot net
> Ontario Institute for Cancer Research
> http://gmod.org/
> 216 392 3087
> On Sep 24, 2010, at 4:04 AM, Anja Friedrich <[hidden email]> wrote:
>
> Hi,
>
> I thought it might be better to use a database as I'm storing my data
> (reference sequence and taro) in it. I tried to find soemthing about the
> "local cv" you mentioned, but was not successfully yet. I will keep looking
> or ask someone of the gff people if I can use it in my case.
> But anyway, thank you for your help.
>
> Anja
>
>
> ________________________________
> Date: Thu, 23 Sep 2010 15:47:03 -0700
> From: [hidden email]
> To: [hidden email]
> Subject: Re: problems loading data using gmod_bulk_load_gff3.pl
>
> Yes, sorry for not elaborating on that earlier.  JBrowse is currently able
> to make different features visually distinct within a track only if they
> have different types.  So I set the different motifs to have different types
> in the GFF I sent.  I didn't use chado; I just used the SeqFeature store
> memory adapter to get the GFF data into a JBrowse instance.
>
> In the future, we plan to make it possible to make features look different
> based on other criteria than just type.  But for now, I think you have two
> options.
>
> If you only want to visualize the features, then you could just take the
> approach that I did in the taro.json config file I sent, and not use chado.
>
> On the other hand, if it's important to have your data in chado, then I
> think you can create a local CV for those types?  Scott could tell you for
> sure.
>
> Sorry for the extra complication,
> Mitch
>
> On 09/22/2010 02:00 PM, Anja Friedrich wrote:
>
> Yes I understand that, but that would mean that Mitch did not use chado.
> But I can't ask the SO people to add all the motifs to the vocabulary...
>
> Anja
>
> ________________________________
> Date: Wed, 22 Sep 2010 13:55:19 -0700
> From: [hidden email]
> To: [hidden email]
> Subject: Re: FW: problems loading data using gmod_bulk_load_gff3.pl
>
> It's just that Chado is very strict about what it will allow: since it
> is intended as a data warehouse where your "important" data goes, it
> tries to make sure your data are clean.  Visualization tools like
> JBrowse and GBrowse don't care nearly so much, and will let you do
> things that aren't technically allowed by the GFF3 specification.
>
> Scott
>
>
> On Wed, Sep 22, 2010 at 4:25 PM, Anja Friedrich
> <[hidden email]> wrote:
>> I asked them to add nested_tandem_repeat. I never asked for motif_small_b.
>> But Mitch managed to visualise it using this feature. Wondering how. Thank
>> for your work and patience Scott.
>>
>> Anja
>>
>>> Date: Wed, 22 Sep 2010 14:22:00 -0400
>>> Subject: Re: [Gmod-schema] FW: problems loading data using
>>> gmod_bulk_load_gff3.pl
>>> From: [hidden email]
>>> To: [hidden email]
>>> CC: [hidden email]
>>>
>>> I just checked http://sequenceontology.org/cgi-bin/miso.cgi and the
>>> term motif_small_b is not found. I seem to remember you asking the SO
>>> people to add terms, is that right? If so, it doesn't appear to have
>>> happened yet.
>>>
>>> Scott
>>>
>>>
>>> On Wed, Sep 22, 2010 at 2:05 PM, Anja Friedrich
>>> <[hidden email]> wrote:
>>> > I did load the sequence ontology into chado. I will try to restore the
>>> > database
>>> >
>>> >> Date: Wed, 22 Sep 2010 14:00:00 -0400
>>> >> Subject: Re: [Gmod-schema] FW: problems loading data using
>>> >> gmod_bulk_load_gff3.pl
>>> >> From: [hidden email]
>>> >> To: [hidden email]
>>> >> CC: [hidden email]
>>> >>
>>> >> Right--the terms must be in the Sequence Ontology which must be loaded
>>> >> into Chado.
>>> >>
>>> >>
>>> >>
>>> >> On Wed, Sep 22, 2010 at 1:41 PM, Anja Friedrich
>>> >> <[hidden email]> wrote:
>>> >> > Hi Scott,
>>> >> >
>>> >> > the error message changed. now its saying
>>> >> >
>>> >> > MSG: no cvterm for motif_small_b
>>> >> >
>>> >> > Anja
>>> >> >
>>> >> >> Date: Wed, 22 Sep 2010 13:27:43 -0400
>>> >> >> Subject: Re: [Gmod-schema] FW: problems loading data using
>>> >> >> gmod_bulk_load_gff3.pl
>>> >> >> From: [hidden email]
>>> >> >> To: [hidden email]
>>> >> >> CC: [hidden email]
>>> >> >>
>>> >> >> Hi Anja,
>>> >> >>
>>> >> >> I saw the email on that list but didn't look closely at what Mitch
>>> >> >> did. What Mitch wrote is very close to what would be acceptable.
>>> >> >> The
>>> >> >> only change that would be need would be the addition of the GFF
>>> >> >> line
>>> >> >> for "1". The sequence-region directive is fine for display, but is
>>> >> >> not OK for Chado, where every feature needs to be typed, like
>>> >> >> "chromosome" or "contig".
>>> >> >>
>>> >> >> Scott
>>> >> >>
>>> >> >>
>>> >> >> On Wed, Sep 22, 2010 at 12:57 PM, Anja Friedrich
>>> >> >> <[hidden email]> wrote:
>>> >> >> >
>>> >> >> >
>>> >> >> > ________________________________
>>> >> >> > From: [hidden email]
>>> >> >> > To: [hidden email]
>>> >> >> > Subject: RE: [Gmod-schema] problems loading data using
>>> >> >> > gmod_bulk_load_gff3.pl
>>> >> >> > Date: Wed, 22 Sep 2010 18:56:32 +0200
>>> >> >> >
>>> >> >> > Hi Scott,
>>> >> >> >
>>> >> >> > thanks for the explanation. I can give it a try and change it.
>>> >> >> > Well I just extended the gff file Mitch Skinner send me don't
>>> >> >> > know
>>> >> >> > if
>>> >> >> > you
>>> >> >> > have seen the post),  and he used to display the feature. Thats
>>> >> >> > how
>>> >> >> > he
>>> >> >> > set
>>> >> >> > the file up, so I thought its fine.
>>> >> >> >
>>> >> >> > Anja
>>> >> >> >
>>> >> >> >> Date: Wed, 22 Sep 2010 12:45:47 -0400
>>> >> >> >> Subject: Re: [Gmod-schema] problems loading data using
>>> >> >> >> gmod_bulk_load_gff3.pl
>>> >> >> >> From: [hidden email]
>>> >> >> >> To: [hidden email]
>>> >> >> >> CC: [hidden email]
>>> >> >> >>
>>> >> >> >> Hi Anja,
>>> >> >> >>
>>> >> >> >> In order to refer to a reference sequence in the first column,
>>> >> >> >> the
>>> >> >> >> first thing you must do is to provide a GFF line that identifies
>>> >> >> >> that
>>> >> >> >> sequence. For example, I'm guessing whatever "1" is, it has a
>>> >> >> >> length
>>> >> >> >> of 2000 (because you have a sequence-region directive in the
>>> >> >> >> file).
>>> >> >> >> So, you would need a gff line something like this:
>>> >> >> >>
>>> >> >> >> 1 . contig 1 2000 . . . ID=1;Name=1
>>> >> >> >>
>>> >> >> >> Of course, the remaining lines in your GFF file aren't valid
>>> >> >> >> either,
>>> >> >> >> because they have "NTR" as a reference sequence, but there is
>>> >> >> >> not
>>> >> >> >> a
>>> >> >> >> line defining the feature called "NTR" in this file (well, it's
>>> >> >> >> not
>>> >> >> >> valid assuming there is not already a feature call "NTR" in your
>>> >> >> >> database; if that were the case it would be fine).
>>> >> >> >>
>>> >> >> >> Scott
>>> >> >> >>
>>> >> >> >>
>>> >> >> >> On Wed, Sep 22, 2010 at 12:33 PM, Anja Friedrich
>>> >> >> >> <[hidden email]> wrote:
>>> >> >> >> > Hi all,
>>> >> >> >> >
>>> >> >> >> > I got an error message I can't interpret by using
>>> >> >> >> > gmod_bulk_load_gff3.pl
>>> >> >> >> >
>>> >> >> >> > anou@anou-laptop:~$ gmod_bulk_load_gff3.pl --organism taro
>>> >> >> >> > --gfffile
>>> >> >> >> > taro.gff
>>> >> >> >> > Preparing data for inserting into the chado database
>>> >> >> >> > (This may take a while ...)
>>> >> >> >> > Unable to find srcfeature 1 in the database.
>>> >> >> >> > Perhaps you need to rerun your data load with the
>>> >> >> >> > '--recreate_cache'
>>> >> >> >> > option.
>>> >> >> >> > at /usr/local/share/perl/5.10.1/Bio/GMOD/DB/Adapter.pm line
>>> >> >> >> > 4555
>>> >> >> >> >
>>> >> >> >> >
>>> >> >> >> >
>>> >> >> >> >
>>> >> >> >> >
>>> >> >> >> >
>>> >> >> >> > Bio::GMOD::DB::Adapter::src_second_chance('Bio::GMOD::DB::Adapter=HASH(0x994b7d0)',
>>> >> >> >> > 'Bio::SeqFeature::Annotated=HASH(0x9b74258)') called at
>>> >> >> >> > /usr/local/bin/gmod_bulk_load_gff3.pl line 841
>>> >> >> >> >
>>> >> >> >> > Abnormal termination, trying to clean up...
>>> >> >> >> >
>>> >> >> >> > Attempting to clean up the loader temp table (so that
>>> >> >> >> > --recreate_cache
>>> >> >> >> > won't be needed)...
>>> >> >> >> > Trying to remove the run lock (so that --remove_lock won't be
>>> >> >> >> > needed)...
>>> >> >> >> > Exiting...
>>> >> >> >> >
>>> >> >> >> > Anyone an idea? I attached the file
>>> >> >> >> >
>>> >> >> >> > Cheers,
>>> >> >> >> > Anja
>>> >> >> >> >
>>> >> >> >> >
>>> >> >> >> >
>>> >> >> >> >
>>> >> >> >> >
>>> >> >> >> >
>>> >> >> >> > ------------------------------------------------------------------------------
>>> >> >> >> > Start uncovering the many advantages of virtual appliances
>>> >> >> >> > and start using them to simplify application deployment and
>>> >> >> >> > accelerate your shift to cloud computing.
>>> >> >> >> > http://p.sf.net/sfu/novell-sfdev2dev
>>> >> >> >> > _______________________________________________
>>> >> >> >> > Gmod-schema mailing list
>>> >> >> >> > [hidden email]
>>> >> >> >> > https://lists.sourceforge.net/lists/listinfo/gmod-schema
>>> >> >> >> >
>>> >> >> >> >
>>> >> >> >>
>>> >> >> >>
>>> >> >> >>
>>> >> >> >> --
>>> >> >> >>
>>> >> >> >>
>>> >> >> >>
>>> >> >> >>
>>> >> >> >> ------------------------------------------------------------------------
>>> >> >> >> Scott Cain, Ph. D.                                   scott at
>>> >> >> >> scottcain
>>> >> >> >> dot net
>>> >> >> >> GMOD Coordinator (http://gmod.org/)
>>> >> >> >> 216-392-3087
>>> >> >> >> Ontario Institute for Cancer Research
>>> >> >> >
>>> >> >> >
>>> >> >> >
>>> >> >> >
>>> >> >> >
>>> >> >> > ------------------------------------------------------------------------------
>>> >> >> > Start uncovering the many advantages of virtual appliances
>>> >> >> > and start using them to simplify application deployment and
>>> >> >> > accelerate your shift to cloud computing.
>>> >> >> > http://p.sf.net/sfu/novell-sfdev2dev
>>> >> >> > _______________________________________________
>>> >> >> > Gmod-schema mailing list
>>> >> >> > [hidden email]
>>> >> >> > https://lists.sourceforge.net/lists/listinfo/gmod-schema
>>> >> >> >
>>> >> >> >
>>> >> >>
>>> >> >>
>>> >> >>
>>> >> >> --
>>> >> >>
>>> >> >>
>>> >> >>
>>> >> >> ------------------------------------------------------------------------
>>> >> >> Scott Cain, Ph. D.                                   scott at
>>> >> >> scottcain
>>> >> >> dot net
>>> >> >> GMOD Coordinator (http://gmod.org/)
>>> >> >> 216-392-3087
>>> >> >> Ontario Institute for Cancer Research
>>> >> >
>>> >>
>>> >>
>>> >>
>>> >> --
>>> >>
>>> >>
>>> >> ------------------------------------------------------------------------
>>> >> Scott Cain, Ph. D.                                   scott at
>>> >> scottcain
>>> >> dot net
>>> >> GMOD Coordinator (http://gmod.org/)                     216-392-3087
>>> >> Ontario Institute for Cancer Research
>>> >
>>>
>>>
>>>
>>> --
>>> ------------------------------------------------------------------------
>>> Scott Cain, Ph. D.                                   scott at scottcain
>>> dot net
>>> GMOD Coordinator (http://gmod.org/)                     216-392-3087
>>> Ontario Institute for Cancer Research
>>
>
>
> --
> ------------------------------------------------------------------------
> Scott Cain, Ph. D.                                   scott at scottcain dot
> net
> GMOD Coordinator (http://gmod.org/)                     216-392-3087
> Ontario Institute for Cancer Research
>
> ------------------------------------------------------------------------------
> Start uncovering the many advantages of virtual appliances
> and start using them to simplify application deployment and
> accelerate your shift to cloud computing.
> http://p.sf.net/sfu/novell-sfdev2dev
> _______________________________________________
> Gmod-schema mailing list
> [hidden email]
> https://lists.sourceforge.net/lists/listinfo/gmod-schema
>
>
> ________________________________
> View message @
> http://gmod.827538.n3.nabble.com/problems-loading-data-using-gmod-bulk-load-gff3-pl-tp1562357p1563926.html
> To unsubscribe from GMOD, click here.
>
> ------------------------------------------------------------------------------
> Start uncovering the many advantages of virtual appliances
> and start using them to simplify application deployment and
> accelerate your shift to cloud computing.
> http://p.sf.net/sfu/novell-sfdev2dev
>
> _______________________________________________
> Gmod-schema mailing list
> [hidden email]
> https://lists.sourceforge.net/lists/listinfo/gmod-schema
>
>
> ------------------------------------------------------------------------------
> Nokia and AT&T present the 2010 Calling All Innovators-North America contest
> Create new apps & games for the Nokia N8 for consumers in  U.S. and Canada
> $10 million total in prizes - $4M cash, 500 devices, nearly $6M in marketing
> Develop with Nokia Qt SDK, Web Runtime, or Java and Publish to Ovi Store
> http://p.sf.net/sfu/nokia-dev2dev
> _______________________________________________
> Gmod-schema mailing list
> [hidden email]
> https://lists.sourceforge.net/lists/listinfo/gmod-schema
>
>
> ________________________________
> View message @
> http://gmod.827538.n3.nabble.com/problems-loading-data-using-gmod-bulk-load-gff3-pl-tp1562357p1570927.html
> To unsubscribe from GMOD, click here.
>
> ------------------------------------------------------------------------------
> Nokia and AT&T present the 2010 Calling All Innovators-North America contest
> Create new apps & games for the Nokia N8 for consumers in  U.S. and Canada
> $10 million total in prizes - $4M cash, 500 devices, nearly $6M in marketing
> Develop with Nokia Qt SDK, Web Runtime, or Java and Publish to Ovi Store
> http://p.sf.net/sfu/nokia-dev2dev
>
> _______________________________________________
> Gmod-schema mailing list
> [hidden email]
> https://lists.sourceforge.net/lists/listinfo/gmod-schema
>
> ------------------------------------------------------------------------------
> Nokia and AT&T present the 2010 Calling All Innovators-North America contest
> Create new apps & games for the Nokia N8 for consumers in  U.S. and Canada
> $10 million total in prizes - $4M cash, 500 devices, nearly $6M in marketing
> Develop with Nokia Qt SDK, Web Runtime, or Java and Publish to Ovi Store
> http://p.sf.net/sfu/nokia-dev2dev
> _______________________________________________
> Gmod-schema mailing list
> [hidden email]
> https://lists.sourceforge.net/lists/listinfo/gmod-schema
>
>
> ________________________________
> View message @
> http://gmod.827538.n3.nabble.com/problems-loading-data-using-gmod-bulk-load-gff3-pl-tp1562357p1573628.html
> To unsubscribe from GMOD, click here.
>



--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research

------------------------------------------------------------------------------
Start uncovering the many advantages of virtual appliances
and start using them to simplify application deployment and
accelerate your shift to cloud computing.
http://p.sf.net/sfu/novell-sfdev2dev
_______________________________________________
Gmod-schema mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-schema
Reply | Threaded
Open this post in threaded view
|

RE: problems loading data using gmod_bulk_load_gff3.pl

anja
CONTENTS DELETED
The author has deleted this message.
Reply | Threaded
Open this post in threaded view
|

Re: problems loading data using gmod_bulk_load_gff3.pl

anja
In reply to this post by Scott Cain
CONTENTS DELETED
The author has deleted this message.
Reply | Threaded
Open this post in threaded view
|

RE: problems loading data using gmod_bulk_load_gff3.pl

anja
CONTENTS DELETED
The author has deleted this message.
Reply | Threaded
Open this post in threaded view
|

Re: problems loading data using gmod_bulk_load_gff3.pl

anja
In reply to this post by Scott Cain
CONTENTS DELETED
The author has deleted this message.
Reply | Threaded
Open this post in threaded view
|

Re: problems loading data using gmod_bulk_load_gff3.pl

Scott Cain
In reply to this post by anja
Ah, you didn't specify that you were using a posgres database; the
default for the SeqFeature::Store loader is mysql.  In order to load a
postgres database, the command has to look something like this:

  bp_seqfeature_load.pl --dns "dbi:Pg:dbname=somename" --adaptor
DBI::Pg --create somefile.gff3

(I'm not on a computer with bioperl loaded at the moment, so I may not
have gotten those flags right.)

Also, I added the GBrowse mailing list to the cc list, and follow ups
to this can trim off the schema mailing list, since this doesn't have
anything to do with Chado.

Scott


On Sun, Sep 26, 2010 at 3:34 PM, anja <[hidden email]> wrote:

> okay, I upgraded it to BioPerl 1.6.1 but get still the same message. I tried
> GRANT ALL ON chado.* TO 'anou'@'localhost'; to get all permission but get
> Syntaxerror by »TO«
> Furthermore by installing BioPerl and making perl Build.PL I chose [P]g as
> the database, not mysql. So I dont know why it appears in the error message?
>
> Anja
>
> ________________________________
> Date: Sun, 26 Sep 2010 11:40:15 -0700
> From: [hidden email]
> To: [hidden email]
> Subject: Re: problems loading data using gmod_bulk_load_gff3.pl
>
> Hi Scott,
>
> thanks, I'm upgrading it. Maybe it solves the problem
>
> Anja
>
>> Date: Sun, 26 Sep 2010 14:34:45 -0400
>> Subject: Re: problems loading data using gmod_bulk_load_gff3.pl
>> From: [hidden email]
>> To: [hidden email]
>> CC: [hidden email]
>>
>> Hi Anja,
>>
>> Getting access denied is a mysql problem; I'm not a mysql person, so I
>> can't say for sure, but looking at the end of the GBrowse tutorial for
>> using MySQL. In particular, make sure you grant all permissions for
>> your user.
>>
>> More importantly--you are using a very old version of BioPerl. At the
>> very least, you should be using version 1.6.1.
>>
>> Scott
>>
>>
>> On Sun, Sep 26, 2010 at 12:47 PM, Anja Friedrich
>> <[hidden email]> wrote:
>> > Hi Scott,
>> > I tried the bp_load_seqfeature.pl as you told me, but I get no access,
>> > not
>> > even with password. Am I doing something wrong?
>> >
>> > anou@anou-laptop:~/bioperl-1.5.2_102/scripts/Bio-SeqFeature-Store$ perl
>> > bp_load_seqfeature.pl -p ****
>> > DBI connect('test','',...) failed: Access denied for user
>> > 'anou'@'localhost'
>> > (using password: YES) at
>> > /usr/local/share/perl/5.10.1/Bio/DB/SeqFeature/Store/DBI/mysql.pm line
>> > 212
>> >
>> > -------------------- EXCEPTION --------------------
>> > MSG: Access denied for user 'anou'@'localhost' (using password: YES)
>> > STACK Bio::DB::SeqFeature::Store::DBI::mysql::init
>> > /usr/local/share/perl/5.10.1/Bio/DB/SeqFeature/Store/DBI/mysql.pm:212
>> > STACK Bio::DB::SeqFeature::Store::new
>> > /usr/local/share/perl/5.10.1/Bio/DB/SeqFeature/Store.pm:370
>> > STACK toplevel bp_load_seqfeature.pl:56
>> > -------------------------------------------
>> >
>> > Anja
>> > ________________________________
>> > Date: Fri, 24 Sep 2010 05:38:24 -0700
>> > From: [hidden email]
>> > To: [hidden email]
>> > Subject: Re: problems loading data using gmod_bulk_load_gff3.pl
>> >
>> > Hi Anja,
>> > If all you want is to use a browser with your data, you don't really
>> > want
>> > chado anyway. Try using Bio::DB::SeqFeature::Store which comes with
>> > BioPerl.
>> > The loader is called bp_load_seqfeature.pl. It won't mind that your
>> > types
>> > aren't part of SO and is much faster than chado.
>> > Scott
>> >
>> > --
>> > Scott Cain, Ph. D.
>> > scott at scottcain dot net
>> > Ontario Institute for Cancer Research
>> > http://gmod.org/
>> > 216 392 3087
>> > On Sep 24, 2010, at 4:04 AM, Anja Friedrich <[hidden email]> wrote:
>> >
>> > Hi,
>> >
>> > I thought it might be better to use a database as I'm storing my data
>> > (reference sequence and taro) in it. I tried to find soemthing about the
>> > "local cv" you mentioned, but was not successfully yet. I will keep
>> > looking
>> > or ask someone of the gff people if I can use it in my case.
>> > But anyway, thank you for your help.
>> >
>> > Anja
>> >
>> >
>> > ________________________________
>> > Date: Thu, 23 Sep 2010 15:47:03 -0700
>> > From: [hidden email]
>> > To: [hidden email]
>> > Subject: Re: problems loading data using gmod_bulk_load_gff3.pl
>> >
>> > Yes, sorry for not elaborating on that earlier.  JBrowse is currently
>> > able
>> > to make different features visually distinct within a track only if they
>> > have different types.  So I set the different motifs to have different
>> > types
>> > in the GFF I sent.  I didn't use chado; I just used the SeqFeature store
>> > memory adapter to get the GFF data into a JBrowse instance.
>> >
>> > In the future, we plan to make it possible to make features look
>> > different
>> > based on other criteria than just type.  But for now, I think you have
>> > two
>> > options.
>> >
>> > If you only want to visualize the features, then you could just take the
>> > approach that I did in the taro.json config file I sent, and not use
>> > chado.
>> >
>> > On the other hand, if it's important to have your data in chado, then I
>> > think you can create a local CV for those types?  Scott could tell you
>> > for
>> > sure.
>> >
>> > Sorry for the extra complication,
>> > Mitch
>> >
>> > On 09/22/2010 02:00 PM, Anja Friedrich wrote:
>> >
>> > Yes I understand that, but that would mean that Mitch did not use chado.
>> > But I can't ask the SO people to add all the motifs to the vocabulary...
>> >
>> > Anja
>> >
>> > ________________________________
>> > Date: Wed, 22 Sep 2010 13:55:19 -0700
>> > From: [hidden email]
>> > To: [hidden email]
>> > Subject: Re: FW: problems loading data using gmod_bulk_load_gff3.pl
>> >
>> > It's just that Chado is very strict about what it will allow: since it
>> > is intended as a data warehouse where your "important" data goes, it
>> > tries to make sure your data are clean.  Visualization tools like
>> > JBrowse and GBrowse don't care nearly so much, and will let you do
>> > things that aren't technically allowed by the GFF3 specification.
>> >
>> > Scott
>> >
>> >
>> > On Wed, Sep 22, 2010 at 4:25 PM, Anja Friedrich
>> > <[hidden email]> wrote:
>> >> I asked them to add nested_tandem_repeat. I never asked for
>> >> motif_small_b.
>> >> But Mitch managed to visualise it using this feature. Wondering how.
>> >> Thank
>> >> for your work and patience Scott.
>> >>
>> >> Anja
>> >>
>> >>> Date: Wed, 22 Sep 2010 14:22:00 -0400
>> >>> Subject: Re: [Gmod-schema] FW: problems loading data using
>> >>> gmod_bulk_load_gff3.pl
>> >>> From: [hidden email]
>> >>> To: [hidden email]
>> >>> CC: [hidden email]
>> >>>
>> >>> I just checked http://sequenceontology.org/cgi-bin/miso.cgi and the
>> >>> term motif_small_b is not found. I seem to remember you asking the SO
>> >>> people to add terms, is that right? If so, it doesn't appear to have
>> >>> happened yet.
>> >>>
>> >>> Scott
>> >>>
>> >>>
>> >>> On Wed, Sep 22, 2010 at 2:05 PM, Anja Friedrich
>> >>> <[hidden email]> wrote:
>> >>> > I did load the sequence ontology into chado. I will try to restore
>> >>> > the
>> >>> > database
>> >>> >
>> >>> >> Date: Wed, 22 Sep 2010 14:00:00 -0400
>> >>> >> Subject: Re: [Gmod-schema] FW: problems loading data using
>> >>> >> gmod_bulk_load_gff3.pl
>> >>> >> From: [hidden email]
>> >>> >> To: [hidden email]
>> >>> >> CC: [hidden email]
>> >>> >>
>> >>> >> Right--the terms must be in the Sequence Ontology which must be
>> >>> >> loaded
>> >>> >> into Chado.
>> >>> >>
>> >>> >>
>> >>> >>
>> >>> >> On Wed, Sep 22, 2010 at 1:41 PM, Anja Friedrich
>> >>> >> <[hidden email]> wrote:
>> >>> >> > Hi Scott,
>> >>> >> >
>> >>> >> > the error message changed. now its saying
>> >>> >> >
>> >>> >> > MSG: no cvterm for motif_small_b
>> >>> >> >
>> >>> >> > Anja
>> >>> >> >
>> >>> >> >> Date: Wed, 22 Sep 2010 13:27:43 -0400
>> >>> >> >> Subject: Re: [Gmod-schema] FW: problems loading data using
>> >>> >> >> gmod_bulk_load_gff3.pl
>> >>> >> >> From: [hidden email]
>> >>> >> >> To: [hidden email]
>> >>> >> >> CC: [hidden email]
>> >>> >> >>
>> >>> >> >> Hi Anja,
>> >>> >> >>
>> >>> >> >> I saw the email on that list but didn't look closely at what
>> >>> >> >> Mitch
>> >>> >> >> did. What Mitch wrote is very close to what would be acceptable.
>> >>> >> >> The
>> >>> >> >> only change that would be need would be the addition of the GFF
>> >>> >> >> line
>> >>> >> >> for "1". The sequence-region directive is fine for display, but
>> >>> >> >> is
>> >>> >> >> not OK for Chado, where every feature needs to be typed, like
>> >>> >> >> "chromosome" or "contig".
>> >>> >> >>
>> >>> >> >> Scott
>> >>> >> >>
>> >>> >> >>
>> >>> >> >> On Wed, Sep 22, 2010 at 12:57 PM, Anja Friedrich
>> >>> >> >> <[hidden email]> wrote:
>> >>> >> >> >
>> >>> >> >> >
>> >>> >> >> > ________________________________
>> >>> >> >> > From: [hidden email]
>> >>> >> >> > To: [hidden email]
>> >>> >> >> > Subject: RE: [Gmod-schema] problems loading data using
>> >>> >> >> > gmod_bulk_load_gff3.pl
>> >>> >> >> > Date: Wed, 22 Sep 2010 18:56:32 +0200
>> >>> >> >> >
>> >>> >> >> > Hi Scott,
>> >>> >> >> >
>> >>> >> >> > thanks for the explanation. I can give it a try and change it.
>> >>> >> >> > Well I just extended the gff file Mitch Skinner send me don't
>> >>> >> >> > know
>> >>> >> >> > if
>> >>> >> >> > you
>> >>> >> >> > have seen the post),  and he used to display the feature.
>> >>> >> >> > Thats
>> >>> >> >> > how
>> >>> >> >> > he
>> >>> >> >> > set
>> >>> >> >> > the file up, so I thought its fine.
>> >>> >> >> >
>> >>> >> >> > Anja
>> >>> >> >> >
>> >>> >> >> >> Date: Wed, 22 Sep 2010 12:45:47 -0400
>> >>> >> >> >> Subject: Re: [Gmod-schema] problems loading data using
>> >>> >> >> >> gmod_bulk_load_gff3.pl
>> >>> >> >> >> From: [hidden email]
>> >>> >> >> >> To: [hidden email]
>> >>> >> >> >> CC: [hidden email]
>> >>> >> >> >>
>> >>> >> >> >> Hi Anja,
>> >>> >> >> >>
>> >>> >> >> >> In order to refer to a reference sequence in the first
>> >>> >> >> >> column,
>> >>> >> >> >> the
>> >>> >> >> >> first thing you must do is to provide a GFF line that
>> >>> >> >> >> identifies
>> >>> >> >> >> that
>> >>> >> >> >> sequence. For example, I'm guessing whatever "1" is, it has a
>> >>> >> >> >> length
>> >>> >> >> >> of 2000 (because you have a sequence-region directive in the
>> >>> >> >> >> file).
>> >>> >> >> >> So, you would need a gff line something like this:
>> >>> >> >> >>
>> >>> >> >> >> 1 . contig 1 2000 . . . ID=1;Name=1
>> >>> >> >> >>
>> >>> >> >> >> Of course, the remaining lines in your GFF file aren't valid
>> >>> >> >> >> either,
>> >>> >> >> >> because they have "NTR" as a reference sequence, but there is
>> >>> >> >> >> not
>> >>> >> >> >> a
>> >>> >> >> >> line defining the feature called "NTR" in this file (well,
>> >>> >> >> >> it's
>> >>> >> >> >> not
>> >>> >> >> >> valid assuming there is not already a feature call "NTR" in
>> >>> >> >> >> your
>> >>> >> >> >> database; if that were the case it would be fine).
>> >>> >> >> >>
>> >>> >> >> >> Scott
>> >>> >> >> >>
>> >>> >> >> >>
>> >>> >> >> >> On Wed, Sep 22, 2010 at 12:33 PM, Anja Friedrich
>> >>> >> >> >> <[hidden email]> wrote:
>> >>> >> >> >> > Hi all,
>> >>> >> >> >> >
>> >>> >> >> >> > I got an error message I can't interpret by using
>> >>> >> >> >> > gmod_bulk_load_gff3.pl
>> >>> >> >> >> >
>> >>> >> >> >> > anou@anou-laptop:~$ gmod_bulk_load_gff3.pl --organism taro
>> >>> >> >> >> > --gfffile
>> >>> >> >> >> > taro.gff
>> >>> >> >> >> > Preparing data for inserting into the chado database
>> >>> >> >> >> > (This may take a while ...)
>> >>> >> >> >> > Unable to find srcfeature 1 in the database.
>> >>> >> >> >> > Perhaps you need to rerun your data load with the
>> >>> >> >> >> > '--recreate_cache'
>> >>> >> >> >> > option.
>> >>> >> >> >> > at /usr/local/share/perl/5.10.1/Bio/GMOD/DB/Adapter.pm line
>> >>> >> >> >> > 4555
>> >>> >> >> >> >
>> >>> >> >> >> >
>> >>> >> >> >> >
>> >>> >> >> >> >
>> >>> >> >> >> >
>> >>> >> >> >> >
>> >>> >> >> >> >
>> >>> >> >> >> > Bio::GMOD::DB::Adapter::src_second_chance('Bio::GMOD::DB::Adapter=HASH(0x994b7d0)',
>> >>> >> >> >> > 'Bio::SeqFeature::Annotated=HASH(0x9b74258)') called at
>> >>> >> >> >> > /usr/local/bin/gmod_bulk_load_gff3.pl line 841
>> >>> >> >> >> >
>> >>> >> >> >> > Abnormal termination, trying to clean up...
>> >>> >> >> >> >
>> >>> >> >> >> > Attempting to clean up the loader temp table (so that
>> >>> >> >> >> > --recreate_cache
>> >>> >> >> >> > won't be needed)...
>> >>> >> >> >> > Trying to remove the run lock (so that --remove_lock won't
>> >>> >> >> >> > be
>> >>> >> >> >> > needed)...
>> >>> >> >> >> > Exiting...
>> >>> >> >> >> >
>> >>> >> >> >> > Anyone an idea? I attached the file
>> >>> >> >> >> >
>> >>> >> >> >> > Cheers,
>> >>> >> >> >> > Anja
>> >>> >> >> >> >
>> >>> >> >> >> >
>> >>> >> >> >> >
>> >>> >> >> >> >
>> >>> >> >> >> >
>> >>> >> >> >> >
>> >>> >> >> >> >
>> >>> >> >> >> > ------------------------------------------------------------------------------
>> >>> >> >> >> > Start uncovering the many advantages of virtual appliances
>> >>> >> >> >> > and start using them to simplify application deployment and
>> >>> >> >> >> > accelerate your shift to cloud computing.
>> >>> >> >> >> > http://p.sf.net/sfu/novell-sfdev2dev
>> >>> >> >> >> > _______________________________________________
>> >>> >> >> >> > Gmod-schema mailing list
>> >>> >> >> >> > [hidden email]
>> >>> >> >> >> > https://lists.sourceforge.net/lists/listinfo/gmod-schema
>> >>> >> >> >> >
>> >>> >> >> >> >
>> >>> >> >> >>
>> >>> >> >> >>
>> >>> >> >> >>
>> >>> >> >> >> --
>> >>> >> >> >>
>> >>> >> >> >>
>> >>> >> >> >>
>> >>> >> >> >>
>> >>> >> >> >>
>> >>> >> >> >> ------------------------------------------------------------------------
>> >>> >> >> >> Scott Cain, Ph. D.                                   scott at
>> >>> >> >> >> scottcain
>> >>> >> >> >> dot net
>> >>> >> >> >> GMOD Coordinator (http://gmod.org/)
>> >>> >> >> >> 216-392-3087
>> >>> >> >> >> Ontario Institute for Cancer Research
>> >>> >> >> >
>> >>> >> >> >
>> >>> >> >> >
>> >>> >> >> >
>> >>> >> >> >
>> >>> >> >> >
>> >>> >> >> > ------------------------------------------------------------------------------
>> >>> >> >> > Start uncovering the many advantages of virtual appliances
>> >>> >> >> > and start using them to simplify application deployment and
>> >>> >> >> > accelerate your shift to cloud computing.
>> >>> >> >> > http://p.sf.net/sfu/novell-sfdev2dev
>> >>> >> >> > _______________________________________________
>> >>> >> >> > Gmod-schema mailing list
>> >>> >> >> > [hidden email]
>> >>> >> >> > https://lists.sourceforge.net/lists/listinfo/gmod-schema
>> >>> >> >> >
>> >>> >> >> >
>> >>> >> >>
>> >>> >> >>
>> >>> >> >>
>> >>> >> >> --
>> >>> >> >>
>> >>> >> >>
>> >>> >> >>
>> >>> >> >>
>> >>> >> >> ------------------------------------------------------------------------
>> >>> >> >> Scott Cain, Ph. D.                                   scott at
>> >>> >> >> scottcain
>> >>> >> >> dot net
>> >>> >> >> GMOD Coordinator (http://gmod.org/)
>> >>> >> >> 216-392-3087
>> >>> >> >> Ontario Institute for Cancer Research
>> >>> >> >
>> >>> >>
>> >>> >>
>> >>> >>
>> >>> >> --
>> >>> >>
>> >>> >>
>> >>> >>
>> >>> >> ------------------------------------------------------------------------
>> >>> >> Scott Cain, Ph. D.                                   scott at
>> >>> >> scottcain
>> >>> >> dot net
>> >>> >> GMOD Coordinator (http://gmod.org/)
>> >>> >> 216-392-3087
>> >>> >> Ontario Institute for Cancer Research
>> >>> >
>> >>>
>> >>>
>> >>>
>> >>> --
>> >>>
>> >>> ------------------------------------------------------------------------
>> >>> Scott Cain, Ph. D.                                   scott at
>> >>> scottcain
>> >>> dot net
>> >>> GMOD Coordinator (http://gmod.org/)                     216-392-3087
>> >>> Ontario Institute for Cancer Research
>> >>
>> >
>> >
>> > --
>> > ------------------------------------------------------------------------
>> > Scott Cain, Ph. D.                                   scott at scottcain
>> > dot
>> > net
>> > GMOD Coordinator (http://gmod.org/)                     216-392-3087
>> > Ontario Institute for Cancer Research
>> >
>> >
>> > ------------------------------------------------------------------------------
>> > Start uncovering the many advantages of virtual appliances
>> > and start using them to simplify application deployment and
>> > accelerate your shift to cloud computing.
>> > http://p.sf.net/sfu/novell-sfdev2dev
>> > _______________________________________________
>> > Gmod-schema mailing list
>> > [hidden email]
>> > https://lists.sourceforge.net/lists/listinfo/gmod-schema
>> >
>> >
>> > ________________________________
>> > View message @
>> >
>> > http://gmod.827538.n3.nabble.com/problems-loading-data-using-gmod-bulk-load-gff3-pl-tp1562357p1563926.html
>> > To unsubscribe from GMOD, click here.
>> >
>> >
>> > ------------------------------------------------------------------------------
>> > Start uncovering the many advantages of virtual appliances
>> > and start using them to simplify application deployment and
>> > accelerate your shift to cloud computing.
>> > http://p.sf.net/sfu/novell-sfdev2dev
>> >
>> > _______________________________________________
>> > Gmod-schema mailing list
>> > [hidden email]
>> > https://lists.sourceforge.net/lists/listinfo/gmod-schema
>> >
>> >
>> >
>> > ------------------------------------------------------------------------------
>> > Nokia and AT&T present the 2010 Calling All Innovators-North America
>> > contest
>> > Create new apps & games for the Nokia N8 for consumers in  U.S. and
>> > Canada
>> > $10 million total in prizes - $4M cash, 500 devices, nearly $6M in
>> > marketing
>> > Develop with Nokia Qt SDK, Web Runtime, or Java and Publish to Ovi Store
>> > http://p.sf.net/sfu/nokia-dev2dev
>> > _______________________________________________
>> > Gmod-schema mailing list
>> > [hidden email]
>> > https://lists.sourceforge.net/lists/listinfo/gmod-schema
>> >
>> >
>> > ________________________________
>> > View message @
>> >
>> > http://gmod.827538.n3.nabble.com/problems-loading-data-using-gmod-bulk-load-gff3-pl-tp1562357p1570927.html
>> > To unsubscribe from GMOD, click here.
>> >
>> >
>> > ------------------------------------------------------------------------------
>> > Nokia and AT&T present the 2010 Calling All Innovators-North America
>> > contest
>> > Create new apps & games for the Nokia N8 for consumers in  U.S. and
>> > Canada
>> > $10 million total in prizes - $4M cash, 500 devices, nearly $6M in
>> > marketing
>> > Develop with Nokia Qt SDK, Web Runtime, or Java and Publish to Ovi Store
>> > http://p.sf.net/sfu/nokia-dev2dev
>> >
>> > _______________________________________________
>> > Gmod-schema mailing list
>> > [hidden email]
>> > https://lists.sourceforge.net/lists/listinfo/gmod-schema
>> >
>> >
>> > ------------------------------------------------------------------------------
>> > Nokia and AT&T present the 2010 Calling All Innovators-North America
>> > contest
>> > Create new apps & games for the Nokia N8 for consumers in  U.S. and
>> > Canada
>> > $10 million total in prizes - $4M cash, 500 devices, nearly $6M in
>> > marketing
>> > Develop with Nokia Qt SDK, Web Runtime, or Java and Publish to Ovi Store
>> > http://p.sf.net/sfu/nokia-dev2dev
>> > _______________________________________________
>> > Gmod-schema mailing list
>> > [hidden email]
>> > https://lists.sourceforge.net/lists/listinfo/gmod-schema
>> >
>> >
>> > ________________________________
>> > View message @
>> >
>> > http://gmod.827538.n3.nabble.com/problems-loading-data-using-gmod-bulk-load-gff3-pl-tp1562357p1573628.html
>> > To unsubscribe from GMOD, click here.
>> >
>>
>>
>>
>> --
>> ------------------------------------------------------------------------
>> Scott Cain, Ph. D.                                   scott at scottcain
>> dot net
>> GMOD Coordinator (http://gmod.org/)                     216-392-3087
>> Ontario Institute for Cancer Research
> ------------------------------------------------------------------------------
> Start uncovering the many advantages of virtual appliances
> and start using them to simplify application deployment and
> accelerate your shift to cloud computing.
> http://p.sf.net/sfu/novell-sfdev2dev
> _______________________________________________
> Gmod-schema mailing list
> [hidden email]
> https://lists.sourceforge.net/lists/listinfo/gmod-schema
>
>
> ________________________________
> View message @
> http://gmod.827538.n3.nabble.com/problems-loading-data-using-gmod-bulk-load-gff3-pl-tp1562357p1584794.html
> To start a new topic under GMOD, email [hidden email]
> To unsubscribe from GMOD, click here.
>
> ________________________________
> View this message in context: RE: problems loading data using
> gmod_bulk_load_gff3.pl
> Sent from the Chado mailing list archive at Nabble.com.
>
> ------------------------------------------------------------------------------
> Start uncovering the many advantages of virtual appliances
> and start using them to simplify application deployment and
> accelerate your shift to cloud computing.
> http://p.sf.net/sfu/novell-sfdev2dev
> _______________________________________________
> Gmod-schema mailing list
> [hidden email]
> https://lists.sourceforge.net/lists/listinfo/gmod-schema
>
>



--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research

------------------------------------------------------------------------------
Start uncovering the many advantages of virtual appliances
and start using them to simplify application deployment and
accelerate your shift to cloud computing.
http://p.sf.net/sfu/novell-sfdev2dev
_______________________________________________
Gmod-schema mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-schema
Reply | Threaded
Open this post in threaded view
|

Re: problems using bp_load_seqfeature.pl

anja
In reply to this post by anja
CONTENTS DELETED
The author has deleted this message.
12