chado-prism

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chado-prism

Mariette
Hi everyone,
I'm trying to make an ergatis annotation pipline linked to gbrowse.
To do so I'm using the chado-prism with the bsml2chado componant.
Everything works fine but the querie looks wrong. I'm guessing I'm
not using the correct chado version. I use the one from gmod1.0. Is
it the correct version to use with ergatis ? I can't figure out which
one is required !

thanks for your help
Jeroem

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Re: chado-prism

Joshua Orvis
Jerome -

We maintain a copy of the schema expected within the software for internal consistency.  The Ergatis component 'initdb' can be used to create a blank Chado instance and load all expected ontologies at once.  That database created can then be the target of bsml2chado runs.

Joshua



On Mon, Jun 14, 2010 at 7:48 AM, Mariette <[hidden email]> wrote:
Hi everyone,
I'm trying to make an ergatis annotation pipline linked to gbrowse.
To do so I'm using the chado-prism with the bsml2chado componant.
Everything works fine but the querie looks wrong. I'm guessing I'm
not using the correct chado version. I use the one from gmod1.0. Is
it the correct version to use with ergatis ? I can't figure out which
one is required !

thanks for your help
Jeroem

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Re: chado-prism

Mariette


Thanks for that,
so I run the componant which worked just fine and filled
the database.
Now when I use the bsml2chado I'm getting the following errors :
at step
  failed  Cache primary keys
Died with 'cvterm_id was not defined for class 'chromosome'' at  
/usr/local/bioinfo/src/ergatis//lib/perl5/Prism.pm line 909

there is some other cvterm to add to chado before to use it ?
It sounds to me like ok when I run the initDB component.

thanks for your answer,
Jerome



Joshua Orvis <[hidden email]> a écrit :

> Jerome -
>
> We maintain a copy of the schema expected within the software for internal
> consistency.  The Ergatis component 'initdb' can be used to create a blank
> Chado instance and load all expected ontologies at once.  That database
> created can then be the target of bsml2chado runs.
>
> Joshua
>
>
>
> On Mon, Jun 14, 2010 at 7:48 AM, Mariette <[hidden email]> wrote:
>
>> Hi everyone,
>> I'm trying to make an ergatis annotation pipline linked to gbrowse.
>> To do so I'm using the chado-prism with the bsml2chado componant.
>> Everything works fine but the querie looks wrong. I'm guessing I'm
>> not using the correct chado version. I use the one from gmod1.0. Is
>> it the correct version to use with ergatis ? I can't figure out which
>> one is required !
>>
>> thanks for your help
>> Jeroem
>>
>>
>> ------------------------------------------------------------------------------
>> ThinkGeek and WIRED's GeekDad team up for the Ultimate
>> GeekDad Father's Day Giveaway. ONE MASSIVE PRIZE to the
>> lucky parental unit.  See the prize list and enter to win:
>> http://p.sf.net/sfu/thinkgeek-promo
>> _______________________________________________
>> Ergatis-users mailing list
>> [hidden email]
>> https://lists.sourceforge.net/lists/listinfo/ergatis-users
>>
>


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Re: chado-prism

Mariette

Joshua,

We are pretty new in chado but we're gessing that
we're facing this error because we haven't load our
seq ref yet, would that make sense ?

If yes there is an ergatis componant to do so ? I take
a look at all components available but can't find any.

thanks for your help,
Jerome






jmariett a écrit :

> Thanks for that,
> so I run the componant which worked just fine and filled
> the database.
> Now when I use the bsml2chado I'm getting the following errors :
> at step
>   failed  Cache primary keys
> Died with 'cvterm_id was not defined for class 'chromosome'' at  
> /usr/local/bioinfo/src/ergatis//lib/perl5/Prism.pm line 909
>
> there is some other cvterm to add to chado before to use it ?
> It sounds to me like ok when I run the initDB component.
>
> thanks for your answer,
> Jerome
>
>
>
> Joshua Orvis <[hidden email]> a écrit :
>
>  
>> Jerome -
>>
>> We maintain a copy of the schema expected within the software for internal
>> consistency.  The Ergatis component 'initdb' can be used to create a blank
>> Chado instance and load all expected ontologies at once.  That database
>> created can then be the target of bsml2chado runs.
>>
>> Joshua
>>
>>
>>
>> On Mon, Jun 14, 2010 at 7:48 AM, Mariette <[hidden email]> wrote:
>>
>>    
>>> Hi everyone,
>>> I'm trying to make an ergatis annotation pipline linked to gbrowse.
>>> To do so I'm using the chado-prism with the bsml2chado componant.
>>> Everything works fine but the querie looks wrong. I'm guessing I'm
>>> not using the correct chado version. I use the one from gmod1.0. Is
>>> it the correct version to use with ergatis ? I can't figure out which
>>> one is required !
>>>
>>> thanks for your help
>>> Jeroem
>>>
>>>
>>> ------------------------------------------------------------------------------
>>> ThinkGeek and WIRED's GeekDad team up for the Ultimate
>>> GeekDad Father's Day Giveaway. ONE MASSIVE PRIZE to the
>>> lucky parental unit.  See the prize list and enter to win:
>>> http://p.sf.net/sfu/thinkgeek-promo
>>> _______________________________________________
>>> Ergatis-users mailing list
>>> [hidden email]
>>> https://lists.sourceforge.net/lists/listinfo/ergatis-users
>>>
>>>      
>
>
> ------------------------------------------------------------------------------
> ThinkGeek and WIRED's GeekDad team up for the Ultimate
> GeekDad Father's Day Giveaway. ONE MASSIVE PRIZE to the
> lucky parental unit.  See the prize list and enter to win:
> http://p.sf.net/sfu/thinkgeek-promo
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> Ergatis-users mailing list
> [hidden email]
> https://lists.sourceforge.net/lists/listinfo/ergatis-users
>  


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Re: chado-prism

Joshua Orvis
It looks like your database is missing the ontology term for 'chromosome'.  Can you log in to the chado database you created and issue this query?

SELECT cvterm_id, cv_id, name FROM cvterm WHERE name = 'chromosome';

You should get at least one row.

Joshua


On Wed, Jun 16, 2010 at 3:22 AM, Mariette <[hidden email]> wrote:

Joshua,

We are pretty new in chado but we're gessing that
we're facing this error because we haven't load our
seq ref yet, would that make sense ?

If yes there is an ergatis componant to do so ? I take
a look at all components available but can't find any.

thanks for your help,
Jerome






jmariett a écrit :

Thanks for that,
so I run the componant which worked just fine and filled
the database.
Now when I use the bsml2chado I'm getting the following errors :
at step
 failed  Cache primary keys
Died with 'cvterm_id was not defined for class 'chromosome'' at  /usr/local/bioinfo/src/ergatis//lib/perl5/Prism.pm line 909

there is some other cvterm to add to chado before to use it ?
It sounds to me like ok when I run the initDB component.

thanks for your answer,
Jerome



Joshua Orvis <[hidden email]> a écrit :

 
Jerome -

We maintain a copy of the schema expected within the software for internal
consistency.  The Ergatis component 'initdb' can be used to create a blank
Chado instance and load all expected ontologies at once.  That database
created can then be the target of bsml2chado runs.

Joshua



On Mon, Jun 14, 2010 at 7:48 AM, Mariette <[hidden email]> wrote:

   
Hi everyone,
I'm trying to make an ergatis annotation pipline linked to gbrowse.
To do so I'm using the chado-prism with the bsml2chado componant.
Everything works fine but the querie looks wrong. I'm guessing I'm
not using the correct chado version. I use the one from gmod1.0. Is
it the correct version to use with ergatis ? I can't figure out which
one is required !

thanks for your help
Jeroem


------------------------------------------------------------------------------
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GeekDad Father's Day Giveaway. ONE MASSIVE PRIZE to the
lucky parental unit.  See the prize list and enter to win:
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_______________________________________________
Ergatis-users mailing list
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https://lists.sourceforge.net/lists/listinfo/ergatis-users

     


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Re: chado-prism

Mariette

the querie gave me :

cvterm_id cv_id name
9739
       
10
        chromosome
34229
       
13
        chromosome


thx for your help,
Jerome




Joshua Orvis a écrit :

> It looks like your database is missing the ontology term for
> 'chromosome'.  Can you log in to the chado database you created and
> issue this query?
>
> SELECT cvterm_id, cv_id, name FROM cvterm WHERE name = 'chromosome';
>
> You should get at least one row.
>
> Joshua
>
>
> On Wed, Jun 16, 2010 at 3:22 AM, Mariette <[hidden email]
> <mailto:[hidden email]>> wrote:
>
>
>     Joshua,
>
>     We are pretty new in chado but we're gessing that
>     we're facing this error because we haven't load our
>     seq ref yet, would that make sense ?
>
>     If yes there is an ergatis componant to do so ? I take
>     a look at all components available but can't find any.
>
>     thanks for your help,
>     Jerome
>
>
>
>
>
>
>     jmariett a écrit :
>
>         Thanks for that,
>         so I run the componant which worked just fine and filled
>         the database.
>         Now when I use the bsml2chado I'm getting the following errors :
>         at step
>          failed  Cache primary keys
>         Died with 'cvterm_id was not defined for class 'chromosome''
>         at  /usr/local/bioinfo/src/ergatis//lib/perl5/Prism.pm line 909
>
>         there is some other cvterm to add to chado before to use it ?
>         It sounds to me like ok when I run the initDB component.
>
>         thanks for your answer,
>         Jerome
>
>
>
>         Joshua Orvis <[hidden email] <mailto:[hidden email]>> a
>         écrit :
>
>          
>
>             Jerome -
>
>             We maintain a copy of the schema expected within the
>             software for internal
>             consistency.  The Ergatis component 'initdb' can be used
>             to create a blank
>             Chado instance and load all expected ontologies at once.
>              That database
>             created can then be the target of bsml2chado runs.
>
>             Joshua
>
>
>
>             On Mon, Jun 14, 2010 at 7:48 AM, Mariette
>             <[hidden email]
>             <mailto:[hidden email]>> wrote:
>
>                
>
>                 Hi everyone,
>                 I'm trying to make an ergatis annotation pipline
>                 linked to gbrowse.
>                 To do so I'm using the chado-prism with the bsml2chado
>                 componant.
>                 Everything works fine but the querie looks wrong. I'm
>                 guessing I'm
>                 not using the correct chado version. I use the one
>                 from gmod1.0. Is
>                 it the correct version to use with ergatis ? I can't
>                 figure out which
>                 one is required !
>
>                 thanks for your help
>                 Jeroem
>
>
>                 ------------------------------------------------------------------------------
>                 ThinkGeek and WIRED's GeekDad team up for the Ultimate
>                 GeekDad Father's Day Giveaway. ONE MASSIVE PRIZE to the
>                 lucky parental unit.  See the prize list and enter to win:
>                 http://p.sf.net/sfu/thinkgeek-promo
>                 _______________________________________________
>                 Ergatis-users mailing list
>                 [hidden email]
>                 <mailto:[hidden email]>
>                 https://lists.sourceforge.net/lists/listinfo/ergatis-users
>
>                      
>
>
>
>         ------------------------------------------------------------------------------
>         ThinkGeek and WIRED's GeekDad team up for the Ultimate GeekDad
>         Father's Day Giveaway. ONE MASSIVE PRIZE to the lucky parental
>         unit.  See the prize list and enter to win:
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>         [hidden email]
>         <mailto:[hidden email]>
>         https://lists.sourceforge.net/lists/listinfo/ergatis-users
>          
>
>
>


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Re: chado-prism

Joshua Orvis
Jerome -

I'm not sure where this is going wrong, but unfortunately we might need to add some debugging steps in the code to try to track it down. Here is the process I can see:

In lib/perl5/Prism/ChadoPrismDB.pm there is a subroutine called "get_cvterm_id_by_class_lookup" that creates a lookup of all the terms in the database that are part of either the SO or ARD ontologies.  The error you are getting is from within the "master_feature_id_lookup" subroutine in /lib/perl5/Prism.pm that is trying to look up the ID for the term 'chromosome'.  Your query from the database directly shows that the terms are present in your database.

We need to see now why that lookup is failing.  Can you use the interface to find the exact command line string of the step that is failing and then, reading the perldoc on the script if necessary, run it again with logging enabled and set at a high level?  We can try using the logs to see where this went wrong.

Alternatively, if you're feeling adventurous, you could start inserting debug steps on your own in the code but the logs may be an easier first step, depending on your comfort with Perl.

Joshua



On Wed, Jun 16, 2010 at 9:31 AM, Mariette <[hidden email]> wrote:

the querie gave me :


cvterm_id       cv_id   name
9739
       
10
       chromosome
34229
       
13
       chromosome


thx for your help,
Jerome




Joshua Orvis a écrit :
It looks like your database is missing the ontology term for 'chromosome'.  Can you log in to the chado database you created and issue this query?

SELECT cvterm_id, cv_id, name FROM cvterm WHERE name = 'chromosome';

You should get at least one row.

Joshua


On Wed, Jun 16, 2010 at 3:22 AM, Mariette <[hidden email] <mailto:[hidden email]>> wrote:


   Joshua,

   We are pretty new in chado but we're gessing that
   we're facing this error because we haven't load our
   seq ref yet, would that make sense ?

   If yes there is an ergatis componant to do so ? I take
   a look at all components available but can't find any.

   thanks for your help,
   Jerome






   jmariett a écrit :

       Thanks for that,
       so I run the componant which worked just fine and filled
       the database.
       Now when I use the bsml2chado I'm getting the following errors :
       at step
        failed  Cache primary keys
       Died with 'cvterm_id was not defined for class 'chromosome''
       at  /usr/local/bioinfo/src/ergatis//lib/perl5/Prism.pm line 909

       there is some other cvterm to add to chado before to use it ?
       It sounds to me like ok when I run the initDB component.

       thanks for your answer,
       Jerome



       Joshua Orvis <[hidden email] <mailto:[hidden email]>> a

       écrit :

       
           Jerome -

           We maintain a copy of the schema expected within the
           software for internal
           consistency.  The Ergatis component 'initdb' can be used
           to create a blank
           Chado instance and load all expected ontologies at once.
            That database
           created can then be the target of bsml2chado runs.

           Joshua



           On Mon, Jun 14, 2010 at 7:48 AM, Mariette
           <[hidden email]
           <mailto:[hidden email]>> wrote:

             
               Hi everyone,
               I'm trying to make an ergatis annotation pipline
               linked to gbrowse.
               To do so I'm using the chado-prism with the bsml2chado
               componant.
               Everything works fine but the querie looks wrong. I'm
               guessing I'm
               not using the correct chado version. I use the one
               from gmod1.0. Is
               it the correct version to use with ergatis ? I can't
               figure out which
               one is required !

               thanks for your help
               Jeroem


               ------------------------------------------------------------------------------
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               GeekDad Father's Day Giveaway. ONE MASSIVE PRIZE to the
               lucky parental unit.  See the prize list and enter to win:
               http://p.sf.net/sfu/thinkgeek-promo
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               <mailto:[hidden email]>

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       unit.  See the prize list and enter to win:
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Re: chado-prism

Mariette

Ok I'm gonna try this,
Just so you know, I was gessing the probleme could come from the fact
we haven't load anythink so far in the chado database. When I installed
gbrowse in an order database, I remember that I had to add a reference
sequence. So far I hadn't done this step ... could that be the probleme ?






Joshua Orvis <[hidden email]> a écrit :

> Jerome -
>
> I'm not sure where this is going wrong, but unfortunately we might need to
> add some debugging steps in the code to try to track it down. Here is the
> process I can see:
>
> In lib/perl5/Prism/ChadoPrismDB.pm there is a subroutine called
> "get_cvterm_id_by_class_lookup" that creates a lookup of all the terms in
> the database that are part of either the SO or ARD ontologies.  The error
> you are getting is from within the "master_feature_id_lookup" subroutine in
> /lib/perl5/Prism.pm that is trying to look up the ID for the term
> 'chromosome'.  Your query from the database directly shows that the terms
> are present in your database.
>
> We need to see now why that lookup is failing.  Can you use the interface to
> find the exact command line string of the step that is failing and then,
> reading the perldoc on the script if necessary, run it again with logging
> enabled and set at a high level?  We can try using the logs to see where
> this went wrong.
>
> Alternatively, if you're feeling adventurous, you could start inserting
> debug steps on your own in the code but the logs may be an easier first
> step, depending on your comfort with Perl.
>
> Joshua
>
>
>
> On Wed, Jun 16, 2010 at 9:31 AM, Mariette <[hidden email]> wrote:
>
>>
>> the querie gave me :
>>
>>
>> cvterm_id       cv_id   name
>> 9739
>>
>> 10
>>        chromosome
>> 34229
>>
>> 13
>>        chromosome
>>
>>
>> thx for your help,
>> Jerome
>>
>>
>>
>>
>> Joshua Orvis a écrit :
>>
>>> It looks like your database is missing the ontology term for 'chromosome'.
>>>  Can you log in to the chado database you created and issue this query?
>>>
>>> SELECT cvterm_id, cv_id, name FROM cvterm WHERE name = 'chromosome';
>>>
>>> You should get at least one row.
>>>
>>> Joshua
>>>
>>>
>>> On Wed, Jun 16, 2010 at 3:22 AM, Mariette  
>>> <[hidden email]<mailto:
>>> [hidden email]>> wrote:
>>>
>>>
>>>    Joshua,
>>>
>>>    We are pretty new in chado but we're gessing that
>>>    we're facing this error because we haven't load our
>>>    seq ref yet, would that make sense ?
>>>
>>>    If yes there is an ergatis componant to do so ? I take
>>>    a look at all components available but can't find any.
>>>
>>>    thanks for your help,
>>>    Jerome
>>>
>>>
>>>
>>>
>>>
>>>
>>>    jmariett a écrit :
>>>
>>>        Thanks for that,
>>>        so I run the componant which worked just fine and filled
>>>        the database.
>>>        Now when I use the bsml2chado I'm getting the following errors :
>>>        at step
>>>         failed  Cache primary keys
>>>        Died with 'cvterm_id was not defined for class 'chromosome''
>>>        at  /usr/local/bioinfo/src/ergatis//lib/perl5/Prism.pm line 909
>>>
>>>        there is some other cvterm to add to chado before to use it ?
>>>        It sounds to me like ok when I run the initDB component.
>>>
>>>        thanks for your answer,
>>>        Jerome
>>>
>>>
>>>
>>>        Joshua Orvis <[hidden email] <mailto:[hidden email]>> a
>>>
>>>        écrit :
>>>
>>>
>>>            Jerome -
>>>
>>>            We maintain a copy of the schema expected within the
>>>            software for internal
>>>            consistency.  The Ergatis component 'initdb' can be used
>>>            to create a blank
>>>            Chado instance and load all expected ontologies at once.
>>>             That database
>>>            created can then be the target of bsml2chado runs.
>>>
>>>            Joshua
>>>
>>>
>>>
>>>            On Mon, Jun 14, 2010 at 7:48 AM, Mariette
>>>            <[hidden email]
>>>            <mailto:[hidden email]>> wrote:
>>>
>>>
>>>                Hi everyone,
>>>                I'm trying to make an ergatis annotation pipline
>>>                linked to gbrowse.
>>>                To do so I'm using the chado-prism with the bsml2chado
>>>                componant.
>>>                Everything works fine but the querie looks wrong. I'm
>>>                guessing I'm
>>>                not using the correct chado version. I use the one
>>>                from gmod1.0. Is
>>>                it the correct version to use with ergatis ? I can't
>>>                figure out which
>>>                one is required !
>>>
>>>                thanks for your help
>>>                Jeroem
>>>
>>>
>>>
>>>  
>>> ------------------------------------------------------------------------------
>>>                ThinkGeek and WIRED's GeekDad team up for the Ultimate
>>>                GeekDad Father's Day Giveaway. ONE MASSIVE PRIZE to the
>>>                lucky parental unit.  See the prize list and enter to win:
>>>                http://p.sf.net/sfu/thinkgeek-promo
>>>                _______________________________________________
>>>                Ergatis-users mailing list
>>>                [hidden email]
>>>                <mailto:[hidden email]>
>>>
>>>                https://lists.sourceforge.net/lists/listinfo/ergatis-users
>>>
>>>
>>>
>>>
>>>
>>>  
>>> ------------------------------------------------------------------------------
>>>        ThinkGeek and WIRED's GeekDad team up for the Ultimate GeekDad
>>>        Father's Day Giveaway. ONE MASSIVE PRIZE to the lucky parental
>>>        unit.  See the prize list and enter to win:
>>>        http://p.sf.net/sfu/thinkgeek-promo
>>>        _______________________________________________
>>>        Ergatis-users mailing list
>>>        [hidden email]
>>>        <mailto:[hidden email]>
>>>
>>>        https://lists.sourceforge.net/lists/listinfo/ergatis-users
>>>
>>>
>>>
>>>
>>
>


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chado-prism

Joshua Orvis




Jerome -

I'm not sure exactly what BSML you're attempting to load, but it should have a reference to the sequence within it.  If the loader sees that sequence ID already in the database it will just attach your new data to it.  If it's a new sequence it will be loaded automatically.

Joshua



On Wed, Jun 16, 2010 at 11:55 AM, jmariett <[hidden email]> wrote:

Ok I'm gonna try this,
Just so you know, I was gessing the probleme could come from the fact
we haven't load anythink so far in the chado database. When I installed
gbrowse in an order database, I remember that I had to add a reference
sequence. So far I hadn't done this step ... could that be the probleme ?






Joshua Orvis <[hidden email]> a écrit :


Jerome -

I'm not sure where this is going wrong, but unfortunately we might need to
add some debugging steps in the code to try to track it down. Here is the
process I can see:

In lib/perl5/Prism/ChadoPrismDB.pm there is a subroutine called
"get_cvterm_id_by_class_lookup" that creates a lookup of all the terms in
the database that are part of either the SO or ARD ontologies.  The error
you are getting is from within the "master_feature_id_lookup" subroutine in
/lib/perl5/Prism.pm that is trying to look up the ID for the term
'chromosome'.  Your query from the database directly shows that the terms
are present in your database.

We need to see now why that lookup is failing.  Can you use the interface to
find the exact command line string of the step that is failing and then,
reading the perldoc on the script if necessary, run it again with logging
enabled and set at a high level?  We can try using the logs to see where
this went wrong.

Alternatively, if you're feeling adventurous, you could start inserting
debug steps on your own in the code but the logs may be an easier first
step, depending on your comfort with Perl.

Joshua



On Wed, Jun 16, 2010 at 9:31 AM, Mariette <[hidden email]> wrote:


the querie gave me :


cvterm_id       cv_id   name
9739

10
      chromosome
34229

13
      chromosome


thx for your help,
Jerome




Joshua Orvis a écrit :

It looks like your database is missing the ontology term for 'chromosome'.
 Can you log in to the chado database you created and issue this query?

SELECT cvterm_id, cv_id, name FROM cvterm WHERE name = 'chromosome';

You should get at least one row.

Joshua


On Wed, Jun 16, 2010 at 3:22 AM, Mariette <[hidden email]<mailto:
[hidden email]>> wrote:


  Joshua,

  We are pretty new in chado but we're gessing that
  we're facing this error because we haven't load our
  seq ref yet, would that make sense ?

  If yes there is an ergatis componant to do so ? I take
  a look at all components available but can't find any.

  thanks for your help,
  Jerome






  jmariett a écrit :

      Thanks for that,
      so I run the componant which worked just fine and filled
      the database.
      Now when I use the bsml2chado I'm getting the following errors :
      at step
       failed  Cache primary keys
      Died with 'cvterm_id was not defined for class 'chromosome''
      at  /usr/local/bioinfo/src/ergatis//lib/perl5/Prism.pm line 909

      there is some other cvterm to add to chado before to use it ?
      It sounds to me like ok when I run the initDB component.

      thanks for your answer,
      Jerome



      Joshua Orvis <[hidden email] <mailto:[hidden email]>> a

      écrit :


          Jerome -

          We maintain a copy of the schema expected within the
          software for internal
          consistency.  The Ergatis component 'initdb' can be used
          to create a blank
          Chado instance and load all expected ontologies at once.
           That database
          created can then be the target of bsml2chado runs.

          Joshua



          On Mon, Jun 14, 2010 at 7:48 AM, Mariette
          <[hidden email]
          <mailto:[hidden email]>> wrote:


              Hi everyone,
              I'm trying to make an ergatis annotation pipline
              linked to gbrowse.
              To do so I'm using the chado-prism with the bsml2chado
              componant.
              Everything works fine but the querie looks wrong. I'm
              guessing I'm
              not using the correct chado version. I use the one
              from gmod1.0. Is
              it the correct version to use with ergatis ? I can't
              figure out which
              one is required !

              thanks for your help
              Jeroem



 ------------------------------------------------------------------------------
              ThinkGeek and WIRED's GeekDad team up for the Ultimate
              GeekDad Father's Day Giveaway. ONE MASSIVE PRIZE to the
              lucky parental unit.  See the prize list and enter to win:
              http://p.sf.net/sfu/thinkgeek-promo
              _______________________________________________
              Ergatis-users mailing list
              [hidden email]
              <mailto:[hidden email]>

              https://lists.sourceforge.net/lists/listinfo/ergatis-users





 ------------------------------------------------------------------------------
      ThinkGeek and WIRED's GeekDad team up for the Ultimate GeekDad
      Father's Day Giveaway. ONE MASSIVE PRIZE to the lucky parental
      unit.  See the prize list and enter to win:
      http://p.sf.net/sfu/thinkgeek-promo
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      [hidden email]
      <mailto:[hidden email]>

      https://lists.sourceforge.net/lists/listinfo/ergatis-users










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Re: chado-prism

Mariette

Well what I did is basicly a fasta2bsml, then
I try to load it into chado ... I might haven't
understand how to use ergatis with galaxy ?

Jerome





Joshua Orvis <[hidden email]> a écrit :

> Jerome -
>
> I'm not sure exactly what BSML you're attempting to load, but it should have
> a reference to the sequence within it.  If the loader sees that sequence ID
> already in the database it will just attach your new data to it.  If it's a
> new sequence it will be loaded automatically.
>
> Joshua
>
>
>
> On Wed, Jun 16, 2010 at 11:55 AM, jmariett <[hidden email]>wrote:
>
>>
>> Ok I'm gonna try this,
>> Just so you know, I was gessing the probleme could come from the fact
>> we haven't load anythink so far in the chado database. When I installed
>> gbrowse in an order database, I remember that I had to add a reference
>> sequence. So far I hadn't done this step ... could that be the probleme ?
>>
>>
>>
>>
>>
>>
>> Joshua Orvis <[hidden email]> a écrit :
>>
>>
>>  Jerome -
>>>
>>> I'm not sure where this is going wrong, but unfortunately we might need to
>>> add some debugging steps in the code to try to track it down. Here is the
>>> process I can see:
>>>
>>> In lib/perl5/Prism/ChadoPrismDB.pm there is a subroutine called
>>> "get_cvterm_id_by_class_lookup" that creates a lookup of all the terms in
>>> the database that are part of either the SO or ARD ontologies.  The error
>>> you are getting is from within the "master_feature_id_lookup" subroutine
>>> in
>>> /lib/perl5/Prism.pm that is trying to look up the ID for the term
>>> 'chromosome'.  Your query from the database directly shows that the terms
>>> are present in your database.
>>>
>>> We need to see now why that lookup is failing.  Can you use the interface
>>> to
>>> find the exact command line string of the step that is failing and then,
>>> reading the perldoc on the script if necessary, run it again with logging
>>> enabled and set at a high level?  We can try using the logs to see where
>>> this went wrong.
>>>
>>> Alternatively, if you're feeling adventurous, you could start inserting
>>> debug steps on your own in the code but the logs may be an easier first
>>> step, depending on your comfort with Perl.
>>>
>>> Joshua
>>>
>>>
>>>
>>> On Wed, Jun 16, 2010 at 9:31 AM, Mariette <[hidden email]>
>>> wrote:
>>>
>>>
>>>> the querie gave me :
>>>>
>>>>
>>>> cvterm_id       cv_id   name
>>>> 9739
>>>>
>>>> 10
>>>>       chromosome
>>>> 34229
>>>>
>>>> 13
>>>>       chromosome
>>>>
>>>>
>>>> thx for your help,
>>>> Jerome
>>>>
>>>>
>>>>
>>>>
>>>> Joshua Orvis a écrit :
>>>>
>>>>  It looks like your database is missing the ontology term for
>>>>> 'chromosome'.
>>>>>  Can you log in to the chado database you created and issue this query?
>>>>>
>>>>> SELECT cvterm_id, cv_id, name FROM cvterm WHERE name = 'chromosome';
>>>>>
>>>>> You should get at least one row.
>>>>>
>>>>> Joshua
>>>>>
>>>>>
>>>>> On Wed, Jun 16, 2010 at 3:22 AM, Mariette <[hidden email]
>>>>> <mailto:
>>>>> [hidden email]>> wrote:
>>>>>
>>>>>
>>>>>   Joshua,
>>>>>
>>>>>   We are pretty new in chado but we're gessing that
>>>>>   we're facing this error because we haven't load our
>>>>>   seq ref yet, would that make sense ?
>>>>>
>>>>>   If yes there is an ergatis componant to do so ? I take
>>>>>   a look at all components available but can't find any.
>>>>>
>>>>>   thanks for your help,
>>>>>   Jerome
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>   jmariett a écrit :
>>>>>
>>>>>       Thanks for that,
>>>>>       so I run the componant which worked just fine and filled
>>>>>       the database.
>>>>>       Now when I use the bsml2chado I'm getting the following errors :
>>>>>       at step
>>>>>        failed  Cache primary keys
>>>>>       Died with 'cvterm_id was not defined for class 'chromosome''
>>>>>       at  /usr/local/bioinfo/src/ergatis//lib/perl5/Prism.pm line 909
>>>>>
>>>>>       there is some other cvterm to add to chado before to use it ?
>>>>>       It sounds to me like ok when I run the initDB component.
>>>>>
>>>>>       thanks for your answer,
>>>>>       Jerome
>>>>>
>>>>>
>>>>>
>>>>>       Joshua Orvis <[hidden email] <mailto:[hidden email]>> a
>>>>>
>>>>>       écrit :
>>>>>
>>>>>
>>>>>           Jerome -
>>>>>
>>>>>           We maintain a copy of the schema expected within the
>>>>>           software for internal
>>>>>           consistency.  The Ergatis component 'initdb' can be used
>>>>>           to create a blank
>>>>>           Chado instance and load all expected ontologies at once.
>>>>>            That database
>>>>>           created can then be the target of bsml2chado runs.
>>>>>
>>>>>           Joshua
>>>>>
>>>>>
>>>>>
>>>>>           On Mon, Jun 14, 2010 at 7:48 AM, Mariette
>>>>>           <[hidden email]
>>>>>           <mailto:[hidden email]>> wrote:
>>>>>
>>>>>
>>>>>               Hi everyone,
>>>>>               I'm trying to make an ergatis annotation pipline
>>>>>               linked to gbrowse.
>>>>>               To do so I'm using the chado-prism with the bsml2chado
>>>>>               componant.
>>>>>               Everything works fine but the querie looks wrong. I'm
>>>>>               guessing I'm
>>>>>               not using the correct chado version. I use the one
>>>>>               from gmod1.0. Is
>>>>>               it the correct version to use with ergatis ? I can't
>>>>>               figure out which
>>>>>               one is required !
>>>>>
>>>>>               thanks for your help
>>>>>               Jeroem
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>  
>>>>> ------------------------------------------------------------------------------
>>>>>               ThinkGeek and WIRED's GeekDad team up for the Ultimate
>>>>>               GeekDad Father's Day Giveaway. ONE MASSIVE PRIZE to the
>>>>>               lucky parental unit.  See the prize list and enter to win:
>>>>>               http://p.sf.net/sfu/thinkgeek-promo
>>>>>               _______________________________________________
>>>>>               Ergatis-users mailing list
>>>>>               [hidden email]
>>>>>               <mailto:[hidden email]>
>>>>>
>>>>>
>>>>> https://lists.sourceforge.net/lists/listinfo/ergatis-users
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>  
>>>>> ------------------------------------------------------------------------------
>>>>>       ThinkGeek and WIRED's GeekDad team up for the Ultimate GeekDad
>>>>>       Father's Day Giveaway. ONE MASSIVE PRIZE to the lucky parental
>>>>>       unit.  See the prize list and enter to win:
>>>>>       http://p.sf.net/sfu/thinkgeek-promo
>>>>>       _______________________________________________
>>>>>       Ergatis-users mailing list
>>>>>       [hidden email]
>>>>>       <mailto:[hidden email]>
>>>>>
>>>>>       https://lists.sourceforge.net/lists/listinfo/ergatis-users
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>
>>>
>>
>


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Re: chado-prism

Joshua Orvis
Jerome -

That should be pretty straight forward, so trying the debugging step I mentioned might be useful.  I'm not sure what your last sentence about Galaxy meant.  They're separate tools.

JO

On Wed, Jun 16, 2010 at 12:02 PM, jmariett <[hidden email]> wrote:

Well what I did is basicly a fasta2bsml, then
I try to load it into chado ... I might haven't
understand how to use ergatis with galaxy ?

Jerome





Joshua Orvis <[hidden email]> a écrit :

> Jerome -
>
> I'm not sure exactly what BSML you're attempting to load, but it should have
> a reference to the sequence within it.  If the loader sees that sequence ID
> already in the database it will just attach your new data to it.  If it's a
> new sequence it will be loaded automatically.
>
> Joshua
>
>
>
> On Wed, Jun 16, 2010 at 11:55 AM, jmariett <[hidden email]>wrote:
>
>>
>> Ok I'm gonna try this,
>> Just so you know, I was gessing the probleme could come from the fact
>> we haven't load anythink so far in the chado database. When I installed
>> gbrowse in an order database, I remember that I had to add a reference
>> sequence. So far I hadn't done this step ... could that be the probleme ?
>>
>>
>>
>>
>>
>>
>> Joshua Orvis <[hidden email]> a écrit :
>>
>>
>>  Jerome -
>>>
>>> I'm not sure where this is going wrong, but unfortunately we might need to
>>> add some debugging steps in the code to try to track it down. Here is the
>>> process I can see:
>>>
>>> In lib/perl5/Prism/ChadoPrismDB.pm there is a subroutine called
>>> "get_cvterm_id_by_class_lookup" that creates a lookup of all the terms in
>>> the database that are part of either the SO or ARD ontologies.  The error
>>> you are getting is from within the "master_feature_id_lookup" subroutine
>>> in
>>> /lib/perl5/Prism.pm that is trying to look up the ID for the term
>>> 'chromosome'.  Your query from the database directly shows that the terms
>>> are present in your database.
>>>
>>> We need to see now why that lookup is failing.  Can you use the interface
>>> to
>>> find the exact command line string of the step that is failing and then,
>>> reading the perldoc on the script if necessary, run it again with logging
>>> enabled and set at a high level?  We can try using the logs to see where
>>> this went wrong.
>>>
>>> Alternatively, if you're feeling adventurous, you could start inserting
>>> debug steps on your own in the code but the logs may be an easier first
>>> step, depending on your comfort with Perl.
>>>
>>> Joshua
>>>
>>>
>>>
>>> On Wed, Jun 16, 2010 at 9:31 AM, Mariette <[hidden email]>
>>> wrote:
>>>
>>>
>>>> the querie gave me :
>>>>
>>>>
>>>> cvterm_id       cv_id   name
>>>> 9739
>>>>
>>>> 10
>>>>       chromosome
>>>> 34229
>>>>
>>>> 13
>>>>       chromosome
>>>>
>>>>
>>>> thx for your help,
>>>> Jerome
>>>>
>>>>
>>>>
>>>>
>>>> Joshua Orvis a écrit :
>>>>
>>>>  It looks like your database is missing the ontology term for
>>>>> 'chromosome'.
>>>>>  Can you log in to the chado database you created and issue this query?
>>>>>
>>>>> SELECT cvterm_id, cv_id, name FROM cvterm WHERE name = 'chromosome';
>>>>>
>>>>> You should get at least one row.
>>>>>
>>>>> Joshua
>>>>>
>>>>>
>>>>> On Wed, Jun 16, 2010 at 3:22 AM, Mariette <[hidden email]
>>>>> <mailto:
>>>>> [hidden email]>> wrote:
>>>>>
>>>>>
>>>>>   Joshua,
>>>>>
>>>>>   We are pretty new in chado but we're gessing that
>>>>>   we're facing this error because we haven't load our
>>>>>   seq ref yet, would that make sense ?
>>>>>
>>>>>   If yes there is an ergatis componant to do so ? I take
>>>>>   a look at all components available but can't find any.
>>>>>
>>>>>   thanks for your help,
>>>>>   Jerome
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>   jmariett a écrit :
>>>>>
>>>>>       Thanks for that,
>>>>>       so I run the componant which worked just fine and filled
>>>>>       the database.
>>>>>       Now when I use the bsml2chado I'm getting the following errors :
>>>>>       at step
>>>>>        failed  Cache primary keys
>>>>>       Died with 'cvterm_id was not defined for class 'chromosome''
>>>>>       at  /usr/local/bioinfo/src/ergatis//lib/perl5/Prism.pm line 909
>>>>>
>>>>>       there is some other cvterm to add to chado before to use it ?
>>>>>       It sounds to me like ok when I run the initDB component.
>>>>>
>>>>>       thanks for your answer,
>>>>>       Jerome
>>>>>
>>>>>
>>>>>
>>>>>       Joshua Orvis <[hidden email] <mailto:[hidden email]>> a
>>>>>
>>>>>       écrit :
>>>>>
>>>>>
>>>>>           Jerome -
>>>>>
>>>>>           We maintain a copy of the schema expected within the
>>>>>           software for internal
>>>>>           consistency.  The Ergatis component 'initdb' can be used
>>>>>           to create a blank
>>>>>           Chado instance and load all expected ontologies at once.
>>>>>            That database
>>>>>           created can then be the target of bsml2chado runs.
>>>>>
>>>>>           Joshua
>>>>>
>>>>>
>>>>>
>>>>>           On Mon, Jun 14, 2010 at 7:48 AM, Mariette
>>>>>           <[hidden email]
>>>>>           <mailto:[hidden email]>> wrote:
>>>>>
>>>>>
>>>>>               Hi everyone,
>>>>>               I'm trying to make an ergatis annotation pipline
>>>>>               linked to gbrowse.
>>>>>               To do so I'm using the chado-prism with the bsml2chado
>>>>>               componant.
>>>>>               Everything works fine but the querie looks wrong. I'm
>>>>>               guessing I'm
>>>>>               not using the correct chado version. I use the one
>>>>>               from gmod1.0. Is
>>>>>               it the correct version to use with ergatis ? I can't
>>>>>               figure out which
>>>>>               one is required !
>>>>>
>>>>>               thanks for your help
>>>>>               Jeroem
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>> ------------------------------------------------------------------------------
>>>>>               ThinkGeek and WIRED's GeekDad team up for the Ultimate
>>>>>               GeekDad Father's Day Giveaway. ONE MASSIVE PRIZE to the
>>>>>               lucky parental unit.  See the prize list and enter to win:
>>>>>               http://p.sf.net/sfu/thinkgeek-promo
>>>>>               _______________________________________________
>>>>>               Ergatis-users mailing list
>>>>>               [hidden email]
>>>>>               <mailto:[hidden email]>
>>>>>
>>>>>
>>>>> https://lists.sourceforge.net/lists/listinfo/ergatis-users
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>> ------------------------------------------------------------------------------
>>>>>       ThinkGeek and WIRED's GeekDad team up for the Ultimate GeekDad
>>>>>       Father's Day Giveaway. ONE MASSIVE PRIZE to the lucky parental
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>>>>>       <mailto:[hidden email]>
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>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>
>>>
>>
>


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Re: chado-prism

Mariette

Hi,
I made a mistake, I wanted to say chado instead of galaxy. Sorry for
the missunderstanding.

Here are the last line of the highest debug level :

....
Logger::PrismAPI DEBUG Thu Jun 17 09:57:34 2010 vm-bioinfo:28607
/usr/local/bioinfo/src/ergatis//lib/perl5/Prism.pm:Prism:Log::Cabin::Foundation::debug:9881
|| Args:
Logger::Coati::Coati::CoatiDB DEBUG Thu Jun 17 09:57:34 2010
vm-bioinfo:28607
/usr/local/bioinfo/src/ergatis//lib/perl5/Coati/Coati/CoatiDB.pm:Coati::Coati::CoatiDB:Log::Cabin::Foundation::debug:138
|| Args:
Logger::Coati::Coati::CoatiDB DEBUG Thu Jun 17 09:57:34 2010
vm-bioinfo:28607
/usr/local/bioinfo/src/ergatis//lib/perl5/Coati/Coati/CoatiDB.pm:Coati::Coati::CoatiDB:Log::Cabin::Foundation::debug:184
|| Opened lookup in read-write mode fo
r SELECT  lower(synonym), cvterm_id FROM cvtermsynonym  gntl_chado,

Logger::PrismAPI DEBUG Thu Jun 17 09:57:34 2010 vm-bioinfo:28607
/usr/local/bioinfo/src/ergatis//lib/perl5/Prism.pm:Prism:Log::Cabin::Foundation::debug:10353
|| Args:
Logger::Coati::Coati::CoatiDB DEBUG Thu Jun 17 09:57:34 2010
vm-bioinfo:28607
/usr/local/bioinfo/src/ergatis//lib/perl5/Coati/Coati/CoatiDB.pm:Coati::Coati::CoatiDB:Log::Cabin::Foundation::debug:138
|| Args:
Logger::Coati::Coati::CoatiDB DEBUG Thu Jun 17 09:57:34 2010
vm-bioinfo:28607
/usr/local/bioinfo/src/ergatis//lib/perl5/Coati/Coati/CoatiDB.pm:Coati::Coati::CoatiDB:Log::Cabin::Foundation::debug:184
|| Opened lookup in read-write mode fo
r SELECT lower(c.name), c.cvterm_id FROM cvterm c, cv WHERE cv.name =
'evidence_code' AND cv.cv_id = c.cv_id  gntl_chado,

Logger::PrismAPI DEBUG Thu Jun 17 09:57:34 2010 vm-bioinfo:28607
/usr/local/bioinfo/src/ergatis//lib/perl5/Prism.pm:Prism:Log::Cabin::Foundation::debug:904
|| Args:
Logger::PrismAPI FATAL Thu Jun 17 09:57:34 2010 vm-bioinfo:28607
/usr/local/bioinfo/src/ergatis//lib/perl5/Prism.pm:Prism:Log::Cabin::Foundation::logdie:909
|| cvterm_id was not defined for class 'chromosome'


thanks,
Jerome







Joshua Orvis a écrit :

> Jerome -
>
> That should be pretty straight forward, so trying the debugging step I
> mentioned might be useful.  I'm not sure what your last sentence about
> Galaxy meant.  They're separate tools.
>
> JO
>
> On Wed, Jun 16, 2010 at 12:02 PM, jmariett <[hidden email]
> <mailto:[hidden email]>> wrote:
>
>
>     Well what I did is basicly a fasta2bsml, then
>     I try to load it into chado ... I might haven't
>     understand how to use ergatis with galaxy ?
>
>     Jerome
>
>
>
>
>
>     Joshua Orvis <[hidden email] <mailto:[hidden email]>> a écrit :
>
>     > Jerome -
>     >
>     > I'm not sure exactly what BSML you're attempting to load, but it
>     should have
>     > a reference to the sequence within it.  If the loader sees that
>     sequence ID
>     > already in the database it will just attach your new data to it.
>      If it's a
>     > new sequence it will be loaded automatically.
>     >
>     > Joshua
>     >
>     >
>     >
>     > On Wed, Jun 16, 2010 at 11:55 AM, jmariett
>     <[hidden email] <mailto:[hidden email]>>wrote:
>     >
>     >>
>     >> Ok I'm gonna try this,
>     >> Just so you know, I was gessing the probleme could come from
>     the fact
>     >> we haven't load anythink so far in the chado database. When I
>     installed
>     >> gbrowse in an order database, I remember that I had to add a
>     reference
>     >> sequence. So far I hadn't done this step ... could that be the
>     probleme ?
>     >>
>     >>
>     >>
>     >>
>     >>
>     >>
>     >> Joshua Orvis <[hidden email] <mailto:[hidden email]>> a écrit :
>     >>
>     >>
>     >>  Jerome -
>     >>>
>     >>> I'm not sure where this is going wrong, but unfortunately we
>     might need to
>     >>> add some debugging steps in the code to try to track it down.
>     Here is the
>     >>> process I can see:
>     >>>
>     >>> In lib/perl5/Prism/ChadoPrismDB.pm there is a subroutine called
>     >>> "get_cvterm_id_by_class_lookup" that creates a lookup of all
>     the terms in
>     >>> the database that are part of either the SO or ARD ontologies.
>      The error
>     >>> you are getting is from within the "master_feature_id_lookup"
>     subroutine
>     >>> in
>     >>> /lib/perl5/Prism.pm that is trying to look up the ID for the term
>     >>> 'chromosome'.  Your query from the database directly shows
>     that the terms
>     >>> are present in your database.
>     >>>
>     >>> We need to see now why that lookup is failing.  Can you use
>     the interface
>     >>> to
>     >>> find the exact command line string of the step that is failing
>     and then,
>     >>> reading the perldoc on the script if necessary, run it again
>     with logging
>     >>> enabled and set at a high level?  We can try using the logs to
>     see where
>     >>> this went wrong.
>     >>>
>     >>> Alternatively, if you're feeling adventurous, you could start
>     inserting
>     >>> debug steps on your own in the code but the logs may be an
>     easier first
>     >>> step, depending on your comfort with Perl.
>     >>>
>     >>> Joshua
>     >>>
>     >>>
>     >>>
>     >>> On Wed, Jun 16, 2010 at 9:31 AM, Mariette
>     <[hidden email] <mailto:[hidden email]>>
>     >>> wrote:
>     >>>
>     >>>
>     >>>> the querie gave me :
>     >>>>
>     >>>>
>     >>>> cvterm_id       cv_id   name
>     >>>> 9739
>     >>>>
>     >>>> 10
>     >>>>       chromosome
>     >>>> 34229
>     >>>>
>     >>>> 13
>     >>>>       chromosome
>     >>>>
>     >>>>
>     >>>> thx for your help,
>     >>>> Jerome
>     >>>>
>     >>>>
>     >>>>
>     >>>>
>     >>>> Joshua Orvis a écrit :
>     >>>>
>     >>>>  It looks like your database is missing the ontology term for
>     >>>>> 'chromosome'.
>     >>>>>  Can you log in to the chado database you created and issue
>     this query?
>     >>>>>
>     >>>>> SELECT cvterm_id, cv_id, name FROM cvterm WHERE name =
>     'chromosome';
>     >>>>>
>     >>>>> You should get at least one row.
>     >>>>>
>     >>>>> Joshua
>     >>>>>
>     >>>>>
>     >>>>> On Wed, Jun 16, 2010 at 3:22 AM, Mariette
>     <[hidden email] <mailto:[hidden email]>
>     >>>>> <mailto:
>     >>>>> [hidden email]
>     <mailto:[hidden email]>>> wrote:
>     >>>>>
>     >>>>>
>     >>>>>   Joshua,
>     >>>>>
>     >>>>>   We are pretty new in chado but we're gessing that
>     >>>>>   we're facing this error because we haven't load our
>     >>>>>   seq ref yet, would that make sense ?
>     >>>>>
>     >>>>>   If yes there is an ergatis componant to do so ? I take
>     >>>>>   a look at all components available but can't find any.
>     >>>>>
>     >>>>>   thanks for your help,
>     >>>>>   Jerome
>     >>>>>
>     >>>>>
>     >>>>>
>     >>>>>
>     >>>>>
>     >>>>>
>     >>>>>   jmariett a écrit :
>     >>>>>
>     >>>>>       Thanks for that,
>     >>>>>       so I run the componant which worked just fine and filled
>     >>>>>       the database.
>     >>>>>       Now when I use the bsml2chado I'm getting the
>     following errors :
>     >>>>>       at step
>     >>>>>        failed  Cache primary keys
>     >>>>>       Died with 'cvterm_id was not defined for class
>     'chromosome''
>     >>>>>       at  /usr/local/bioinfo/src/ergatis//lib/perl5/Prism.pm
>     line 909
>     >>>>>
>     >>>>>       there is some other cvterm to add to chado before to
>     use it ?
>     >>>>>       It sounds to me like ok when I run the initDB component.
>     >>>>>
>     >>>>>       thanks for your answer,
>     >>>>>       Jerome
>     >>>>>
>     >>>>>
>     >>>>>
>     >>>>>       Joshua Orvis <[hidden email]
>     <mailto:[hidden email]> <mailto:[hidden email]
>     <mailto:[hidden email]>>> a
>     >>>>>
>     >>>>>       écrit :
>     >>>>>
>     >>>>>
>     >>>>>           Jerome -
>     >>>>>
>     >>>>>           We maintain a copy of the schema expected within the
>     >>>>>           software for internal
>     >>>>>           consistency.  The Ergatis component 'initdb' can
>     be used
>     >>>>>           to create a blank
>     >>>>>           Chado instance and load all expected ontologies at
>     once.
>     >>>>>            That database
>     >>>>>           created can then be the target of bsml2chado runs.
>     >>>>>
>     >>>>>           Joshua
>     >>>>>
>     >>>>>
>     >>>>>
>     >>>>>           On Mon, Jun 14, 2010 at 7:48 AM, Mariette
>     >>>>>           <[hidden email]
>     <mailto:[hidden email]>
>     >>>>>           <mailto:[hidden email]
>     <mailto:[hidden email]>>> wrote:
>     >>>>>
>     >>>>>
>     >>>>>               Hi everyone,
>     >>>>>               I'm trying to make an ergatis annotation pipline
>     >>>>>               linked to gbrowse.
>     >>>>>               To do so I'm using the chado-prism with the
>     bsml2chado
>     >>>>>               componant.
>     >>>>>               Everything works fine but the querie looks
>     wrong. I'm
>     >>>>>               guessing I'm
>     >>>>>               not using the correct chado version. I use the one
>     >>>>>               from gmod1.0. Is
>     >>>>>               it the correct version to use with ergatis ? I
>     can't
>     >>>>>               figure out which
>     >>>>>               one is required !
>     >>>>>
>     >>>>>               thanks for your help
>     >>>>>               Jeroem
>     >>>>>
>     >>>>>
>     >>>>>
>     >>>>>
>     >>>>>
>     >>>>>
>     ------------------------------------------------------------------------------
>     >>>>>               ThinkGeek and WIRED's GeekDad team up for the
>     Ultimate
>     >>>>>               GeekDad Father's Day Giveaway. ONE MASSIVE
>     PRIZE to the
>     >>>>>               lucky parental unit.  See the prize list and
>     enter to win:
>     >>>>>               http://p.sf.net/sfu/thinkgeek-promo
>     >>>>>               _______________________________________________
>     >>>>>               Ergatis-users mailing list
>     >>>>>               [hidden email]
>     <mailto:[hidden email]>
>     >>>>>               <mailto:[hidden email]
>     <mailto:[hidden email]>>
>     >>>>>
>     >>>>>
>     >>>>> https://lists.sourceforge.net/lists/listinfo/ergatis-users
>     >>>>>
>     >>>>>
>     >>>>>
>     >>>>>
>     >>>>>
>     >>>>>
>     >>>>>
>     >>>>>
>     ------------------------------------------------------------------------------
>     >>>>>       ThinkGeek and WIRED's GeekDad team up for the Ultimate
>     GeekDad
>     >>>>>       Father's Day Giveaway. ONE MASSIVE PRIZE to the lucky
>     parental
>     >>>>>       unit.  See the prize list and enter to win:
>     >>>>>       http://p.sf.net/sfu/thinkgeek-promo
>     >>>>>       _______________________________________________
>     >>>>>       Ergatis-users mailing list
>     >>>>>       [hidden email]
>     <mailto:[hidden email]>
>     >>>>>       <mailto:[hidden email]
>     <mailto:[hidden email]>>
>     >>>>>
>     >>>>>       https://lists.sourceforge.net/lists/listinfo/ergatis-users
>     >>>>>
>     >>>>>
>     >>>>>
>     >>>>>
>     >>>>>
>     >>>>
>     >>>
>     >>
>     >
>
>
>     ------------------------------------------------------------------------------
>     ThinkGeek and WIRED's GeekDad team up for the Ultimate
>     GeekDad Father's Day Giveaway. ONE MASSIVE PRIZE to the
>     lucky parental unit.  See the prize list and enter to win:
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>     _______________________________________________
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>     [hidden email]
>     <mailto:[hidden email]>
>     https://lists.sourceforge.net/lists/listinfo/ergatis-users
>
>
> ------------------------------------------------------------------------
>
> ------------------------------------------------------------------------------
> ThinkGeek and WIRED's GeekDad team up for the Ultimate
> GeekDad Father's Day Giveaway. ONE MASSIVE PRIZE to the
> lucky parental unit.  See the prize list and enter to win:
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>
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>  


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Re: chado-prism

Mariette

Hi again ...

So I tryed not to use ergatis to upload my first data set.
I added an organism directly in the database :

INSERT INTO organism (abbreviation, genus, species, common_name) VALUES
('P.basidiomycetes', 'Pycnoporus','basidiomycetes','pycnoporus');

Then I converted my multifasta file in a gff3 format using the gmod
converter.
Finaly I used the bulk_loader and got the same error but with some more log:

[root@genome-browser gmod-1.0]# gmod_bulk_load_gff3.pl --gfffile=out.gff
--organism=pycnoporus
DBD::Pg::st execute failed: ERROR:  relation "feature_feature_id_seq"
does not exist at /usr/lib/perl5/site_perl/5.8.8/Bio/GMOD/DB/Adapter.pm
line 1280.
DBD::Pg::st fetchrow_array failed: no statement executing at
/usr/lib/perl5/site_perl/5.8.8/Bio/GMOD/DB/Adapter.pm line 1281.
DBD::Pg::st execute failed: ERROR:  current transaction is aborted,
commands ignored until end of transaction block at
/usr/lib/perl5/site_perl/5.8.8/Bio/GMOD/DB/Adapter.pm line 1280.
DBD::Pg::st fetchrow_array failed: no statement executing at
/usr/lib/perl5/site_perl/5.8.8/Bio/GMOD/DB/Adapter.pm line 1281.
DBD::Pg::st execute failed: ERROR:  current transaction is aborted,
commands ignored until end of transaction block at
/usr/lib/perl5/site_perl/5.8.8/Bio/GMOD/DB/Adapter.pm line 1280.
DBD::Pg::st fetchrow_array failed: no statement executing at
/usr/lib/perl5/site_perl/5.8.8/Bio/GMOD/DB/Adapter.pm line 1281.
DBD::Pg::st execute failed: ERROR:  current transaction is aborted,
commands ignored until end of transaction block at
/usr/lib/perl5/site_perl/5.8.8/Bio/GMOD/DB/Adapter.pm line 1280.
DBD::Pg::st fetchrow_array failed: no statement executing at
/usr/lib/perl5/site_perl/5.8.8/Bio/GMOD/DB/Adapter.pm line 1281.
DBD::Pg::st execute failed: ERROR:  current transaction is aborted,
commands ignored until end of transaction block at
/usr/lib/perl5/site_perl/5.8.8/Bio/GMOD/DB/Adapter.pm line 1280.
DBD::Pg::st fetchrow_array failed: no statement executing at
/usr/lib/perl5/site_perl/5.8.8/Bio/GMOD/DB/Adapter.pm line 1281.
DBD::Pg::st execute failed: ERROR:  current transaction is aborted,
commands ignored until end of transaction block at
/usr/lib/perl5/site_perl/5.8.8/Bio/GMOD/DB/Adapter.pm line 1280.
DBD::Pg::st fetchrow_array failed: no statement executing at
/usr/lib/perl5/site_perl/5.8.8/Bio/GMOD/DB/Adapter.pm line 1281.
DBD::Pg::st execute failed: ERROR:  current transaction is aborted,
commands ignored until end of transaction block at
/usr/lib/perl5/site_perl/5.8.8/Bio/GMOD/DB/Adapter.pm line 1280.
DBD::Pg::st fetchrow_array failed: no statement executing at
/usr/lib/perl5/site_perl/5.8.8/Bio/GMOD/DB/Adapter.pm line 1281.
DBD::Pg::st execute failed: ERROR:  current transaction is aborted,
commands ignored until end of transaction block at
/usr/lib/perl5/site_perl/5.8.8/Bio/GMOD/DB/Adapter.pm line 1280.
DBD::Pg::st fetchrow_array failed: no statement executing at
/usr/lib/perl5/site_perl/5.8.8/Bio/GMOD/DB/Adapter.pm line 1281.
DBD::Pg::st execute failed: ERROR:  current transaction is aborted,
commands ignored until end of transaction block at
/usr/lib/perl5/site_perl/5.8.8/Bio/GMOD/DB/Adapter.pm line 1280.
DBD::Pg::st fetchrow_array failed: no statement executing at
/usr/lib/perl5/site_perl/5.8.8/Bio/GMOD/DB/Adapter.pm line 1281.
DBD::Pg::st execute failed: ERROR:  current transaction is aborted,
commands ignored until end of transaction block at
/usr/lib/perl5/site_perl/5.8.8/Bio/GMOD/DB/Adapter.pm line 1280.
DBD::Pg::st fetchrow_array failed: no statement executing at
/usr/lib/perl5/site_perl/5.8.8/Bio/GMOD/DB/Adapter.pm line 1281.
DBD::Pg::st execute failed: ERROR:  current transaction is aborted,
commands ignored until end of transaction block at
/usr/lib/perl5/site_perl/5.8.8/Bio/GMOD/DB/Adapter.pm line 1280.
DBD::Pg::st fetchrow_array failed: no statement executing at
/usr/lib/perl5/site_perl/5.8.8/Bio/GMOD/DB/Adapter.pm line 1281.
DBD::Pg::st execute failed: ERROR:  current transaction is aborted,
commands ignored until end of transaction block at
/usr/lib/perl5/site_perl/5.8.8/Bio/GMOD/DB/Adapter.pm line 1280.
DBD::Pg::st fetchrow_array failed: no statement executing at
/usr/lib/perl5/site_perl/5.8.8/Bio/GMOD/DB/Adapter.pm line 1281.
DBD::Pg::st execute failed: ERROR:  current transaction is aborted,
commands ignored until end of transaction block at
/usr/lib/perl5/site_perl/5.8.8/Bio/GMOD/DB/Adapter.pm line 1280.
DBD::Pg::st fetchrow_array failed: no statement executing at
/usr/lib/perl5/site_perl/5.8.8/Bio/GMOD/DB/Adapter.pm line 1281.
DBD::Pg::st execute failed: ERROR:  current transaction is aborted,
commands ignored until end of transaction block at
/usr/lib/perl5/site_perl/5.8.8/Bio/GMOD/DB/Adapter.pm line 1280.
DBD::Pg::st fetchrow_array failed: no statement executing at
/usr/lib/perl5/site_perl/5.8.8/Bio/GMOD/DB/Adapter.pm line 1281.
DBD::Pg::st execute failed: ERROR:  current transaction is aborted,
commands ignored until end of transaction block at
/usr/lib/perl5/site_perl/5.8.8/Bio/GMOD/DB/Adapter.pm line 1280.
DBD::Pg::st fetchrow_array failed: no statement executing at
/usr/lib/perl5/site_perl/5.8.8/Bio/GMOD/DB/Adapter.pm line 1281.
DBD::Pg::st execute failed: ERROR:  current transaction is aborted,
commands ignored until end of transaction block at
/usr/lib/perl5/site_perl/5.8.8/Bio/GMOD/DB/Adapter.pm line 1159.
DBD::Pg::st fetchrow_array failed: no statement executing at
/usr/lib/perl5/site_perl/5.8.8/Bio/GMOD/DB/Adapter.pm line 1161.
(Re)creating the uniquename cache in the database...
Creating table...
DBD::Pg::db do failed: ERROR:  current transaction is aborted, commands
ignored until end of transaction block at
/usr/lib/perl5/site_perl/5.8.8/Bio/GMOD/DB/Adapter.pm line 1168.
Populating table...
DBD::Pg::db do failed: ERROR:  current transaction is aborted, commands
ignored until end of transaction block at
/usr/lib/perl5/site_perl/5.8.8/Bio/GMOD/DB/Adapter.pm line 1171.
Creating indexes...DBD::Pg::db do failed: ERROR:  current transaction is
aborted, commands ignored until end of transaction block at
/usr/lib/perl5/site_perl/5.8.8/Bio/GMOD/DB/Adapter.pm line 1174.
DBD::Pg::db do failed: ERROR:  current transaction is aborted, commands
ignored until end of transaction block at
/usr/lib/perl5/site_perl/5.8.8/Bio/GMOD/DB/Adapter.pm line 1175.
DBD::Pg::db do failed: ERROR:  current transaction is aborted, commands
ignored until end of transaction block at
/usr/lib/perl5/site_perl/5.8.8/Bio/GMOD/DB/Adapter.pm line 1176.
Done.
Preparing data for inserting into the gntl_chado database
(This may take a while ...)

------------- EXCEPTION: Bio::Root::Exception -------------
*MSG: no cvterm for chromosome*
STACK: Error::throw
STACK: Bio::Root::Root::throw
/usr/lib/perl5/site_perl/5.8.8/Bio/Root/Root.pm:368
STACK: Bio::GMOD::DB::Adapter::get_type
/usr/lib/perl5/site_perl/5.8.8/Bio/GMOD/DB/Adapter.pm:4050
STACK: /usr/bin/gmod_bulk_load_gff3.pl:755
-----------------------------------------------------------
Issuing rollback() due to DESTROY without explicit disconnect() of
DBD::Pg::db handle dbname=gntl_chado;port=5432;host=147.99.108.44.


I tryed to rerun the initdb component, which worked fine again ... but I'm
still getting this error !

thanks,
Jerome





Mariette a écrit :

> Hi,
> I made a mistake, I wanted to say chado instead of galaxy. Sorry for
> the missunderstanding.
>
> Here are the last line of the highest debug level :
>
> ....
> Logger::PrismAPI DEBUG Thu Jun 17 09:57:34 2010 vm-bioinfo:28607
> /usr/local/bioinfo/src/ergatis//lib/perl5/Prism.pm:Prism:Log::Cabin::Foundation::debug:9881
> || Args:
> Logger::Coati::Coati::CoatiDB DEBUG Thu Jun 17 09:57:34 2010
> vm-bioinfo:28607
> /usr/local/bioinfo/src/ergatis//lib/perl5/Coati/Coati/CoatiDB.pm:Coati::Coati::CoatiDB:Log::Cabin::Foundation::debug:138
> || Args:
> Logger::Coati::Coati::CoatiDB DEBUG Thu Jun 17 09:57:34 2010
> vm-bioinfo:28607
> /usr/local/bioinfo/src/ergatis//lib/perl5/Coati/Coati/CoatiDB.pm:Coati::Coati::CoatiDB:Log::Cabin::Foundation::debug:184
> || Opened lookup in read-write mode fo
> r SELECT  lower(synonym), cvterm_id FROM cvtermsynonym  gntl_chado,
>
> Logger::PrismAPI DEBUG Thu Jun 17 09:57:34 2010 vm-bioinfo:28607
> /usr/local/bioinfo/src/ergatis//lib/perl5/Prism.pm:Prism:Log::Cabin::Foundation::debug:10353
> || Args:
> Logger::Coati::Coati::CoatiDB DEBUG Thu Jun 17 09:57:34 2010
> vm-bioinfo:28607
> /usr/local/bioinfo/src/ergatis//lib/perl5/Coati/Coati/CoatiDB.pm:Coati::Coati::CoatiDB:Log::Cabin::Foundation::debug:138
> || Args:
> Logger::Coati::Coati::CoatiDB DEBUG Thu Jun 17 09:57:34 2010
> vm-bioinfo:28607
> /usr/local/bioinfo/src/ergatis//lib/perl5/Coati/Coati/CoatiDB.pm:Coati::Coati::CoatiDB:Log::Cabin::Foundation::debug:184
> || Opened lookup in read-write mode fo
> r SELECT lower(c.name), c.cvterm_id FROM cvterm c, cv WHERE cv.name =
> 'evidence_code' AND cv.cv_id = c.cv_id  gntl_chado,
>
> Logger::PrismAPI DEBUG Thu Jun 17 09:57:34 2010 vm-bioinfo:28607
> /usr/local/bioinfo/src/ergatis//lib/perl5/Prism.pm:Prism:Log::Cabin::Foundation::debug:904
> || Args:
> Logger::PrismAPI FATAL Thu Jun 17 09:57:34 2010 vm-bioinfo:28607
> /usr/local/bioinfo/src/ergatis//lib/perl5/Prism.pm:Prism:Log::Cabin::Foundation::logdie:909
> || cvterm_id was not defined for class 'chromosome'
>
>
> thanks,
> Jerome
>
>
>
>
>
>
>
> Joshua Orvis a écrit :
>  
>> Jerome -
>>
>> That should be pretty straight forward, so trying the debugging step I
>> mentioned might be useful.  I'm not sure what your last sentence about
>> Galaxy meant.  They're separate tools.
>>
>> JO
>>
>> On Wed, Jun 16, 2010 at 12:02 PM, jmariett <[hidden email]
>> <mailto:[hidden email]>> wrote:
>>
>>
>>     Well what I did is basicly a fasta2bsml, then
>>     I try to load it into chado ... I might haven't
>>     understand how to use ergatis with galaxy ?
>>
>>     Jerome
>>
>>
>>
>>
>>
>>     Joshua Orvis <[hidden email] <mailto:[hidden email]>> a écrit :
>>
>>     > Jerome -
>>     >
>>     > I'm not sure exactly what BSML you're attempting to load, but it
>>     should have
>>     > a reference to the sequence within it.  If the loader sees that
>>     sequence ID
>>     > already in the database it will just attach your new data to it.
>>      If it's a
>>     > new sequence it will be loaded automatically.
>>     >
>>     > Joshua
>>     >
>>     >
>>     >
>>     > On Wed, Jun 16, 2010 at 11:55 AM, jmariett
>>     <[hidden email] <mailto:[hidden email]>>wrote:
>>     >
>>     >>
>>     >> Ok I'm gonna try this,
>>     >> Just so you know, I was gessing the probleme could come from
>>     the fact
>>     >> we haven't load anythink so far in the chado database. When I
>>     installed
>>     >> gbrowse in an order database, I remember that I had to add a
>>     reference
>>     >> sequence. So far I hadn't done this step ... could that be the
>>     probleme ?
>>     >>
>>     >>
>>     >>
>>     >>
>>     >>
>>     >>
>>     >> Joshua Orvis <[hidden email] <mailto:[hidden email]>> a écrit :
>>     >>
>>     >>
>>     >>  Jerome -
>>     >>>
>>     >>> I'm not sure where this is going wrong, but unfortunately we
>>     might need to
>>     >>> add some debugging steps in the code to try to track it down.
>>     Here is the
>>     >>> process I can see:
>>     >>>
>>     >>> In lib/perl5/Prism/ChadoPrismDB.pm there is a subroutine called
>>     >>> "get_cvterm_id_by_class_lookup" that creates a lookup of all
>>     the terms in
>>     >>> the database that are part of either the SO or ARD ontologies.
>>      The error
>>     >>> you are getting is from within the "master_feature_id_lookup"
>>     subroutine
>>     >>> in
>>     >>> /lib/perl5/Prism.pm that is trying to look up the ID for the term
>>     >>> 'chromosome'.  Your query from the database directly shows
>>     that the terms
>>     >>> are present in your database.
>>     >>>
>>     >>> We need to see now why that lookup is failing.  Can you use
>>     the interface
>>     >>> to
>>     >>> find the exact command line string of the step that is failing
>>     and then,
>>     >>> reading the perldoc on the script if necessary, run it again
>>     with logging
>>     >>> enabled and set at a high level?  We can try using the logs to
>>     see where
>>     >>> this went wrong.
>>     >>>
>>     >>> Alternatively, if you're feeling adventurous, you could start
>>     inserting
>>     >>> debug steps on your own in the code but the logs may be an
>>     easier first
>>     >>> step, depending on your comfort with Perl.
>>     >>>
>>     >>> Joshua
>>     >>>
>>     >>>
>>     >>>
>>     >>> On Wed, Jun 16, 2010 at 9:31 AM, Mariette
>>     <[hidden email] <mailto:[hidden email]>>
>>     >>> wrote:
>>     >>>
>>     >>>
>>     >>>> the querie gave me :
>>     >>>>
>>     >>>>
>>     >>>> cvterm_id       cv_id   name
>>     >>>> 9739
>>     >>>>
>>     >>>> 10
>>     >>>>       chromosome
>>     >>>> 34229
>>     >>>>
>>     >>>> 13
>>     >>>>       chromosome
>>     >>>>
>>     >>>>
>>     >>>> thx for your help,
>>     >>>> Jerome
>>     >>>>
>>     >>>>
>>     >>>>
>>     >>>>
>>     >>>> Joshua Orvis a écrit :
>>     >>>>
>>     >>>>  It looks like your database is missing the ontology term for
>>     >>>>> 'chromosome'.
>>     >>>>>  Can you log in to the chado database you created and issue
>>     this query?
>>     >>>>>
>>     >>>>> SELECT cvterm_id, cv_id, name FROM cvterm WHERE name =
>>     'chromosome';
>>     >>>>>
>>     >>>>> You should get at least one row.
>>     >>>>>
>>     >>>>> Joshua
>>     >>>>>
>>     >>>>>
>>     >>>>> On Wed, Jun 16, 2010 at 3:22 AM, Mariette
>>     <[hidden email] <mailto:[hidden email]>
>>     >>>>> <mailto:
>>     >>>>> [hidden email]
>>     <mailto:[hidden email]>>> wrote:
>>     >>>>>
>>     >>>>>
>>     >>>>>   Joshua,
>>     >>>>>
>>     >>>>>   We are pretty new in chado but we're gessing that
>>     >>>>>   we're facing this error because we haven't load our
>>     >>>>>   seq ref yet, would that make sense ?
>>     >>>>>
>>     >>>>>   If yes there is an ergatis componant to do so ? I take
>>     >>>>>   a look at all components available but can't find any.
>>     >>>>>
>>     >>>>>   thanks for your help,
>>     >>>>>   Jerome
>>     >>>>>
>>     >>>>>
>>     >>>>>
>>     >>>>>
>>     >>>>>
>>     >>>>>
>>     >>>>>   jmariett a écrit :
>>     >>>>>
>>     >>>>>       Thanks for that,
>>     >>>>>       so I run the componant which worked just fine and filled
>>     >>>>>       the database.
>>     >>>>>       Now when I use the bsml2chado I'm getting the
>>     following errors :
>>     >>>>>       at step
>>     >>>>>        failed  Cache primary keys
>>     >>>>>       Died with 'cvterm_id was not defined for class
>>     'chromosome''
>>     >>>>>       at  /usr/local/bioinfo/src/ergatis//lib/perl5/Prism.pm
>>     line 909
>>     >>>>>
>>     >>>>>       there is some other cvterm to add to chado before to
>>     use it ?
>>     >>>>>       It sounds to me like ok when I run the initDB component.
>>     >>>>>
>>     >>>>>       thanks for your answer,
>>     >>>>>       Jerome
>>     >>>>>
>>     >>>>>
>>     >>>>>
>>     >>>>>       Joshua Orvis <[hidden email]
>>     <mailto:[hidden email]> <mailto:[hidden email]
>>     <mailto:[hidden email]>>> a
>>     >>>>>
>>     >>>>>       écrit :
>>     >>>>>
>>     >>>>>
>>     >>>>>           Jerome -
>>     >>>>>
>>     >>>>>           We maintain a copy of the schema expected within the
>>     >>>>>           software for internal
>>     >>>>>           consistency.  The Ergatis component 'initdb' can
>>     be used
>>     >>>>>           to create a blank
>>     >>>>>           Chado instance and load all expected ontologies at
>>     once.
>>     >>>>>            That database
>>     >>>>>           created can then be the target of bsml2chado runs.
>>     >>>>>
>>     >>>>>           Joshua
>>     >>>>>
>>     >>>>>
>>     >>>>>
>>     >>>>>           On Mon, Jun 14, 2010 at 7:48 AM, Mariette
>>     >>>>>           <[hidden email]
>>     <mailto:[hidden email]>
>>     >>>>>           <mailto:[hidden email]
>>     <mailto:[hidden email]>>> wrote:
>>     >>>>>
>>     >>>>>
>>     >>>>>               Hi everyone,
>>     >>>>>               I'm trying to make an ergatis annotation pipline
>>     >>>>>               linked to gbrowse.
>>     >>>>>               To do so I'm using the chado-prism with the
>>     bsml2chado
>>     >>>>>               componant.
>>     >>>>>               Everything works fine but the querie looks
>>     wrong. I'm
>>     >>>>>               guessing I'm
>>     >>>>>               not using the correct chado version. I use the one
>>     >>>>>               from gmod1.0. Is
>>     >>>>>               it the correct version to use with ergatis ? I
>>     can't
>>     >>>>>               figure out which
>>     >>>>>               one is required !
>>     >>>>>
>>     >>>>>               thanks for your help
>>     >>>>>               Jeroem
>>     >>>>>
>>     >>>>>
>>     >>>>>
>>     >>>>>
>>     >>>>>
>>     >>>>>
>>     ------------------------------------------------------------------------------
>>     >>>>>               ThinkGeek and WIRED's GeekDad team up for the
>>     Ultimate
>>     >>>>>               GeekDad Father's Day Giveaway. ONE MASSIVE
>>     PRIZE to the
>>     >>>>>               lucky parental unit.  See the prize list and
>>     enter to win:
>>     >>>>>               http://p.sf.net/sfu/thinkgeek-promo
>>     >>>>>               _______________________________________________
>>     >>>>>               Ergatis-users mailing list
>>     >>>>>               [hidden email]
>>     <mailto:[hidden email]>
>>     >>>>>               <mailto:[hidden email]
>>     <mailto:[hidden email]>>
>>     >>>>>
>>     >>>>>
>>     >>>>> https://lists.sourceforge.net/lists/listinfo/ergatis-users
>>     >>>>>
>>     >>>>>
>>     >>>>>
>>     >>>>>
>>     >>>>>
>>     >>>>>
>>     >>>>>
>>     >>>>>
>>     ------------------------------------------------------------------------------
>>     >>>>>       ThinkGeek and WIRED's GeekDad team up for the Ultimate
>>     GeekDad
>>     >>>>>       Father's Day Giveaway. ONE MASSIVE PRIZE to the lucky
>>     parental
>>     >>>>>       unit.  See the prize list and enter to win:
>>     >>>>>       http://p.sf.net/sfu/thinkgeek-promo
>>     >>>>>       _______________________________________________
>>     >>>>>       Ergatis-users mailing list
>>     >>>>>       [hidden email]
>>     <mailto:[hidden email]>
>>     >>>>>       <mailto:[hidden email]
>>     <mailto:[hidden email]>>
>>     >>>>>
>>     >>>>>       https://lists.sourceforge.net/lists/listinfo/ergatis-users
>>     >>>>>
>>     >>>>>
>>     >>>>>
>>     >>>>>
>>     >>>>>
>>     >>>>
>>     >>>
>>     >>
>>     >
>>
>>
>>     ------------------------------------------------------------------------------
>>     ThinkGeek and WIRED's GeekDad team up for the Ultimate
>>     GeekDad Father's Day Giveaway. ONE MASSIVE PRIZE to the
>>     lucky parental unit.  See the prize list and enter to win:
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>>     https://lists.sourceforge.net/lists/listinfo/ergatis-users
>>
>>
>> ------------------------------------------------------------------------
>>
>> ------------------------------------------------------------------------------
>> ThinkGeek and WIRED's GeekDad team up for the Ultimate
>> GeekDad Father's Day Giveaway. ONE MASSIVE PRIZE to the
>> lucky parental unit.  See the prize list and enter to win:
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>
>
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> GeekDad Father's Day Giveaway. ONE MASSIVE PRIZE to the
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Re: chado-prism

Joshua Orvis
Jerome -

This is a little hard to debug remotely.  It seems like you have the term in your database and the queries are correct.  I mentioned the "get_cvterm_id_by_class_lookup" subroutine that builds the ontology term lookup.  Have you tried using Data::Dumper or some other tool to inspect the lookup and see if the term for 'chromosome' is present?

Joshua

On Thu, Jun 17, 2010 at 5:02 AM, Mariette <[hidden email]> wrote:

Hi again ...

So I tryed not to use ergatis to upload my first data set.
I added an organism directly in the database :

INSERT INTO organism (abbreviation, genus, species, common_name) VALUES
('P.basidiomycetes', 'Pycnoporus','basidiomycetes','pycnoporus');

Then I converted my multifasta file in a gff3 format using the gmod
converter.
Finaly I used the bulk_loader and got the same error but with some more log:

[root@genome-browser gmod-1.0]# gmod_bulk_load_gff3.pl --gfffile=out.gff
--organism=pycnoporus
DBD::Pg::st execute failed: ERROR:  relation "feature_feature_id_seq"
does not exist at /usr/lib/perl5/site_perl/5.8.8/Bio/GMOD/DB/Adapter.pm
line 1280.
DBD::Pg::st fetchrow_array failed: no statement executing at
/usr/lib/perl5/site_perl/5.8.8/Bio/GMOD/DB/Adapter.pm line 1281.
DBD::Pg::st execute failed: ERROR:  current transaction is aborted,
commands ignored until end of transaction block at
/usr/lib/perl5/site_perl/5.8.8/Bio/GMOD/DB/Adapter.pm line 1280.
DBD::Pg::st fetchrow_array failed: no statement executing at
/usr/lib/perl5/site_perl/5.8.8/Bio/GMOD/DB/Adapter.pm line 1281.
DBD::Pg::st execute failed: ERROR:  current transaction is aborted,
commands ignored until end of transaction block at
/usr/lib/perl5/site_perl/5.8.8/Bio/GMOD/DB/Adapter.pm line 1280.
DBD::Pg::st fetchrow_array failed: no statement executing at
/usr/lib/perl5/site_perl/5.8.8/Bio/GMOD/DB/Adapter.pm line 1281.
DBD::Pg::st execute failed: ERROR:  current transaction is aborted,
commands ignored until end of transaction block at
/usr/lib/perl5/site_perl/5.8.8/Bio/GMOD/DB/Adapter.pm line 1280.
DBD::Pg::st fetchrow_array failed: no statement executing at
/usr/lib/perl5/site_perl/5.8.8/Bio/GMOD/DB/Adapter.pm line 1281.
DBD::Pg::st execute failed: ERROR:  current transaction is aborted,
commands ignored until end of transaction block at
/usr/lib/perl5/site_perl/5.8.8/Bio/GMOD/DB/Adapter.pm line 1280.
DBD::Pg::st fetchrow_array failed: no statement executing at
/usr/lib/perl5/site_perl/5.8.8/Bio/GMOD/DB/Adapter.pm line 1281.
DBD::Pg::st execute failed: ERROR:  current transaction is aborted,
commands ignored until end of transaction block at
/usr/lib/perl5/site_perl/5.8.8/Bio/GMOD/DB/Adapter.pm line 1280.
DBD::Pg::st fetchrow_array failed: no statement executing at
/usr/lib/perl5/site_perl/5.8.8/Bio/GMOD/DB/Adapter.pm line 1281.
DBD::Pg::st execute failed: ERROR:  current transaction is aborted,
commands ignored until end of transaction block at
/usr/lib/perl5/site_perl/5.8.8/Bio/GMOD/DB/Adapter.pm line 1280.
DBD::Pg::st fetchrow_array failed: no statement executing at
/usr/lib/perl5/site_perl/5.8.8/Bio/GMOD/DB/Adapter.pm line 1281.
DBD::Pg::st execute failed: ERROR:  current transaction is aborted,
commands ignored until end of transaction block at
/usr/lib/perl5/site_perl/5.8.8/Bio/GMOD/DB/Adapter.pm line 1280.
DBD::Pg::st fetchrow_array failed: no statement executing at
/usr/lib/perl5/site_perl/5.8.8/Bio/GMOD/DB/Adapter.pm line 1281.
DBD::Pg::st execute failed: ERROR:  current transaction is aborted,
commands ignored until end of transaction block at
/usr/lib/perl5/site_perl/5.8.8/Bio/GMOD/DB/Adapter.pm line 1280.
DBD::Pg::st fetchrow_array failed: no statement executing at
/usr/lib/perl5/site_perl/5.8.8/Bio/GMOD/DB/Adapter.pm line 1281.
DBD::Pg::st execute failed: ERROR:  current transaction is aborted,
commands ignored until end of transaction block at
/usr/lib/perl5/site_perl/5.8.8/Bio/GMOD/DB/Adapter.pm line 1280.
DBD::Pg::st fetchrow_array failed: no statement executing at
/usr/lib/perl5/site_perl/5.8.8/Bio/GMOD/DB/Adapter.pm line 1281.
DBD::Pg::st execute failed: ERROR:  current transaction is aborted,
commands ignored until end of transaction block at
/usr/lib/perl5/site_perl/5.8.8/Bio/GMOD/DB/Adapter.pm line 1280.
DBD::Pg::st fetchrow_array failed: no statement executing at
/usr/lib/perl5/site_perl/5.8.8/Bio/GMOD/DB/Adapter.pm line 1281.
DBD::Pg::st execute failed: ERROR:  current transaction is aborted,
commands ignored until end of transaction block at
/usr/lib/perl5/site_perl/5.8.8/Bio/GMOD/DB/Adapter.pm line 1280.
DBD::Pg::st fetchrow_array failed: no statement executing at
/usr/lib/perl5/site_perl/5.8.8/Bio/GMOD/DB/Adapter.pm line 1281.
DBD::Pg::st execute failed: ERROR:  current transaction is aborted,
commands ignored until end of transaction block at
/usr/lib/perl5/site_perl/5.8.8/Bio/GMOD/DB/Adapter.pm line 1280.
DBD::Pg::st fetchrow_array failed: no statement executing at
/usr/lib/perl5/site_perl/5.8.8/Bio/GMOD/DB/Adapter.pm line 1281.
DBD::Pg::st execute failed: ERROR:  current transaction is aborted,
commands ignored until end of transaction block at
/usr/lib/perl5/site_perl/5.8.8/Bio/GMOD/DB/Adapter.pm line 1280.
DBD::Pg::st fetchrow_array failed: no statement executing at
/usr/lib/perl5/site_perl/5.8.8/Bio/GMOD/DB/Adapter.pm line 1281.
DBD::Pg::st execute failed: ERROR:  current transaction is aborted,
commands ignored until end of transaction block at
/usr/lib/perl5/site_perl/5.8.8/Bio/GMOD/DB/Adapter.pm line 1280.
DBD::Pg::st fetchrow_array failed: no statement executing at
/usr/lib/perl5/site_perl/5.8.8/Bio/GMOD/DB/Adapter.pm line 1281.
DBD::Pg::st execute failed: ERROR:  current transaction is aborted,
commands ignored until end of transaction block at
/usr/lib/perl5/site_perl/5.8.8/Bio/GMOD/DB/Adapter.pm line 1159.
DBD::Pg::st fetchrow_array failed: no statement executing at
/usr/lib/perl5/site_perl/5.8.8/Bio/GMOD/DB/Adapter.pm line 1161.
(Re)creating the uniquename cache in the database...
Creating table...
DBD::Pg::db do failed: ERROR:  current transaction is aborted, commands
ignored until end of transaction block at
/usr/lib/perl5/site_perl/5.8.8/Bio/GMOD/DB/Adapter.pm line 1168.
Populating table...
DBD::Pg::db do failed: ERROR:  current transaction is aborted, commands
ignored until end of transaction block at
/usr/lib/perl5/site_perl/5.8.8/Bio/GMOD/DB/Adapter.pm line 1171.
Creating indexes...DBD::Pg::db do failed: ERROR:  current transaction is
aborted, commands ignored until end of transaction block at
/usr/lib/perl5/site_perl/5.8.8/Bio/GMOD/DB/Adapter.pm line 1174.
DBD::Pg::db do failed: ERROR:  current transaction is aborted, commands
ignored until end of transaction block at
/usr/lib/perl5/site_perl/5.8.8/Bio/GMOD/DB/Adapter.pm line 1175.
DBD::Pg::db do failed: ERROR:  current transaction is aborted, commands
ignored until end of transaction block at
/usr/lib/perl5/site_perl/5.8.8/Bio/GMOD/DB/Adapter.pm line 1176.
Done.
Preparing data for inserting into the gntl_chado database
(This may take a while ...)

------------- EXCEPTION: Bio::Root::Exception -------------
*MSG: no cvterm for chromosome*
STACK: Error::throw
STACK: Bio::Root::Root::throw
/usr/lib/perl5/site_perl/5.8.8/Bio/Root/Root.pm:368
STACK: Bio::GMOD::DB::Adapter::get_type
/usr/lib/perl5/site_perl/5.8.8/Bio/GMOD/DB/Adapter.pm:4050
STACK: /usr/bin/gmod_bulk_load_gff3.pl:755
-----------------------------------------------------------
Issuing rollback() due to DESTROY without explicit disconnect() of
DBD::Pg::db handle dbname=gntl_chado;port=5432;host=147.99.108.44.


I tryed to rerun the initdb component, which worked fine again ... but I'm
still getting this error !

thanks,
Jerome





Mariette a écrit :
> Hi,
> I made a mistake, I wanted to say chado instead of galaxy. Sorry for
> the missunderstanding.
>
> Here are the last line of the highest debug level :
>
> ....
> Logger::PrismAPI DEBUG Thu Jun 17 09:57:34 2010 vm-bioinfo:28607
> /usr/local/bioinfo/src/ergatis//lib/perl5/Prism.pm:Prism:Log::Cabin::Foundation::debug:9881
> || Args:
> Logger::Coati::Coati::CoatiDB DEBUG Thu Jun 17 09:57:34 2010
> vm-bioinfo:28607
> /usr/local/bioinfo/src/ergatis//lib/perl5/Coati/Coati/CoatiDB.pm:Coati::Coati::CoatiDB:Log::Cabin::Foundation::debug:138
> || Args:
> Logger::Coati::Coati::CoatiDB DEBUG Thu Jun 17 09:57:34 2010
> vm-bioinfo:28607
> /usr/local/bioinfo/src/ergatis//lib/perl5/Coati/Coati/CoatiDB.pm:Coati::Coati::CoatiDB:Log::Cabin::Foundation::debug:184
> || Opened lookup in read-write mode fo
> r SELECT  lower(synonym), cvterm_id FROM cvtermsynonym  gntl_chado,
>
> Logger::PrismAPI DEBUG Thu Jun 17 09:57:34 2010 vm-bioinfo:28607
> /usr/local/bioinfo/src/ergatis//lib/perl5/Prism.pm:Prism:Log::Cabin::Foundation::debug:10353
> || Args:
> Logger::Coati::Coati::CoatiDB DEBUG Thu Jun 17 09:57:34 2010
> vm-bioinfo:28607
> /usr/local/bioinfo/src/ergatis//lib/perl5/Coati/Coati/CoatiDB.pm:Coati::Coati::CoatiDB:Log::Cabin::Foundation::debug:138
> || Args:
> Logger::Coati::Coati::CoatiDB DEBUG Thu Jun 17 09:57:34 2010
> vm-bioinfo:28607
> /usr/local/bioinfo/src/ergatis//lib/perl5/Coati/Coati/CoatiDB.pm:Coati::Coati::CoatiDB:Log::Cabin::Foundation::debug:184
> || Opened lookup in read-write mode fo
> r SELECT lower(c.name), c.cvterm_id FROM cvterm c, cv WHERE cv.name =
> 'evidence_code' AND cv.cv_id = c.cv_id  gntl_chado,
>
> Logger::PrismAPI DEBUG Thu Jun 17 09:57:34 2010 vm-bioinfo:28607
> /usr/local/bioinfo/src/ergatis//lib/perl5/Prism.pm:Prism:Log::Cabin::Foundation::debug:904
> || Args:
> Logger::PrismAPI FATAL Thu Jun 17 09:57:34 2010 vm-bioinfo:28607
> /usr/local/bioinfo/src/ergatis//lib/perl5/Prism.pm:Prism:Log::Cabin::Foundation::logdie:909
> || cvterm_id was not defined for class 'chromosome'
>
>
> thanks,
> Jerome
>
>
>
>
>
>
>
> Joshua Orvis a écrit :
>
>> Jerome -
>>
>> That should be pretty straight forward, so trying the debugging step I
>> mentioned might be useful.  I'm not sure what your last sentence about
>> Galaxy meant.  They're separate tools.
>>
>> JO
>>
>> On Wed, Jun 16, 2010 at 12:02 PM, jmariett <[hidden email]
>> <mailto:[hidden email]>> wrote:
>>
>>
>>     Well what I did is basicly a fasta2bsml, then
>>     I try to load it into chado ... I might haven't
>>     understand how to use ergatis with galaxy ?
>>
>>     Jerome
>>
>>
>>
>>
>>
>>     Joshua Orvis <[hidden email] <mailto:[hidden email]>> a écrit :
>>
>>     > Jerome -
>>     >
>>     > I'm not sure exactly what BSML you're attempting to load, but it
>>     should have
>>     > a reference to the sequence within it.  If the loader sees that
>>     sequence ID
>>     > already in the database it will just attach your new data to it.
>>      If it's a
>>     > new sequence it will be loaded automatically.
>>     >
>>     > Joshua
>>     >
>>     >
>>     >
>>     > On Wed, Jun 16, 2010 at 11:55 AM, jmariett
>>     <[hidden email] <mailto:[hidden email]>>wrote:
>>     >
>>     >>
>>     >> Ok I'm gonna try this,
>>     >> Just so you know, I was gessing the probleme could come from
>>     the fact
>>     >> we haven't load anythink so far in the chado database. When I
>>     installed
>>     >> gbrowse in an order database, I remember that I had to add a
>>     reference
>>     >> sequence. So far I hadn't done this step ... could that be the
>>     probleme ?
>>     >>
>>     >>
>>     >>
>>     >>
>>     >>
>>     >>
>>     >> Joshua Orvis <[hidden email] <mailto:[hidden email]>> a écrit :
>>     >>
>>     >>
>>     >>  Jerome -
>>     >>>
>>     >>> I'm not sure where this is going wrong, but unfortunately we
>>     might need to
>>     >>> add some debugging steps in the code to try to track it down.
>>     Here is the
>>     >>> process I can see:
>>     >>>
>>     >>> In lib/perl5/Prism/ChadoPrismDB.pm there is a subroutine called
>>     >>> "get_cvterm_id_by_class_lookup" that creates a lookup of all
>>     the terms in
>>     >>> the database that are part of either the SO or ARD ontologies.
>>      The error
>>     >>> you are getting is from within the "master_feature_id_lookup"
>>     subroutine
>>     >>> in
>>     >>> /lib/perl5/Prism.pm that is trying to look up the ID for the term
>>     >>> 'chromosome'.  Your query from the database directly shows
>>     that the terms
>>     >>> are present in your database.
>>     >>>
>>     >>> We need to see now why that lookup is failing.  Can you use
>>     the interface
>>     >>> to
>>     >>> find the exact command line string of the step that is failing
>>     and then,
>>     >>> reading the perldoc on the script if necessary, run it again
>>     with logging
>>     >>> enabled and set at a high level?  We can try using the logs to
>>     see where
>>     >>> this went wrong.
>>     >>>
>>     >>> Alternatively, if you're feeling adventurous, you could start
>>     inserting
>>     >>> debug steps on your own in the code but the logs may be an
>>     easier first
>>     >>> step, depending on your comfort with Perl.
>>     >>>
>>     >>> Joshua
>>     >>>
>>     >>>
>>     >>>
>>     >>> On Wed, Jun 16, 2010 at 9:31 AM, Mariette
>>     <[hidden email] <mailto:[hidden email]>>
>>     >>> wrote:
>>     >>>
>>     >>>
>>     >>>> the querie gave me :
>>     >>>>
>>     >>>>
>>     >>>> cvterm_id       cv_id   name
>>     >>>> 9739
>>     >>>>
>>     >>>> 10
>>     >>>>       chromosome
>>     >>>> 34229
>>     >>>>
>>     >>>> 13
>>     >>>>       chromosome
>>     >>>>
>>     >>>>
>>     >>>> thx for your help,
>>     >>>> Jerome
>>     >>>>
>>     >>>>
>>     >>>>
>>     >>>>
>>     >>>> Joshua Orvis a écrit :
>>     >>>>
>>     >>>>  It looks like your database is missing the ontology term for
>>     >>>>> 'chromosome'.
>>     >>>>>  Can you log in to the chado database you created and issue
>>     this query?
>>     >>>>>
>>     >>>>> SELECT cvterm_id, cv_id, name FROM cvterm WHERE name =
>>     'chromosome';
>>     >>>>>
>>     >>>>> You should get at least one row.
>>     >>>>>
>>     >>>>> Joshua
>>     >>>>>
>>     >>>>>
>>     >>>>> On Wed, Jun 16, 2010 at 3:22 AM, Mariette
>>     <[hidden email] <mailto:[hidden email]>
>>     >>>>> <mailto:
>>     >>>>> [hidden email]
>>     <mailto:[hidden email]>>> wrote:
>>     >>>>>
>>     >>>>>
>>     >>>>>   Joshua,
>>     >>>>>
>>     >>>>>   We are pretty new in chado but we're gessing that
>>     >>>>>   we're facing this error because we haven't load our
>>     >>>>>   seq ref yet, would that make sense ?
>>     >>>>>
>>     >>>>>   If yes there is an ergatis componant to do so ? I take
>>     >>>>>   a look at all components available but can't find any.
>>     >>>>>
>>     >>>>>   thanks for your help,
>>     >>>>>   Jerome
>>     >>>>>
>>     >>>>>
>>     >>>>>
>>     >>>>>
>>     >>>>>
>>     >>>>>
>>     >>>>>   jmariett a écrit :
>>     >>>>>
>>     >>>>>       Thanks for that,
>>     >>>>>       so I run the componant which worked just fine and filled
>>     >>>>>       the database.
>>     >>>>>       Now when I use the bsml2chado I'm getting the
>>     following errors :
>>     >>>>>       at step
>>     >>>>>        failed  Cache primary keys
>>     >>>>>       Died with 'cvterm_id was not defined for class
>>     'chromosome''
>>     >>>>>       at  /usr/local/bioinfo/src/ergatis//lib/perl5/Prism.pm
>>     line 909
>>     >>>>>
>>     >>>>>       there is some other cvterm to add to chado before to
>>     use it ?
>>     >>>>>       It sounds to me like ok when I run the initDB component.
>>     >>>>>
>>     >>>>>       thanks for your answer,
>>     >>>>>       Jerome
>>     >>>>>
>>     >>>>>
>>     >>>>>
>>     >>>>>       Joshua Orvis <[hidden email]
>>     <mailto:[hidden email]> <mailto:[hidden email]
>>     <mailto:[hidden email]>>> a
>>     >>>>>
>>     >>>>>       écrit :
>>     >>>>>
>>     >>>>>
>>     >>>>>           Jerome -
>>     >>>>>
>>     >>>>>           We maintain a copy of the schema expected within the
>>     >>>>>           software for internal
>>     >>>>>           consistency.  The Ergatis component 'initdb' can
>>     be used
>>     >>>>>           to create a blank
>>     >>>>>           Chado instance and load all expected ontologies at
>>     once.
>>     >>>>>            That database
>>     >>>>>           created can then be the target of bsml2chado runs.
>>     >>>>>
>>     >>>>>           Joshua
>>     >>>>>
>>     >>>>>
>>     >>>>>
>>     >>>>>           On Mon, Jun 14, 2010 at 7:48 AM, Mariette
>>     >>>>>           <[hidden email]
>>     <mailto:[hidden email]>
>>     >>>>>           <mailto:[hidden email]
>>     <mailto:[hidden email]>>> wrote:
>>     >>>>>
>>     >>>>>
>>     >>>>>               Hi everyone,
>>     >>>>>               I'm trying to make an ergatis annotation pipline
>>     >>>>>               linked to gbrowse.
>>     >>>>>               To do so I'm using the chado-prism with the
>>     bsml2chado
>>     >>>>>               componant.
>>     >>>>>               Everything works fine but the querie looks
>>     wrong. I'm
>>     >>>>>               guessing I'm
>>     >>>>>               not using the correct chado version. I use the one
>>     >>>>>               from gmod1.0. Is
>>     >>>>>               it the correct version to use with ergatis ? I
>>     can't
>>     >>>>>               figure out which
>>     >>>>>               one is required !
>>     >>>>>
>>     >>>>>               thanks for your help
>>     >>>>>               Jeroem
>>     >>>>>
>>     >>>>>
>>     >>>>>
>>     >>>>>
>>     >>>>>
>>     >>>>>
>>     ------------------------------------------------------------------------------
>>     >>>>>               ThinkGeek and WIRED's GeekDad team up for the
>>     Ultimate
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>>     >>>>>               _______________________________________________
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>>     <mailto:[hidden email]>
>>     >>>>>               <mailto:[hidden email]
>>     <mailto:[hidden email]>>
>>     >>>>>
>>     >>>>>
>>     >>>>> https://lists.sourceforge.net/lists/listinfo/ergatis-users
>>     >>>>>
>>     >>>>>
>>     >>>>>
>>     >>>>>
>>     >>>>>
>>     >>>>>
>>     >>>>>
>>     >>>>>
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>>
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Re: chado-prism

Mariette

Joshua,

I found what was wrong, I was using a user able to create database but not
able to create language so the database was not properly loaded !! I should
have being warned by the tag ADMIN user of the initdb component.

So I reloaded my database and tryed tu upload some fastas using the
fata2bsml
and then the bsml2chado.

I'm getting a weird error at step :
error assign primary keys
/usr/local/bioinfo/src/ergatis/bin/assign_pks ...
Died with 'table was not defined' at
/usr/local/bioinfo/src/ergatis//lib/perl5/Prism/ChadoPrismDB.pm line 30

I figured out that the
--checksum_file=/work/tmp/ergatis/cbrowser/bsml2chado/5_default/checksums.out.sorted
was not correct !
more /work/tmp/ergatis/cbrowser/bsml2chado/5_default/checksums.out.sorted
hostname=n37.cluster
job_owner=contig
sge_id=575178
job_name=sort
queue=wflowq
000807e9b47a47f6e64d62d764831a87 0 featureprop 39630
000b3b621aafa22c3bef5bdba0d198bd 0 feature 13632863
....
fffb219e482eacdea90bad34d46fee8f 1 featureprop 122642
hostname=n24.cluster
job_owner=contig
sge_id=575649
job_name=sort
queue=wflowq

If I do the command line which generate this file, it looks to me like
ok ... those lines are not in !
Have you already faced this probleme ???

thanks,
Jerome











Joshua Orvis a écrit :

> Jerome -
>
> This is a little hard to debug remotely.  It seems like you have the
> term in your database and the queries are correct.  I mentioned the
> "get_cvterm_id_by_class_lookup" subroutine that builds the ontology
> term lookup.  Have you tried using Data::Dumper or some other tool to
> inspect the lookup and see if the term for 'chromosome' is present?
>
> Joshua
>
> On Thu, Jun 17, 2010 at 5:02 AM, Mariette <[hidden email]
> <mailto:[hidden email]>> wrote:
>
>
>     Hi again ...
>
>     So I tryed not to use ergatis to upload my first data set.
>     I added an organism directly in the database :
>
>     INSERT INTO organism (abbreviation, genus, species, common_name)
>     VALUES
>     ('P.basidiomycetes', 'Pycnoporus','basidiomycetes','pycnoporus');
>
>     Then I converted my multifasta file in a gff3 format using the gmod
>     converter.
>     Finaly I used the bulk_loader and got the same error but with some
>     more log:
>
>     [root@genome-browser gmod-1.0]# gmod_bulk_load_gff3.pl
>     <http://gmod_bulk_load_gff3.pl> --gfffile=out.gff
>     --organism=pycnoporus
>     DBD::Pg::st execute failed: ERROR:  relation "feature_feature_id_seq"
>     does not exist at
>     /usr/lib/perl5/site_perl/5.8.8/Bio/GMOD/DB/Adapter.pm
>     line 1280.
>     DBD::Pg::st fetchrow_array failed: no statement executing at
>     /usr/lib/perl5/site_perl/5.8.8/Bio/GMOD/DB/Adapter.pm line 1281.
>     DBD::Pg::st execute failed: ERROR:  current transaction is aborted,
>     commands ignored until end of transaction block at
>     /usr/lib/perl5/site_perl/5.8.8/Bio/GMOD/DB/Adapter.pm line 1280.
>     DBD::Pg::st fetchrow_array failed: no statement executing at
>     /usr/lib/perl5/site_perl/5.8.8/Bio/GMOD/DB/Adapter.pm line 1281.
>     DBD::Pg::st execute failed: ERROR:  current transaction is aborted,
>     commands ignored until end of transaction block at
>     /usr/lib/perl5/site_perl/5.8.8/Bio/GMOD/DB/Adapter.pm line 1280.
>     DBD::Pg::st fetchrow_array failed: no statement executing at
>     /usr/lib/perl5/site_perl/5.8.8/Bio/GMOD/DB/Adapter.pm line 1281.
>     DBD::Pg::st execute failed: ERROR:  current transaction is aborted,
>     commands ignored until end of transaction block at
>     /usr/lib/perl5/site_perl/5.8.8/Bio/GMOD/DB/Adapter.pm line 1280.
>     DBD::Pg::st fetchrow_array failed: no statement executing at
>     /usr/lib/perl5/site_perl/5.8.8/Bio/GMOD/DB/Adapter.pm line 1281.
>     DBD::Pg::st execute failed: ERROR:  current transaction is aborted,
>     commands ignored until end of transaction block at
>     /usr/lib/perl5/site_perl/5.8.8/Bio/GMOD/DB/Adapter.pm line 1280.
>     DBD::Pg::st fetchrow_array failed: no statement executing at
>     /usr/lib/perl5/site_perl/5.8.8/Bio/GMOD/DB/Adapter.pm line 1281.
>     DBD::Pg::st execute failed: ERROR:  current transaction is aborted,
>     commands ignored until end of transaction block at
>     /usr/lib/perl5/site_perl/5.8.8/Bio/GMOD/DB/Adapter.pm line 1280.
>     DBD::Pg::st fetchrow_array failed: no statement executing at
>     /usr/lib/perl5/site_perl/5.8.8/Bio/GMOD/DB/Adapter.pm line 1281.
>     DBD::Pg::st execute failed: ERROR:  current transaction is aborted,
>     commands ignored until end of transaction block at
>     /usr/lib/perl5/site_perl/5.8.8/Bio/GMOD/DB/Adapter.pm line 1280.
>     DBD::Pg::st fetchrow_array failed: no statement executing at
>     /usr/lib/perl5/site_perl/5.8.8/Bio/GMOD/DB/Adapter.pm line 1281.
>     DBD::Pg::st execute failed: ERROR:  current transaction is aborted,
>     commands ignored until end of transaction block at
>     /usr/lib/perl5/site_perl/5.8.8/Bio/GMOD/DB/Adapter.pm line 1280.
>     DBD::Pg::st fetchrow_array failed: no statement executing at
>     /usr/lib/perl5/site_perl/5.8.8/Bio/GMOD/DB/Adapter.pm line 1281.
>     DBD::Pg::st execute failed: ERROR:  current transaction is aborted,
>     commands ignored until end of transaction block at
>     /usr/lib/perl5/site_perl/5.8.8/Bio/GMOD/DB/Adapter.pm line 1280.
>     DBD::Pg::st fetchrow_array failed: no statement executing at
>     /usr/lib/perl5/site_perl/5.8.8/Bio/GMOD/DB/Adapter.pm line 1281.
>     DBD::Pg::st execute failed: ERROR:  current transaction is aborted,
>     commands ignored until end of transaction block at
>     /usr/lib/perl5/site_perl/5.8.8/Bio/GMOD/DB/Adapter.pm line 1280.
>     DBD::Pg::st fetchrow_array failed: no statement executing at
>     /usr/lib/perl5/site_perl/5.8.8/Bio/GMOD/DB/Adapter.pm line 1281.
>     DBD::Pg::st execute failed: ERROR:  current transaction is aborted,
>     commands ignored until end of transaction block at
>     /usr/lib/perl5/site_perl/5.8.8/Bio/GMOD/DB/Adapter.pm line 1280.
>     DBD::Pg::st fetchrow_array failed: no statement executing at
>     /usr/lib/perl5/site_perl/5.8.8/Bio/GMOD/DB/Adapter.pm line 1281.
>     DBD::Pg::st execute failed: ERROR:  current transaction is aborted,
>     commands ignored until end of transaction block at
>     /usr/lib/perl5/site_perl/5.8.8/Bio/GMOD/DB/Adapter.pm line 1280.
>     DBD::Pg::st fetchrow_array failed: no statement executing at
>     /usr/lib/perl5/site_perl/5.8.8/Bio/GMOD/DB/Adapter.pm line 1281.
>     DBD::Pg::st execute failed: ERROR:  current transaction is aborted,
>     commands ignored until end of transaction block at
>     /usr/lib/perl5/site_perl/5.8.8/Bio/GMOD/DB/Adapter.pm line 1280.
>     DBD::Pg::st fetchrow_array failed: no statement executing at
>     /usr/lib/perl5/site_perl/5.8.8/Bio/GMOD/DB/Adapter.pm line 1281.
>     DBD::Pg::st execute failed: ERROR:  current transaction is aborted,
>     commands ignored until end of transaction block at
>     /usr/lib/perl5/site_perl/5.8.8/Bio/GMOD/DB/Adapter.pm line 1280.
>     DBD::Pg::st fetchrow_array failed: no statement executing at
>     /usr/lib/perl5/site_perl/5.8.8/Bio/GMOD/DB/Adapter.pm line 1281.
>     DBD::Pg::st execute failed: ERROR:  current transaction is aborted,
>     commands ignored until end of transaction block at
>     /usr/lib/perl5/site_perl/5.8.8/Bio/GMOD/DB/Adapter.pm line 1280.
>     DBD::Pg::st fetchrow_array failed: no statement executing at
>     /usr/lib/perl5/site_perl/5.8.8/Bio/GMOD/DB/Adapter.pm line 1281.
>     DBD::Pg::st execute failed: ERROR:  current transaction is aborted,
>     commands ignored until end of transaction block at
>     /usr/lib/perl5/site_perl/5.8.8/Bio/GMOD/DB/Adapter.pm line 1159.
>     DBD::Pg::st fetchrow_array failed: no statement executing at
>     /usr/lib/perl5/site_perl/5.8.8/Bio/GMOD/DB/Adapter.pm line 1161.
>     (Re)creating the uniquename cache in the database...
>     Creating table...
>     DBD::Pg::db do failed: ERROR:  current transaction is aborted,
>     commands
>     ignored until end of transaction block at
>     /usr/lib/perl5/site_perl/5.8.8/Bio/GMOD/DB/Adapter.pm line 1168.
>     Populating table...
>     DBD::Pg::db do failed: ERROR:  current transaction is aborted,
>     commands
>     ignored until end of transaction block at
>     /usr/lib/perl5/site_perl/5.8.8/Bio/GMOD/DB/Adapter.pm line 1171.
>     Creating indexes...DBD::Pg::db do failed: ERROR:  current
>     transaction is
>     aborted, commands ignored until end of transaction block at
>     /usr/lib/perl5/site_perl/5.8.8/Bio/GMOD/DB/Adapter.pm line 1174.
>     DBD::Pg::db do failed: ERROR:  current transaction is aborted,
>     commands
>     ignored until end of transaction block at
>     /usr/lib/perl5/site_perl/5.8.8/Bio/GMOD/DB/Adapter.pm line 1175.
>     DBD::Pg::db do failed: ERROR:  current transaction is aborted,
>     commands
>     ignored until end of transaction block at
>     /usr/lib/perl5/site_perl/5.8.8/Bio/GMOD/DB/Adapter.pm line 1176.
>     Done.
>     Preparing data for inserting into the gntl_chado database
>     (This may take a while ...)
>
>     ------------- EXCEPTION: Bio::Root::Exception -------------
>     *MSG: no cvterm for chromosome*
>     STACK: Error::throw
>     STACK: Bio::Root::Root::throw
>     /usr/lib/perl5/site_perl/5.8.8/Bio/Root/Root.pm:368
>     STACK: Bio::GMOD::DB::Adapter::get_type
>     /usr/lib/perl5/site_perl/5.8.8/Bio/GMOD/DB/Adapter.pm:4050
>     STACK: /usr/bin/gmod_bulk_load_gff3.pl:755
>     <http://gmod_bulk_load_gff3.pl:755>
>     -----------------------------------------------------------
>     Issuing rollback() due to DESTROY without explicit disconnect() of
>     DBD::Pg::db handle dbname=gntl_chado;port=5432;host=147.99.108.44.
>
>
>     I tryed to rerun the initdb component, which worked fine again ...
>     but I'm
>     still getting this error !
>
>     thanks,
>     Jerome
>
>
>
>
>
>     Mariette a écrit :
>     > Hi,
>     > I made a mistake, I wanted to say chado instead of galaxy. Sorry for
>     > the missunderstanding.
>     >
>     > Here are the last line of the highest debug level :
>     >
>     > ....
>     > Logger::PrismAPI DEBUG Thu Jun 17 09:57:34 2010 vm-bioinfo:28607
>     >
>     /usr/local/bioinfo/src/ergatis//lib/perl5/Prism.pm:Prism:Log::Cabin::Foundation::debug:9881
>     > || Args:
>     > Logger::Coati::Coati::CoatiDB DEBUG Thu Jun 17 09:57:34 2010
>     > vm-bioinfo:28607
>     >
>     /usr/local/bioinfo/src/ergatis//lib/perl5/Coati/Coati/CoatiDB.pm:Coati::Coati::CoatiDB:Log::Cabin::Foundation::debug:138
>     > || Args:
>     > Logger::Coati::Coati::CoatiDB DEBUG Thu Jun 17 09:57:34 2010
>     > vm-bioinfo:28607
>     >
>     /usr/local/bioinfo/src/ergatis//lib/perl5/Coati/Coati/CoatiDB.pm:Coati::Coati::CoatiDB:Log::Cabin::Foundation::debug:184
>     > || Opened lookup in read-write mode fo
>     > r SELECT  lower(synonym), cvterm_id FROM cvtermsynonym  gntl_chado,
>     >
>     > Logger::PrismAPI DEBUG Thu Jun 17 09:57:34 2010 vm-bioinfo:28607
>     >
>     /usr/local/bioinfo/src/ergatis//lib/perl5/Prism.pm:Prism:Log::Cabin::Foundation::debug:10353
>     > || Args:
>     > Logger::Coati::Coati::CoatiDB DEBUG Thu Jun 17 09:57:34 2010
>     > vm-bioinfo:28607
>     >
>     /usr/local/bioinfo/src/ergatis//lib/perl5/Coati/Coati/CoatiDB.pm:Coati::Coati::CoatiDB:Log::Cabin::Foundation::debug:138
>     > || Args:
>     > Logger::Coati::Coati::CoatiDB DEBUG Thu Jun 17 09:57:34 2010
>     > vm-bioinfo:28607
>     >
>     /usr/local/bioinfo/src/ergatis//lib/perl5/Coati/Coati/CoatiDB.pm:Coati::Coati::CoatiDB:Log::Cabin::Foundation::debug:184
>     > || Opened lookup in read-write mode fo
>     > r SELECT lower(c.name <http://c.name>), c.cvterm_id FROM cvterm
>     c, cv WHERE cv.name <http://cv.name> =
>     > 'evidence_code' AND cv.cv_id = c.cv_id  gntl_chado,
>     >
>     > Logger::PrismAPI DEBUG Thu Jun 17 09:57:34 2010 vm-bioinfo:28607
>     >
>     /usr/local/bioinfo/src/ergatis//lib/perl5/Prism.pm:Prism:Log::Cabin::Foundation::debug:904
>     > || Args:
>     > Logger::PrismAPI FATAL Thu Jun 17 09:57:34 2010 vm-bioinfo:28607
>     >
>     /usr/local/bioinfo/src/ergatis//lib/perl5/Prism.pm:Prism:Log::Cabin::Foundation::logdie:909
>     > || cvterm_id was not defined for class 'chromosome'
>     >
>     >
>     > thanks,
>     > Jerome
>     >
>     >
>     >
>     >
>     >
>     >
>     >
>     > Joshua Orvis a écrit :
>     >
>     >> Jerome -
>     >>
>     >> That should be pretty straight forward, so trying the debugging
>     step I
>     >> mentioned might be useful.  I'm not sure what your last
>     sentence about
>     >> Galaxy meant.  They're separate tools.
>     >>
>     >> JO
>     >>
>     >> On Wed, Jun 16, 2010 at 12:02 PM, jmariett
>     <[hidden email] <mailto:[hidden email]>
>     >> <mailto:[hidden email]
>     <mailto:[hidden email]>>> wrote:
>     >>
>     >>
>     >>     Well what I did is basicly a fasta2bsml, then
>     >>     I try to load it into chado ... I might haven't
>     >>     understand how to use ergatis with galaxy ?
>     >>
>     >>     Jerome
>     >>
>     >>
>     >>
>     >>
>     >>
>     >>     Joshua Orvis <[hidden email] <mailto:[hidden email]>
>     <mailto:[hidden email] <mailto:[hidden email]>>> a écrit :
>     >>
>     >>     > Jerome -
>     >>     >
>     >>     > I'm not sure exactly what BSML you're attempting to load,
>     but it
>     >>     should have
>     >>     > a reference to the sequence within it.  If the loader
>     sees that
>     >>     sequence ID
>     >>     > already in the database it will just attach your new data
>     to it.
>     >>      If it's a
>     >>     > new sequence it will be loaded automatically.
>     >>     >
>     >>     > Joshua
>     >>     >
>     >>     >
>     >>     >
>     >>     > On Wed, Jun 16, 2010 at 11:55 AM, jmariett
>     >>     <[hidden email]
>     <mailto:[hidden email]>
>     <mailto:[hidden email]
>     <mailto:[hidden email]>>>wrote:
>     >>     >
>     >>     >>
>     >>     >> Ok I'm gonna try this,
>     >>     >> Just so you know, I was gessing the probleme could come from
>     >>     the fact
>     >>     >> we haven't load anythink so far in the chado database.
>     When I
>     >>     installed
>     >>     >> gbrowse in an order database, I remember that I had to add a
>     >>     reference
>     >>     >> sequence. So far I hadn't done this step ... could that
>     be the
>     >>     probleme ?
>     >>     >>
>     >>     >>
>     >>     >>
>     >>     >>
>     >>     >>
>     >>     >>
>     >>     >> Joshua Orvis <[hidden email] <mailto:[hidden email]>
>     <mailto:[hidden email] <mailto:[hidden email]>>> a écrit :
>     >>     >>
>     >>     >>
>     >>     >>  Jerome -
>     >>     >>>
>     >>     >>> I'm not sure where this is going wrong, but
>     unfortunately we
>     >>     might need to
>     >>     >>> add some debugging steps in the code to try to track it
>     down.
>     >>     Here is the
>     >>     >>> process I can see:
>     >>     >>>
>     >>     >>> In lib/perl5/Prism/ChadoPrismDB.pm there is a
>     subroutine called
>     >>     >>> "get_cvterm_id_by_class_lookup" that creates a lookup
>     of all
>     >>     the terms in
>     >>     >>> the database that are part of either the SO or ARD
>     ontologies.
>     >>      The error
>     >>     >>> you are getting is from within the
>     "master_feature_id_lookup"
>     >>     subroutine
>     >>     >>> in
>     >>     >>> /lib/perl5/Prism.pm that is trying to look up the ID
>     for the term
>     >>     >>> 'chromosome'.  Your query from the database directly shows
>     >>     that the terms
>     >>     >>> are present in your database.
>     >>     >>>
>     >>     >>> We need to see now why that lookup is failing.  Can you use
>     >>     the interface
>     >>     >>> to
>     >>     >>> find the exact command line string of the step that is
>     failing
>     >>     and then,
>     >>     >>> reading the perldoc on the script if necessary, run it
>     again
>     >>     with logging
>     >>     >>> enabled and set at a high level?  We can try using the
>     logs to
>     >>     see where
>     >>     >>> this went wrong.
>     >>     >>>
>     >>     >>> Alternatively, if you're feeling adventurous, you could
>     start
>     >>     inserting
>     >>     >>> debug steps on your own in the code but the logs may be an
>     >>     easier first
>     >>     >>> step, depending on your comfort with Perl.
>     >>     >>>
>     >>     >>> Joshua
>     >>     >>>
>     >>     >>>
>     >>     >>>
>     >>     >>> On Wed, Jun 16, 2010 at 9:31 AM, Mariette
>     >>     <[hidden email]
>     <mailto:[hidden email]>
>     <mailto:[hidden email] <mailto:[hidden email]>>>
>     >>     >>> wrote:
>     >>     >>>
>     >>     >>>
>     >>     >>>> the querie gave me :
>     >>     >>>>
>     >>     >>>>
>     >>     >>>> cvterm_id       cv_id   name
>     >>     >>>> 9739
>     >>     >>>>
>     >>     >>>> 10
>     >>     >>>>       chromosome
>     >>     >>>> 34229
>     >>     >>>>
>     >>     >>>> 13
>     >>     >>>>       chromosome
>     >>     >>>>
>     >>     >>>>
>     >>     >>>> thx for your help,
>     >>     >>>> Jerome
>     >>     >>>>
>     >>     >>>>
>     >>     >>>>
>     >>     >>>>
>     >>     >>>> Joshua Orvis a écrit :
>     >>     >>>>
>     >>     >>>>  It looks like your database is missing the ontology
>     term for
>     >>     >>>>> 'chromosome'.
>     >>     >>>>>  Can you log in to the chado database you created and
>     issue
>     >>     this query?
>     >>     >>>>>
>     >>     >>>>> SELECT cvterm_id, cv_id, name FROM cvterm WHERE name =
>     >>     'chromosome';
>     >>     >>>>>
>     >>     >>>>> You should get at least one row.
>     >>     >>>>>
>     >>     >>>>> Joshua
>     >>     >>>>>
>     >>     >>>>>
>     >>     >>>>> On Wed, Jun 16, 2010 at 3:22 AM, Mariette
>     >>     <[hidden email]
>     <mailto:[hidden email]>
>     <mailto:[hidden email] <mailto:[hidden email]>>
>     >>     >>>>> <mailto:
>     >>     >>>>> [hidden email]
>     <mailto:[hidden email]>
>     >>     <mailto:[hidden email]
>     <mailto:[hidden email]>>>> wrote:
>     >>     >>>>>
>     >>     >>>>>
>     >>     >>>>>   Joshua,
>     >>     >>>>>
>     >>     >>>>>   We are pretty new in chado but we're gessing that
>     >>     >>>>>   we're facing this error because we haven't load our
>     >>     >>>>>   seq ref yet, would that make sense ?
>     >>     >>>>>
>     >>     >>>>>   If yes there is an ergatis componant to do so ? I take
>     >>     >>>>>   a look at all components available but can't find any.
>     >>     >>>>>
>     >>     >>>>>   thanks for your help,
>     >>     >>>>>   Jerome
>     >>     >>>>>
>     >>     >>>>>
>     >>     >>>>>
>     >>     >>>>>
>     >>     >>>>>
>     >>     >>>>>
>     >>     >>>>>   jmariett a écrit :
>     >>     >>>>>
>     >>     >>>>>       Thanks for that,
>     >>     >>>>>       so I run the componant which worked just fine
>     and filled
>     >>     >>>>>       the database.
>     >>     >>>>>       Now when I use the bsml2chado I'm getting the
>     >>     following errors :
>     >>     >>>>>       at step
>     >>     >>>>>        failed  Cache primary keys
>     >>     >>>>>       Died with 'cvterm_id was not defined for class
>     >>     'chromosome''
>     >>     >>>>>       at
>      /usr/local/bioinfo/src/ergatis//lib/perl5/Prism.pm
>     >>     line 909
>     >>     >>>>>
>     >>     >>>>>       there is some other cvterm to add to chado
>     before to
>     >>     use it ?
>     >>     >>>>>       It sounds to me like ok when I run the initDB
>     component.
>     >>     >>>>>
>     >>     >>>>>       thanks for your answer,
>     >>     >>>>>       Jerome
>     >>     >>>>>
>     >>     >>>>>
>     >>     >>>>>
>     >>     >>>>>       Joshua Orvis <[hidden email]
>     <mailto:[hidden email]>
>     >>     <mailto:[hidden email] <mailto:[hidden email]>>
>     <mailto:[hidden email] <mailto:[hidden email]>
>     >>     <mailto:[hidden email] <mailto:[hidden email]>>>> a
>     >>     >>>>>
>     >>     >>>>>       écrit :
>     >>     >>>>>
>     >>     >>>>>
>     >>     >>>>>           Jerome -
>     >>     >>>>>
>     >>     >>>>>           We maintain a copy of the schema expected
>     within the
>     >>     >>>>>           software for internal
>     >>     >>>>>           consistency.  The Ergatis component
>     'initdb' can
>     >>     be used
>     >>     >>>>>           to create a blank
>     >>     >>>>>           Chado instance and load all expected
>     ontologies at
>     >>     once.
>     >>     >>>>>            That database
>     >>     >>>>>           created can then be the target of
>     bsml2chado runs.
>     >>     >>>>>
>     >>     >>>>>           Joshua
>     >>     >>>>>
>     >>     >>>>>
>     >>     >>>>>
>     >>     >>>>>           On Mon, Jun 14, 2010 at 7:48 AM, Mariette
>     >>     >>>>>           <[hidden email]
>     <mailto:[hidden email]>
>     >>     <mailto:[hidden email]
>     <mailto:[hidden email]>>
>     >>     >>>>>           <mailto:[hidden email]
>     <mailto:[hidden email]>
>     >>     <mailto:[hidden email]
>     <mailto:[hidden email]>>>> wrote:
>     >>     >>>>>
>     >>     >>>>>
>     >>     >>>>>               Hi everyone,
>     >>     >>>>>               I'm trying to make an ergatis
>     annotation pipline
>     >>     >>>>>               linked to gbrowse.
>     >>     >>>>>               To do so I'm using the chado-prism with the
>     >>     bsml2chado
>     >>     >>>>>               componant.
>     >>     >>>>>               Everything works fine but the querie looks
>     >>     wrong. I'm
>     >>     >>>>>               guessing I'm
>     >>     >>>>>               not using the correct chado version. I
>     use the one
>     >>     >>>>>               from gmod1.0. Is
>     >>     >>>>>               it the correct version to use with
>     ergatis ? I
>     >>     can't
>     >>     >>>>>               figure out which
>     >>     >>>>>               one is required !
>     >>     >>>>>
>     >>     >>>>>               thanks for your help
>     >>     >>>>>               Jeroem
>     >>     >>>>>
>     >>     >>>>>
>     >>     >>>>>
>     >>     >>>>>
>     >>     >>>>>
>     >>     >>>>>
>     >>    
>     ------------------------------------------------------------------------------
>     >>     >>>>>               ThinkGeek and WIRED's GeekDad team up
>     for the
>     >>     Ultimate
>     >>     >>>>>               GeekDad Father's Day Giveaway. ONE MASSIVE
>     >>     PRIZE to the
>     >>     >>>>>               lucky parental unit.  See the prize
>     list and
>     >>     enter to win:
>     >>     >>>>>               http://p.sf.net/sfu/thinkgeek-promo
>     >>     >>>>>              
>     _______________________________________________
>     >>     >>>>>               Ergatis-users mailing list
>     >>     >>>>>               [hidden email]
>     <mailto:[hidden email]>
>     >>     <mailto:[hidden email]
>     <mailto:[hidden email]>>
>     >>     >>>>>              
>     <mailto:[hidden email]
>     <mailto:[hidden email]>
>     >>     <mailto:[hidden email]
>     <mailto:[hidden email]>>>
>     >>     >>>>>
>     >>     >>>>>
>     >>     >>>>>
>     https://lists.sourceforge.net/lists/listinfo/ergatis-users
>     >>     >>>>>
>     >>     >>>>>
>     >>     >>>>>
>     >>     >>>>>
>     >>     >>>>>
>     >>     >>>>>
>     >>     >>>>>
>     >>     >>>>>
>     >>    
>     ------------------------------------------------------------------------------
>     >>     >>>>>       ThinkGeek and WIRED's GeekDad team up for the
>     Ultimate
>     >>     GeekDad
>     >>     >>>>>       Father's Day Giveaway. ONE MASSIVE PRIZE to the
>     lucky
>     >>     parental
>     >>     >>>>>       unit.  See the prize list and enter to win:
>     >>     >>>>>       http://p.sf.net/sfu/thinkgeek-promo
>     >>     >>>>>       _______________________________________________
>     >>     >>>>>       Ergatis-users mailing list
>     >>     >>>>>       [hidden email]
>     <mailto:[hidden email]>
>     >>     <mailto:[hidden email]
>     <mailto:[hidden email]>>
>     >>     >>>>>       <mailto:[hidden email]
>     <mailto:[hidden email]>
>     >>     <mailto:[hidden email]
>     <mailto:[hidden email]>>>
>     >>     >>>>>
>     >>     >>>>>      
>     https://lists.sourceforge.net/lists/listinfo/ergatis-users
>     >>     >>>>>
>     >>     >>>>>
>     >>     >>>>>
>     >>     >>>>>
>     >>     >>>>>
>     >>     >>>>
>     >>     >>>
>     >>     >>
>     >>     >
>     >>
>     >>
>     >>    
>     ------------------------------------------------------------------------------
>     >>     ThinkGeek and WIRED's GeekDad team up for the Ultimate
>     >>     GeekDad Father's Day Giveaway. ONE MASSIVE PRIZE to the
>     >>     lucky parental unit.  See the prize list and enter to win:
>     >>     http://p.sf.net/sfu/thinkgeek-promo
>     >>     _______________________________________________
>     >>     Ergatis-users mailing list
>     >>     [hidden email]
>     <mailto:[hidden email]>
>     >>     <mailto:[hidden email]
>     <mailto:[hidden email]>>
>     >>     https://lists.sourceforge.net/lists/listinfo/ergatis-users
>     >>
>     >>
>     >>
>     ------------------------------------------------------------------------
>     >>
>     >>
>     ------------------------------------------------------------------------------
>     >> ThinkGeek and WIRED's GeekDad team up for the Ultimate
>     >> GeekDad Father's Day Giveaway. ONE MASSIVE PRIZE to the
>     >> lucky parental unit.  See the prize list and enter to win:
>     >> http://p.sf.net/sfu/thinkgeek-promo
>     >>
>     ------------------------------------------------------------------------
>     >>
>     >> _______________________________________________
>     >> Ergatis-users mailing list
>     >> [hidden email]
>     <mailto:[hidden email]>
>     >> https://lists.sourceforge.net/lists/listinfo/ergatis-users
>     >>
>     >>
>     >
>     >
>     >
>     ------------------------------------------------------------------------------
>     > ThinkGeek and WIRED's GeekDad team up for the Ultimate
>     > GeekDad Father's Day Giveaway. ONE MASSIVE PRIZE to the
>     > lucky parental unit.  See the prize list and enter to win:
>     > http://p.sf.net/sfu/thinkgeek-promo
>     > _______________________________________________
>     > Ergatis-users mailing list
>     > [hidden email]
>     <mailto:[hidden email]>
>     > https://lists.sourceforge.net/lists/listinfo/ergatis-users
>     >
>
>
>     ------------------------------------------------------------------------------
>     ThinkGeek and WIRED's GeekDad team up for the Ultimate
>     GeekDad Father's Day Giveaway. ONE MASSIVE PRIZE to the
>     lucky parental unit.  See the prize list and enter to win:
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>     _______________________________________________
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>     [hidden email]
>     <mailto:[hidden email]>
>     https://lists.sourceforge.net/lists/listinfo/ergatis-users
>
>
> ------------------------------------------------------------------------
>
> ------------------------------------------------------------------------------
> ThinkGeek and WIRED's GeekDad team up for the Ultimate
> GeekDad Father's Day Giveaway. ONE MASSIVE PRIZE to the
> lucky parental unit.  See the prize list and enter to win:
> http://p.sf.net/sfu/thinkgeek-promo
> ------------------------------------------------------------------------
>
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Re: chado-prism

Mariette

Hi,
I'm getting further ...

first off, I got some trouble with the way the sort command is
used in the bsml2chado component.
I had to do a redirection of the stdin using '>' instead of the
stdin parameter set in this component. It may be specific to
me but in case it can help ...

Then I'm having a probleme still with the bsml2chado component
the : "Restore chado-mart indices" step of the bsml2chado component
doesn't use the $;RDBMS$; variable.
Thus there is an error when using postgresql, an error occured because the
script /usr/local/bioinfo/src/ergatis/bin/ddl2iterator ask for the
database_type
option. So I added it into the bsml2chaod.xml.

Other think, when processing the initdb component, the user has to be a
database
admin. So the table owner is the admin. Even if I granted all privileges
on on other
user, my user didn't have the right to create indexes required in the
bsml2chado
step. So I had to change owner on all my tables. How do you deal with
that ? Is the
admin user the same user than the one who add datas in your system ?? Or
do you
do the same than I did ??

Now it's working but I'm guessing I will need help later on,
so thanks for your help,

Jerome








Mariette a écrit :

> Joshua,
>
> I found what was wrong, I was using a user able to create database but not
> able to create language so the database was not properly loaded !! I should
> have being warned by the tag ADMIN user of the initdb component.
>
> So I reloaded my database and tryed tu upload some fastas using the
> fata2bsml
> and then the bsml2chado.
>
> I'm getting a weird error at step :
> error assign primary keys
> /usr/local/bioinfo/src/ergatis/bin/assign_pks ...
> Died with 'table was not defined' at
> /usr/local/bioinfo/src/ergatis//lib/perl5/Prism/ChadoPrismDB.pm line 30
>
> I figured out that the
> --checksum_file=/work/tmp/ergatis/cbrowser/bsml2chado/5_default/checksums.out.sorted
> was not correct !
> more /work/tmp/ergatis/cbrowser/bsml2chado/5_default/checksums.out.sorted
> hostname=n37.cluster
> job_owner=contig
> sge_id=575178
> job_name=sort
> queue=wflowq
> 000807e9b47a47f6e64d62d764831a87 0 featureprop 39630
> 000b3b621aafa22c3bef5bdba0d198bd 0 feature 13632863
> ....
> fffb219e482eacdea90bad34d46fee8f 1 featureprop 122642
> hostname=n24.cluster
> job_owner=contig
> sge_id=575649
> job_name=sort
> queue=wflowq
>
> If I do the command line which generate this file, it looks to me like
> ok ... those lines are not in !
> Have you already faced this probleme ???
>
> thanks,
> Jerome
>
>
>
>
>
>
>
>
>
>
>
> Joshua Orvis a écrit :
>  
>> Jerome -
>>
>> This is a little hard to debug remotely.  It seems like you have the
>> term in your database and the queries are correct.  I mentioned the
>> "get_cvterm_id_by_class_lookup" subroutine that builds the ontology
>> term lookup.  Have you tried using Data::Dumper or some other tool to
>> inspect the lookup and see if the term for 'chromosome' is present?
>>
>> Joshua
>>
>> On Thu, Jun 17, 2010 at 5:02 AM, Mariette <[hidden email]
>> <mailto:[hidden email]>> wrote:
>>
>>
>>     Hi again ...
>>
>>     So I tryed not to use ergatis to upload my first data set.
>>     I added an organism directly in the database :
>>
>>     INSERT INTO organism (abbreviation, genus, species, common_name)
>>     VALUES
>>     ('P.basidiomycetes', 'Pycnoporus','basidiomycetes','pycnoporus');
>>
>>     Then I converted my multifasta file in a gff3 format using the gmod
>>     converter.
>>     Finaly I used the bulk_loader and got the same error but with some
>>     more log:
>>
>>     [root@genome-browser gmod-1.0]# gmod_bulk_load_gff3.pl
>>     <http://gmod_bulk_load_gff3.pl> --gfffile=out.gff
>>     --organism=pycnoporus
>>     DBD::Pg::st execute failed: ERROR:  relation "feature_feature_id_seq"
>>     does not exist at
>>     /usr/lib/perl5/site_perl/5.8.8/Bio/GMOD/DB/Adapter.pm
>>     line 1280.
>>     DBD::Pg::st fetchrow_array failed: no statement executing at
>>     /usr/lib/perl5/site_perl/5.8.8/Bio/GMOD/DB/Adapter.pm line 1281.
>>     DBD::Pg::st execute failed: ERROR:  current transaction is aborted,
>>     commands ignored until end of transaction block at
>>     /usr/lib/perl5/site_perl/5.8.8/Bio/GMOD/DB/Adapter.pm line 1280.
>>     DBD::Pg::st fetchrow_array failed: no statement executing at
>>     /usr/lib/perl5/site_perl/5.8.8/Bio/GMOD/DB/Adapter.pm line 1281.
>>     DBD::Pg::st execute failed: ERROR:  current transaction is aborted,
>>     commands ignored until end of transaction block at
>>     /usr/lib/perl5/site_perl/5.8.8/Bio/GMOD/DB/Adapter.pm line 1280.
>>     DBD::Pg::st fetchrow_array failed: no statement executing at
>>     /usr/lib/perl5/site_perl/5.8.8/Bio/GMOD/DB/Adapter.pm line 1281.
>>     DBD::Pg::st execute failed: ERROR:  current transaction is aborted,
>>     commands ignored until end of transaction block at
>>     /usr/lib/perl5/site_perl/5.8.8/Bio/GMOD/DB/Adapter.pm line 1280.
>>     DBD::Pg::st fetchrow_array failed: no statement executing at
>>     /usr/lib/perl5/site_perl/5.8.8/Bio/GMOD/DB/Adapter.pm line 1281.
>>     DBD::Pg::st execute failed: ERROR:  current transaction is aborted,
>>     commands ignored until end of transaction block at
>>     /usr/lib/perl5/site_perl/5.8.8/Bio/GMOD/DB/Adapter.pm line 1280.
>>     DBD::Pg::st fetchrow_array failed: no statement executing at
>>     /usr/lib/perl5/site_perl/5.8.8/Bio/GMOD/DB/Adapter.pm line 1281.
>>     DBD::Pg::st execute failed: ERROR:  current transaction is aborted,
>>     commands ignored until end of transaction block at
>>     /usr/lib/perl5/site_perl/5.8.8/Bio/GMOD/DB/Adapter.pm line 1280.
>>     DBD::Pg::st fetchrow_array failed: no statement executing at
>>     /usr/lib/perl5/site_perl/5.8.8/Bio/GMOD/DB/Adapter.pm line 1281.
>>     DBD::Pg::st execute failed: ERROR:  current transaction is aborted,
>>     commands ignored until end of transaction block at
>>     /usr/lib/perl5/site_perl/5.8.8/Bio/GMOD/DB/Adapter.pm line 1280.
>>     DBD::Pg::st fetchrow_array failed: no statement executing at
>>     /usr/lib/perl5/site_perl/5.8.8/Bio/GMOD/DB/Adapter.pm line 1281.
>>     DBD::Pg::st execute failed: ERROR:  current transaction is aborted,
>>     commands ignored until end of transaction block at
>>     /usr/lib/perl5/site_perl/5.8.8/Bio/GMOD/DB/Adapter.pm line 1280.
>>     DBD::Pg::st fetchrow_array failed: no statement executing at
>>     /usr/lib/perl5/site_perl/5.8.8/Bio/GMOD/DB/Adapter.pm line 1281.
>>     DBD::Pg::st execute failed: ERROR:  current transaction is aborted,
>>     commands ignored until end of transaction block at
>>     /usr/lib/perl5/site_perl/5.8.8/Bio/GMOD/DB/Adapter.pm line 1280.
>>     DBD::Pg::st fetchrow_array failed: no statement executing at
>>     /usr/lib/perl5/site_perl/5.8.8/Bio/GMOD/DB/Adapter.pm line 1281.
>>     DBD::Pg::st execute failed: ERROR:  current transaction is aborted,
>>     commands ignored until end of transaction block at
>>     /usr/lib/perl5/site_perl/5.8.8/Bio/GMOD/DB/Adapter.pm line 1280.
>>     DBD::Pg::st fetchrow_array failed: no statement executing at
>>     /usr/lib/perl5/site_perl/5.8.8/Bio/GMOD/DB/Adapter.pm line 1281.
>>     DBD::Pg::st execute failed: ERROR:  current transaction is aborted,
>>     commands ignored until end of transaction block at
>>     /usr/lib/perl5/site_perl/5.8.8/Bio/GMOD/DB/Adapter.pm line 1280.
>>     DBD::Pg::st fetchrow_array failed: no statement executing at
>>     /usr/lib/perl5/site_perl/5.8.8/Bio/GMOD/DB/Adapter.pm line 1281.
>>     DBD::Pg::st execute failed: ERROR:  current transaction is aborted,
>>     commands ignored until end of transaction block at
>>     /usr/lib/perl5/site_perl/5.8.8/Bio/GMOD/DB/Adapter.pm line 1280.
>>     DBD::Pg::st fetchrow_array failed: no statement executing at
>>     /usr/lib/perl5/site_perl/5.8.8/Bio/GMOD/DB/Adapter.pm line 1281.
>>     DBD::Pg::st execute failed: ERROR:  current transaction is aborted,
>>     commands ignored until end of transaction block at
>>     /usr/lib/perl5/site_perl/5.8.8/Bio/GMOD/DB/Adapter.pm line 1280.
>>     DBD::Pg::st fetchrow_array failed: no statement executing at
>>     /usr/lib/perl5/site_perl/5.8.8/Bio/GMOD/DB/Adapter.pm line 1281.
>>     DBD::Pg::st execute failed: ERROR:  current transaction is aborted,
>>     commands ignored until end of transaction block at
>>     /usr/lib/perl5/site_perl/5.8.8/Bio/GMOD/DB/Adapter.pm line 1280.
>>     DBD::Pg::st fetchrow_array failed: no statement executing at
>>     /usr/lib/perl5/site_perl/5.8.8/Bio/GMOD/DB/Adapter.pm line 1281.
>>     DBD::Pg::st execute failed: ERROR:  current transaction is aborted,
>>     commands ignored until end of transaction block at
>>     /usr/lib/perl5/site_perl/5.8.8/Bio/GMOD/DB/Adapter.pm line 1280.
>>     DBD::Pg::st fetchrow_array failed: no statement executing at
>>     /usr/lib/perl5/site_perl/5.8.8/Bio/GMOD/DB/Adapter.pm line 1281.
>>     DBD::Pg::st execute failed: ERROR:  current transaction is aborted,
>>     commands ignored until end of transaction block at
>>     /usr/lib/perl5/site_perl/5.8.8/Bio/GMOD/DB/Adapter.pm line 1159.
>>     DBD::Pg::st fetchrow_array failed: no statement executing at
>>     /usr/lib/perl5/site_perl/5.8.8/Bio/GMOD/DB/Adapter.pm line 1161.
>>     (Re)creating the uniquename cache in the database...
>>     Creating table...
>>     DBD::Pg::db do failed: ERROR:  current transaction is aborted,
>>     commands
>>     ignored until end of transaction block at
>>     /usr/lib/perl5/site_perl/5.8.8/Bio/GMOD/DB/Adapter.pm line 1168.
>>     Populating table...
>>     DBD::Pg::db do failed: ERROR:  current transaction is aborted,
>>     commands
>>     ignored until end of transaction block at
>>     /usr/lib/perl5/site_perl/5.8.8/Bio/GMOD/DB/Adapter.pm line 1171.
>>     Creating indexes...DBD::Pg::db do failed: ERROR:  current
>>     transaction is
>>     aborted, commands ignored until end of transaction block at
>>     /usr/lib/perl5/site_perl/5.8.8/Bio/GMOD/DB/Adapter.pm line 1174.
>>     DBD::Pg::db do failed: ERROR:  current transaction is aborted,
>>     commands
>>     ignored until end of transaction block at
>>     /usr/lib/perl5/site_perl/5.8.8/Bio/GMOD/DB/Adapter.pm line 1175.
>>     DBD::Pg::db do failed: ERROR:  current transaction is aborted,
>>     commands
>>     ignored until end of transaction block at
>>     /usr/lib/perl5/site_perl/5.8.8/Bio/GMOD/DB/Adapter.pm line 1176.
>>     Done.
>>     Preparing data for inserting into the gntl_chado database
>>     (This may take a while ...)
>>
>>     ------------- EXCEPTION: Bio::Root::Exception -------------
>>     *MSG: no cvterm for chromosome*
>>     STACK: Error::throw
>>     STACK: Bio::Root::Root::throw
>>     /usr/lib/perl5/site_perl/5.8.8/Bio/Root/Root.pm:368
>>     STACK: Bio::GMOD::DB::Adapter::get_type
>>     /usr/lib/perl5/site_perl/5.8.8/Bio/GMOD/DB/Adapter.pm:4050
>>     STACK: /usr/bin/gmod_bulk_load_gff3.pl:755
>>     <http://gmod_bulk_load_gff3.pl:755>
>>     -----------------------------------------------------------
>>     Issuing rollback() due to DESTROY without explicit disconnect() of
>>     DBD::Pg::db handle dbname=gntl_chado;port=5432;host=147.99.108.44.
>>
>>
>>     I tryed to rerun the initdb component, which worked fine again ...
>>     but I'm
>>     still getting this error !
>>
>>     thanks,
>>     Jerome
>>
>>
>>
>>
>>
>>     Mariette a écrit :
>>     > Hi,
>>     > I made a mistake, I wanted to say chado instead of galaxy. Sorry for
>>     > the missunderstanding.
>>     >
>>     > Here are the last line of the highest debug level :
>>     >
>>     > ....
>>     > Logger::PrismAPI DEBUG Thu Jun 17 09:57:34 2010 vm-bioinfo:28607
>>     >
>>     /usr/local/bioinfo/src/ergatis//lib/perl5/Prism.pm:Prism:Log::Cabin::Foundation::debug:9881
>>     > || Args:
>>     > Logger::Coati::Coati::CoatiDB DEBUG Thu Jun 17 09:57:34 2010
>>     > vm-bioinfo:28607
>>     >
>>     /usr/local/bioinfo/src/ergatis//lib/perl5/Coati/Coati/CoatiDB.pm:Coati::Coati::CoatiDB:Log::Cabin::Foundation::debug:138
>>     > || Args:
>>     > Logger::Coati::Coati::CoatiDB DEBUG Thu Jun 17 09:57:34 2010
>>     > vm-bioinfo:28607
>>     >
>>     /usr/local/bioinfo/src/ergatis//lib/perl5/Coati/Coati/CoatiDB.pm:Coati::Coati::CoatiDB:Log::Cabin::Foundation::debug:184
>>     > || Opened lookup in read-write mode fo
>>     > r SELECT  lower(synonym), cvterm_id FROM cvtermsynonym  gntl_chado,
>>     >
>>     > Logger::PrismAPI DEBUG Thu Jun 17 09:57:34 2010 vm-bioinfo:28607
>>     >
>>     /usr/local/bioinfo/src/ergatis//lib/perl5/Prism.pm:Prism:Log::Cabin::Foundation::debug:10353
>>     > || Args:
>>     > Logger::Coati::Coati::CoatiDB DEBUG Thu Jun 17 09:57:34 2010
>>     > vm-bioinfo:28607
>>     >
>>     /usr/local/bioinfo/src/ergatis//lib/perl5/Coati/Coati/CoatiDB.pm:Coati::Coati::CoatiDB:Log::Cabin::Foundation::debug:138
>>     > || Args:
>>     > Logger::Coati::Coati::CoatiDB DEBUG Thu Jun 17 09:57:34 2010
>>     > vm-bioinfo:28607
>>     >
>>     /usr/local/bioinfo/src/ergatis//lib/perl5/Coati/Coati/CoatiDB.pm:Coati::Coati::CoatiDB:Log::Cabin::Foundation::debug:184
>>     > || Opened lookup in read-write mode fo
>>     > r SELECT lower(c.name <http://c.name>), c.cvterm_id FROM cvterm
>>     c, cv WHERE cv.name <http://cv.name> =
>>     > 'evidence_code' AND cv.cv_id = c.cv_id  gntl_chado,
>>     >
>>     > Logger::PrismAPI DEBUG Thu Jun 17 09:57:34 2010 vm-bioinfo:28607
>>     >
>>     /usr/local/bioinfo/src/ergatis//lib/perl5/Prism.pm:Prism:Log::Cabin::Foundation::debug:904
>>     > || Args:
>>     > Logger::PrismAPI FATAL Thu Jun 17 09:57:34 2010 vm-bioinfo:28607
>>     >
>>     /usr/local/bioinfo/src/ergatis//lib/perl5/Prism.pm:Prism:Log::Cabin::Foundation::logdie:909
>>     > || cvterm_id was not defined for class 'chromosome'
>>     >
>>     >
>>     > thanks,
>>     > Jerome
>>     >
>>     >
>>     >
>>     >
>>     >
>>     >
>>     >
>>     > Joshua Orvis a écrit :
>>     >
>>     >> Jerome -
>>     >>
>>     >> That should be pretty straight forward, so trying the debugging
>>     step I
>>     >> mentioned might be useful.  I'm not sure what your last
>>     sentence about
>>     >> Galaxy meant.  They're separate tools.
>>     >>
>>     >> JO
>>     >>
>>     >> On Wed, Jun 16, 2010 at 12:02 PM, jmariett
>>     <[hidden email] <mailto:[hidden email]>
>>     >> <mailto:[hidden email]
>>     <mailto:[hidden email]>>> wrote:
>>     >>
>>     >>
>>     >>     Well what I did is basicly a fasta2bsml, then
>>     >>     I try to load it into chado ... I might haven't
>>     >>     understand how to use ergatis with galaxy ?
>>     >>
>>     >>     Jerome
>>     >>
>>     >>
>>     >>
>>     >>
>>     >>
>>     >>     Joshua Orvis <[hidden email] <mailto:[hidden email]>
>>     <mailto:[hidden email] <mailto:[hidden email]>>> a écrit :
>>     >>
>>     >>     > Jerome -
>>     >>     >
>>     >>     > I'm not sure exactly what BSML you're attempting to load,
>>     but it
>>     >>     should have
>>     >>     > a reference to the sequence within it.  If the loader
>>     sees that
>>     >>     sequence ID
>>     >>     > already in the database it will just attach your new data
>>     to it.
>>     >>      If it's a
>>     >>     > new sequence it will be loaded automatically.
>>     >>     >
>>     >>     > Joshua
>>     >>     >
>>     >>     >
>>     >>     >
>>     >>     > On Wed, Jun 16, 2010 at 11:55 AM, jmariett
>>     >>     <[hidden email]
>>     <mailto:[hidden email]>
>>     <mailto:[hidden email]
>>     <mailto:[hidden email]>>>wrote:
>>     >>     >
>>     >>     >>
>>     >>     >> Ok I'm gonna try this,
>>     >>     >> Just so you know, I was gessing the probleme could come from
>>     >>     the fact
>>     >>     >> we haven't load anythink so far in the chado database.
>>     When I
>>     >>     installed
>>     >>     >> gbrowse in an order database, I remember that I had to add a
>>     >>     reference
>>     >>     >> sequence. So far I hadn't done this step ... could that
>>     be the
>>     >>     probleme ?
>>     >>     >>
>>     >>     >>
>>     >>     >>
>>     >>     >>
>>     >>     >>
>>     >>     >>
>>     >>     >> Joshua Orvis <[hidden email] <mailto:[hidden email]>
>>     <mailto:[hidden email] <mailto:[hidden email]>>> a écrit :
>>     >>     >>
>>     >>     >>
>>     >>     >>  Jerome -
>>     >>     >>>
>>     >>     >>> I'm not sure where this is going wrong, but
>>     unfortunately we
>>     >>     might need to
>>     >>     >>> add some debugging steps in the code to try to track it
>>     down.
>>     >>     Here is the
>>     >>     >>> process I can see:
>>     >>     >>>
>>     >>     >>> In lib/perl5/Prism/ChadoPrismDB.pm there is a
>>     subroutine called
>>     >>     >>> "get_cvterm_id_by_class_lookup" that creates a lookup
>>     of all
>>     >>     the terms in
>>     >>     >>> the database that are part of either the SO or ARD
>>     ontologies.
>>     >>      The error
>>     >>     >>> you are getting is from within the
>>     "master_feature_id_lookup"
>>     >>     subroutine
>>     >>     >>> in
>>     >>     >>> /lib/perl5/Prism.pm that is trying to look up the ID
>>     for the term
>>     >>     >>> 'chromosome'.  Your query from the database directly shows
>>     >>     that the terms
>>     >>     >>> are present in your database.
>>     >>     >>>
>>     >>     >>> We need to see now why that lookup is failing.  Can you use
>>     >>     the interface
>>     >>     >>> to
>>     >>     >>> find the exact command line string of the step that is
>>     failing
>>     >>     and then,
>>     >>     >>> reading the perldoc on the script if necessary, run it
>>     again
>>     >>     with logging
>>     >>     >>> enabled and set at a high level?  We can try using the
>>     logs to
>>     >>     see where
>>     >>     >>> this went wrong.
>>     >>     >>>
>>     >>     >>> Alternatively, if you're feeling adventurous, you could
>>     start
>>     >>     inserting
>>     >>     >>> debug steps on your own in the code but the logs may be an
>>     >>     easier first
>>     >>     >>> step, depending on your comfort with Perl.
>>     >>     >>>
>>     >>     >>> Joshua
>>     >>     >>>
>>     >>     >>>
>>     >>     >>>
>>     >>     >>> On Wed, Jun 16, 2010 at 9:31 AM, Mariette
>>     >>     <[hidden email]
>>     <mailto:[hidden email]>
>>     <mailto:[hidden email] <mailto:[hidden email]>>>
>>     >>     >>> wrote:
>>     >>     >>>
>>     >>     >>>
>>     >>     >>>> the querie gave me :
>>     >>     >>>>
>>     >>     >>>>
>>     >>     >>>> cvterm_id       cv_id   name
>>     >>     >>>> 9739
>>     >>     >>>>
>>     >>     >>>> 10
>>     >>     >>>>       chromosome
>>     >>     >>>> 34229
>>     >>     >>>>
>>     >>     >>>> 13
>>     >>     >>>>       chromosome
>>     >>     >>>>
>>     >>     >>>>
>>     >>     >>>> thx for your help,
>>     >>     >>>> Jerome
>>     >>     >>>>
>>     >>     >>>>
>>     >>     >>>>
>>     >>     >>>>
>>     >>     >>>> Joshua Orvis a écrit :
>>     >>     >>>>
>>     >>     >>>>  It looks like your database is missing the ontology
>>     term for
>>     >>     >>>>> 'chromosome'.
>>     >>     >>>>>  Can you log in to the chado database you created and
>>     issue
>>     >>     this query?
>>     >>     >>>>>
>>     >>     >>>>> SELECT cvterm_id, cv_id, name FROM cvterm WHERE name =
>>     >>     'chromosome';
>>     >>     >>>>>
>>     >>     >>>>> You should get at least one row.
>>     >>     >>>>>
>>     >>     >>>>> Joshua
>>     >>     >>>>>
>>     >>     >>>>>
>>     >>     >>>>> On Wed, Jun 16, 2010 at 3:22 AM, Mariette
>>     >>     <[hidden email]
>>     <mailto:[hidden email]>
>>     <mailto:[hidden email] <mailto:[hidden email]>>
>>     >>     >>>>> <mailto:
>>     >>     >>>>> [hidden email]
>>     <mailto:[hidden email]>
>>     >>     <mailto:[hidden email]
>>     <mailto:[hidden email]>>>> wrote:
>>     >>     >>>>>
>>     >>     >>>>>
>>     >>     >>>>>   Joshua,
>>     >>     >>>>>
>>     >>     >>>>>   We are pretty new in chado but we're gessing that
>>     >>     >>>>>   we're facing this error because we haven't load our
>>     >>     >>>>>   seq ref yet, would that make sense ?
>>     >>     >>>>>
>>     >>     >>>>>   If yes there is an ergatis componant to do so ? I take
>>     >>     >>>>>   a look at all components available but can't find any.
>>     >>     >>>>>
>>     >>     >>>>>   thanks for your help,
>>     >>     >>>>>   Jerome
>>     >>     >>>>>
>>     >>     >>>>>
>>     >>     >>>>>
>>     >>     >>>>>
>>     >>     >>>>>
>>     >>     >>>>>
>>     >>     >>>>>   jmariett a écrit :
>>     >>     >>>>>
>>     >>     >>>>>       Thanks for that,
>>     >>     >>>>>       so I run the componant which worked just fine
>>     and filled
>>     >>     >>>>>       the database.
>>     >>     >>>>>       Now when I use the bsml2chado I'm getting the
>>     >>     following errors :
>>     >>     >>>>>       at step
>>     >>     >>>>>        failed  Cache primary keys
>>     >>     >>>>>       Died with 'cvterm_id was not defined for class
>>     >>     'chromosome''
>>     >>     >>>>>       at
>>      /usr/local/bioinfo/src/ergatis//lib/perl5/Prism.pm
>>     >>     line 909
>>     >>     >>>>>
>>     >>     >>>>>       there is some other cvterm to add to chado
>>     before to
>>     >>     use it ?
>>     >>     >>>>>       It sounds to me like ok when I run the initDB
>>     component.
>>     >>     >>>>>
>>     >>     >>>>>       thanks for your answer,
>>     >>     >>>>>       Jerome
>>     >>     >>>>>
>>     >>     >>>>>
>>     >>     >>>>>
>>     >>     >>>>>       Joshua Orvis <[hidden email]
>>     <mailto:[hidden email]>
>>     >>     <mailto:[hidden email] <mailto:[hidden email]>>
>>     <mailto:[hidden email] <mailto:[hidden email]>
>>     >>     <mailto:[hidden email] <mailto:[hidden email]>>>> a
>>     >>     >>>>>
>>     >>     >>>>>       écrit :
>>     >>     >>>>>
>>     >>     >>>>>
>>     >>     >>>>>           Jerome -
>>     >>     >>>>>
>>     >>     >>>>>           We maintain a copy of the schema expected
>>     within the
>>     >>     >>>>>           software for internal
>>     >>     >>>>>           consistency.  The Ergatis component
>>     'initdb' can
>>     >>     be used
>>     >>     >>>>>           to create a blank
>>     >>     >>>>>           Chado instance and load all expected
>>     ontologies at
>>     >>     once.
>>     >>     >>>>>            That database
>>     >>     >>>>>           created can then be the target of
>>     bsml2chado runs.
>>     >>     >>>>>
>>     >>     >>>>>           Joshua
>>     >>     >>>>>
>>     >>     >>>>>
>>     >>     >>>>>
>>     >>     >>>>>           On Mon, Jun 14, 2010 at 7:48 AM, Mariette
>>     >>     >>>>>           <[hidden email]
>>     <mailto:[hidden email]>
>>     >>     <mailto:[hidden email]
>>     <mailto:[hidden email]>>
>>     >>     >>>>>           <mailto:[hidden email]
>>     <mailto:[hidden email]>
>>     >>     <mailto:[hidden email]
>>     <mailto:[hidden email]>>>> wrote:
>>     >>     >>>>>
>>     >>     >>>>>
>>     >>     >>>>>               Hi everyone,
>>     >>     >>>>>               I'm trying to make an ergatis
>>     annotation pipline
>>     >>     >>>>>               linked to gbrowse.
>>     >>     >>>>>               To do so I'm using the chado-prism with the
>>     >>     bsml2chado
>>     >>     >>>>>               componant.
>>     >>     >>>>>               Everything works fine but the querie looks
>>     >>     wrong. I'm
>>     >>     >>>>>               guessing I'm
>>     >>     >>>>>               not using the correct chado version. I
>>     use the one
>>     >>     >>>>>               from gmod1.0. Is
>>     >>     >>>>>               it the correct version to use with
>>     ergatis ? I
>>     >>     can't
>>     >>     >>>>>               figure out which
>>     >>     >>>>>               one is required !
>>     >>     >>>>>
>>     >>     >>>>>               thanks for your help
>>     >>     >>>>>               Jeroem
>>     >>     >>>>>
>>     >>     >>>>>
>>     >>     >>>>>
>>     >>     >>>>>
>>     >>     >>>>>
>>     >>     >>>>>
>>     >>    
>>     ------------------------------------------------------------------------------
>>     >>     >>>>>               ThinkGeek and WIRED's GeekDad team up
>>     for the
>>     >>     Ultimate
>>     >>     >>>>>               GeekDad Father's Day Giveaway. ONE MASSIVE
>>     >>     PRIZE to the
>>     >>     >>>>>               lucky parental unit.  See the prize
>>     list and
>>     >>     enter to win:
>>     >>     >>>>>               http://p.sf.net/sfu/thinkgeek-promo
>>     >>     >>>>>              
>>     _______________________________________________
>>     >>     >>>>>               Ergatis-users mailing list
>>     >>     >>>>>               [hidden email]
>>     <mailto:[hidden email]>
>>     >>     <mailto:[hidden email]
>>     <mailto:[hidden email]>>
>>     >>     >>>>>              
>>     <mailto:[hidden email]
>>     <mailto:[hidden email]>
>>     >>     <mailto:[hidden email]
>>     <mailto:[hidden email]>>>
>>     >>     >>>>>
>>     >>     >>>>>
>>     >>     >>>>>
>>     https://lists.sourceforge.net/lists/listinfo/ergatis-users
>>     >>     >>>>>
>>     >>     >>>>>
>>     >>     >>>>>
>>     >>     >>>>>
>>     >>     >>>>>
>>     >>     >>>>>
>>     >>     >>>>>
>>     >>     >>>>>
>>     >>    
>>     ------------------------------------------------------------------------------
>>     >>     >>>>>       ThinkGeek and WIRED's GeekDad team up for the
>>     Ultimate
>>     >>     GeekDad
>>     >>     >>>>>       Father's Day Giveaway. ONE MASSIVE PRIZE to the
>>     lucky
>>     >>     parental
>>     >>     >>>>>       unit.  See the prize list and enter to win:
>>     >>     >>>>>       http://p.sf.net/sfu/thinkgeek-promo
>>     >>     >>>>>       _______________________________________________
>>     >>     >>>>>       Ergatis-users mailing list
>>     >>     >>>>>       [hidden email]
>>     <mailto:[hidden email]>
>>     >>     <mailto:[hidden email]
>>     <mailto:[hidden email]>>
>>     >>     >>>>>       <mailto:[hidden email]
>>     <mailto:[hidden email]>
>>     >>     <mailto:[hidden email]
>>     <mailto:[hidden email]>>>
>>     >>     >>>>>
>>     >>     >>>>>      
>>     https://lists.sourceforge.net/lists/listinfo/ergatis-users
>>     >>     >>>>>
>>     >>     >>>>>
>>     >>     >>>>>
>>     >>     >>>>>
>>     >>     >>>>>
>>     >>     >>>>
>>     >>     >>>
>>     >>     >>
>>     >>     >
>>     >>
>>     >>
>>     >>    
>>     ------------------------------------------------------------------------------
>>     >>     ThinkGeek and WIRED's GeekDad team up for the Ultimate
>>     >>     GeekDad Father's Day Giveaway. ONE MASSIVE PRIZE to the
>>     >>     lucky parental unit.  See the prize list and enter to win:
>>     >>     http://p.sf.net/sfu/thinkgeek-promo
>>     >>     _______________________________________________
>>     >>     Ergatis-users mailing list
>>     >>     [hidden email]
>>     <mailto:[hidden email]>
>>     >>     <mailto:[hidden email]
>>     <mailto:[hidden email]>>
>>     >>     https://lists.sourceforge.net/lists/listinfo/ergatis-users
>>     >>
>>     >>
>>     >>
>>     ------------------------------------------------------------------------
>>     >>
>>     >>
>>     ------------------------------------------------------------------------------
>>     >> ThinkGeek and WIRED's GeekDad team up for the Ultimate
>>     >> GeekDad Father's Day Giveaway. ONE MASSIVE PRIZE to the
>>     >> lucky parental unit.  See the prize list and enter to win:
>>     >> http://p.sf.net/sfu/thinkgeek-promo
>>     >>
>>     ------------------------------------------------------------------------
>>     >>
>>     >> _______________________________________________
>>     >> Ergatis-users mailing list
>>     >> [hidden email]
>>     <mailto:[hidden email]>
>>     >> https://lists.sourceforge.net/lists/listinfo/ergatis-users
>>     >>
>>     >>
>>     >
>>     >
>>     >
>>     ------------------------------------------------------------------------------
>>     > ThinkGeek and WIRED's GeekDad team up for the Ultimate
>>     > GeekDad Father's Day Giveaway. ONE MASSIVE PRIZE to the
>>     > lucky parental unit.  See the prize list and enter to win:
>>     > http://p.sf.net/sfu/thinkgeek-promo
>>     > _______________________________________________
>>     > Ergatis-users mailing list
>>     > [hidden email]
>>     <mailto:[hidden email]>
>>     > https://lists.sourceforge.net/lists/listinfo/ergatis-users
>>     >
>>
>>
>>     ------------------------------------------------------------------------------
>>     ThinkGeek and WIRED's GeekDad team up for the Ultimate
>>     GeekDad Father's Day Giveaway. ONE MASSIVE PRIZE to the
>>     lucky parental unit.  See the prize list and enter to win:
>>     http://p.sf.net/sfu/thinkgeek-promo
>>     _______________________________________________
>>     Ergatis-users mailing list
>>     [hidden email]
>>     <mailto:[hidden email]>
>>     https://lists.sourceforge.net/lists/listinfo/ergatis-users
>>
>>
>> ------------------------------------------------------------------------
>>
>> ------------------------------------------------------------------------------
>> ThinkGeek and WIRED's GeekDad team up for the Ultimate
>> GeekDad Father's Day Giveaway. ONE MASSIVE PRIZE to the
>> lucky parental unit.  See the prize list and enter to win:
>> http://p.sf.net/sfu/thinkgeek-promo
>> ------------------------------------------------------------------------
>>
>> _______________________________________________
>> Ergatis-users mailing list
>> [hidden email]
>> https://lists.sourceforge.net/lists/listinfo/ergatis-users
>>  
>>    
>
>
> ------------------------------------------------------------------------------
> ThinkGeek and WIRED's GeekDad team up for the Ultimate
> GeekDad Father's Day Giveaway. ONE MASSIVE PRIZE to the
> lucky parental unit.  See the prize list and enter to win:
> http://p.sf.net/sfu/thinkgeek-promo
> _______________________________________________
> Ergatis-users mailing list
> [hidden email]
> https://lists.sourceforge.net/lists/listinfo/ergatis-users
>  


------------------------------------------------------------------------------
ThinkGeek and WIRED's GeekDad team up for the Ultimate
GeekDad Father's Day Giveaway. ONE MASSIVE PRIZE to the
lucky parental unit.  See the prize list and enter to win:
http://p.sf.net/sfu/thinkgeek-promo
_______________________________________________
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