Re: [Gmod-schema] no parent error

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

Re: [Gmod-schema] no parent error

Dino Ienco
Dear Scott,
        I follow your suggestion and I download the svn version of CHADO.
This time I loaded all the files (121 gff files).
But for one files I obtain some error/warning, but the loader also  
loads the file with this errors/warning

The accession number of the file in which I found this error is  
NC_008785.
A sample of this error is the follows:
       
=============
(This may take a while ...)
this shouldn't happen in modified_uniquename at /usr/local/share/perl/
5.10.0/Bio/GMOD/DB/Adapter.pm line 2994
         
Bio
::GMOD
::DB
::Adapter
::modified_uniquename('Bio::GMOD::DB::Adapter=HASH(0x8e38be0)',  
'orig_id', undef, 'organism_id', 26) called at /usr/local/share/perl/
5.10.0/Bio/GMOD/DB/Adapter.pm line 3953
         
Bio
::GMOD
::DB::Adapter::handle_CDS('Bio::GMOD::DB::Adapter=HASH(0x8e38be0)',  
'Bio::SeqFeature::Annotated=HASH(0x9046570)') called at /home/ienco/
Downloads/chado/load/bin/gmod_bulk_load_gff3.pl line 807


There is a CDS feature with no parent (ID:BMASAVP1_A0001)  I think  
that is wrong!


This GFF file has CDS and/or UTR features that do not belong to a
'central dogma' gene (ie, gene/transcript/CDS).  The features of
this type are being stored in the database as is.

this shouldn't happen in modified_uniquename at /usr/local/share/perl/
5.10.0/Bio/GMOD/DB/Adapter.pm line 2994
         
Bio
::GMOD
::DB
::Adapter
::modified_uniquename('Bio::GMOD::DB::Adapter=HASH(0x8e38be0)',  
'orig_id', undef, 'organism_id', 26) called at /usr/local/share/perl/
5.10.0/Bio/GMOD/DB/Adapter.pm line 3953
         
Bio
::GMOD
::DB::Adapter::handle_CDS('Bio::GMOD::DB::Adapter=HASH(0x8e38be0)',  
'Bio::SeqFeature::Annotated=HASH(0x8fa6b28)') called at /home/ienco/
Downloads/chado/load/bin/gmod_bulk_load_gff3.pl line 807


There is a CDS feature with no parent (ID:BMASAVP1_A0001)  I think  
that is wrong!

this shouldn't happen in modified_uniquename at /usr/local/share/perl/
5.10.0/Bio/GMOD/DB/Adapter.pm line 2994
         
Bio
::GMOD
::DB
::Adapter
::modified_uniquename('Bio::GMOD::DB::Adapter=HASH(0x8e38be0)',  
'orig_id', undef, 'organism_id', 26) called at /usr/local/share/perl/
5.10.0/Bio/GMOD/DB/Adapter.pm line 3953
         
Bio
::GMOD
::DB::Adapter::handle_CDS('Bio::GMOD::DB::Adapter=HASH(0x8e38be0)',  
'Bio::SeqFeature::Annotated=HASH(0x9059f28)') called at /home/ienco/
Downloads/chado/load/bin/gmod_bulk_load_gff3.pl line 807


There is a CDS feature with no parent (ID:BMASAVP1_A0002)  I think  
that is wrong!

this shouldn't happen in modified_uniquename at /usr/local/share/perl/
5.10.0/Bio/GMOD/DB/Adapter.pm line 2994
         
Bio
::GMOD
::DB
::Adapter
::modified_uniquename('Bio::GMOD::DB::Adapter=HASH(0x8e38be0)',  
'orig_id', undef, 'organism_id', 26) called at /usr/local/share/perl/
5.10.0/Bio/GMOD/DB/Adapter.pm line 3953
         
Bio
::GMOD
::DB::Adapter::handle_CDS('Bio::GMOD::DB::Adapter=HASH(0x8e38be0)',  
'Bio::SeqFeature::Annotated=HASH(0x90461f0)') called at /home/ienco/
Downloads/chado/load/bin/gmod_bulk_load_gff3.pl line 807

.........


======================

and then there are these warning

======================

There is a CDS feature with no parent (ID:BMASAVP1_A3532)  I think  
that is wrong!

More than one feature found for BMASAVP1_A0002, org_id:26 when trying  
to add sequence at /usr/local/share/perl/5.10.0/Bio/GMOD/DB/Adapter.pm  
line 2531, <GEN0> line 7053.
More than one feature found for BMASAVP1_A0004, org_id:26 when trying  
to add sequence at /usr/local/share/perl/5.10.0/Bio/GMOD/DB/Adapter.pm  
line 2531, <GEN0> line 7054.
More than one feature found for BMASAVP1_A0005, org_id:26 when trying  
to add sequence at /usr/local/share/perl/5.10.0/Bio/GMOD/DB/Adapter.pm  
line 2531, <GEN0> line 7055.
More than one feature found for BMASAVP1_A0006, org_id:26 when trying  
to add sequence at /usr/local/share/perl/5.10.0/Bio/GMOD/DB/Adapter.pm  
line 2531, <GEN0> line 7056.
More than one feature found for BMASAVP1_A0007, org_id:26 when trying  
to add sequence at /usr/local/share/perl/5.10.0/Bio/GMOD/DB/Adapter.pm  
line 2531, <GEN0> line 7057.
More than one feature found for BMASAVP1_A0013, org_id:26 when trying  
to add sequence at /usr/local/share/perl/5.10.0/Bio/GMOD/DB/Adapter.pm  
line 2531, <GEN0> line 7058.
More than one feature found for BMASAVP1_A0017, org_id:26 when trying  
to add sequence at /usr/local/share/perl/5.10.0/Bio/GMOD/DB/Adapter.pm  
line 2531, <GEN0> line 7059.
More than one feature found for BMASAVP1_A0018, org_id:26 when trying  
to add sequence at /usr/local/share/perl/5.10.0/Bio/GMOD/DB/Adapter.pm  
line 2531, <GEN0> line 7060.
More than one feature found for BMASAVP1_A0019, org_id:26 when trying  
to add sequence at /usr/local/share/perl/5.10.0/Bio/GMOD/DB/Adapter.pm  
line 2531, <GEN0> line 7061.
More than one feature found for BMASAVP1_A0021, org_id:26 when trying  
to add sequence at /usr/local/share/perl/5.10.0/Bio/GMOD/DB/Adapter.pm  
line 2531, <GEN0> line 7062.
More than one feature found for BMASAVP1_A0022, org_id:26 when trying  
to add sequence at /usr/local/share/perl/5.10.0/Bio/GMOD/DB/Adapter.pm  
line 2531, <GEN0> line 7063.
More than one feature found for BMASAVP1_A0023, org_id:26 when trying  
to add sequence at /usr/local/share/perl/5.10.0/Bio/GMOD/DB/Adapter.pm  
line 2531, <GEN0> line 7064.
More than one feature found for BMASAVP1_A0024, org_id:26 when trying  
to add sequence at /usr/local/share/perl/5.10.0/Bio/GMOD/DB/Adapter.pm  
line 2531, <GEN0> line 7065.
More than one feature found for BMASAVP1_A0025, org_id:26 when trying  
to add sequence at /usr/local/share/perl/5.10.0/Bio/GMOD/DB/Adapter.pm  
line 2531, <GEN0> line 7066.
More than one feature found for BMASAVP1_A0026, org_id:26 when trying  
to add sequence at /usr/local/share/perl/5.10.0/Bio/GMOD/DB/Adapter.pm  
line 2531, <GEN0> line 7067.
More than one feature found for BMASAVP1_A0027, org_id:26 when trying  
to add sequence at /usr/local/share/perl/5.10.0/Bio/GMOD/DB/Adapter.pm  
line 2531, <GEN0> line 7068.
More than one feature found for BMASAVP1_A0028, org_id:26 when trying  
to add sequence at /usr/local/share/perl/5.10.0/Bio/GMOD/DB/Adapter.pm  
line 2531, <GEN0> line 7069.
More than one feature found for BMASAVP1_A0029, org_id:26 when trying  
to add sequence at /usr/local/share/perl/5.10.0/Bio/GMOD/DB/Adapter.pm  
line 2531, <GEN0> line 7070.
More than one feature found for BMASAVP1_A0030, org_id:26 when trying  
to add sequence at /usr/local/share/perl/5.10.0/Bio/GMOD/DB/Adapter.pm  
line 2531, <GEN0> line 7071.
More than one feature found for BMASAVP1_A0031, org_id:26 when trying  
to add sequence at /usr/local/share/perl/5.10.0/Bio/GMOD/DB/Adapter.pm  
line 2531, <GEN0> line 7072.
More than one feature found for BMASAVP1_A0032, org_id:26 when trying  
to add sequence at /usr/local/share/perl/5.10.0/Bio/GMOD/DB/Adapter.pm  
line 2531, <GEN0> line 7073.
More than one feature found for BMASAVP1_A0033, org_id:26 when trying  
to add sequence at /usr/local/share/perl/5.10.0/Bio/GMOD/DB/Adapter.pm  
line 2531, <GEN0> line 7074.
More than one feature found for BMASAVP1_A0034, org_id:26 when trying  
to add sequence at /usr/local/share/perl/5.10.0/Bio/GMOD/DB/Adapter.pm  
line 2531, <GEN0> line 7075.
More than one feature found for BMASAVP1_A0035, org_id:26 when trying  
to add sequence at /usr/local/share/perl/5.10.0/Bio/GMOD/DB/Adapter.pm  
line 2531, <GEN0> line 7076.
More than one feature found for BMASAVP1_A0036, org_id:26 when trying  
to add sequence at /usr/local/share/perl/5.10.0/Bio/GMOD/DB/Adapter.pm  
line 2531, <GEN0> line 7077.
More than one feature found for BMASAVP1_A0037, org_id:26 when trying  
to add sequence at /usr/local/share/perl/5.10.0/Bio/GMOD/DB/Adapter.pm  
line 2531, <GEN0> line 7078.
More than one feature found for BMASAVP1_A0038, org_id:26 when trying  
to add sequence at /usr/local/share/perl/5.10.0/Bio/GMOD/DB/Adapter.pm  
line 2531, <GEN0> line 7079.
More than one feature found for BMASAVP1_A0039, org_id:26 when trying  
to add sequence at /usr/local/share/perl/5.10.0/Bio/GMOD/DB/Adapter.pm  
line 2531, <GEN0> line 7080.
More than one feature found for BMASAVP1_A0040, org_id:26 when trying  
to add sequence at /usr/local/share/perl/5.10.0/Bio/GMOD/DB/Adapter.pm  
line 2531, <GEN0> line 7081.
More than one feature found for BMASAVP1_A0041, org_id:26 when trying  
to add sequence at /usr/local/share/perl/5.10.0/Bio/GMOD/DB/Adapter.pm  
line 2531, <GEN0> line 7082.
More than one feature found for BMASAVP1_A0042, org_id:26 when trying  
to add sequence at /usr/local/share/perl/5.10.0/Bio/GMOD/DB/Adapter.pm  
line 2531, <GEN0> line 7083.
More than one feature found for BMASAVP1_A0043, org_id:26 when trying  
to add sequence at /usr/local/share/perl/5.10.0/Bio/GMOD/DB/Adapter.pm  
line 2531, <GEN0> line 7084.
More than one feature found for BMASAVP1_A0044, org_id:26 when trying  
to add sequence at /usr/local/share/perl/5.10.0/Bio/GMOD/DB/Adapter.pm  
line 2531, <GEN0> line 7085.
More than one feature found for BMASAVP1_A0045, org_id:26 when trying  
to add sequence at /usr/local/share/perl/5.10.0/Bio/GMOD/DB/Adapter.pm  
line 2531, <GEN0> line 7086.

........
======================

Are there some problems?


Thanks for your attention

Dino


On May 13, 2010, at 12:54 AM, Scott Cain wrote:

> Hi Dino,
>
> It is possible that in that situation that there might be some
> interaction between the data in different GFF files, in fact, I think
> I may have fixed a bug along those lines some time ago.  Are you using
> the 1.0 release, or are you using an svn checkout?  If you are using
> 1.0, please try getting a checkout of the schema repository from svn.
> See this page for more info:
>
>  http://gmod.org/wiki/SVN
>
> If you are already using an svn checkout, please try to create a
> minimal set of GFF files that causes the problem so I can fix this,
> because it shouldn't be happening.
>
> Thanks,
> Scott
>
>
> On Wed, May 12, 2010 at 5:50 PM, Dino Ienco <[hidden email]> wrote:
>> Hi Scott,
>>        my problem is the follows:
>>        I need to load 121 gff files in a chado DB.
>>        This files represent 44 different organism.
>>        I'm trying to load this file in the db with the perl program:
>> gmod_bulk_load_gff3.pl
>>        Before I sort the file with the option indicate on the gmod  
>> site.
>>        It is very strange because if I change the order in which I  
>> load the
>> data file, this change also the error.
>>        All the errors are about "no parent", but I check the files  
>> manually
>> and I find the ID definition reported in the error.
>>        Then I try this solution
>>                for a fixed file that I need to load before I delete  
>> it with
>> the --delete option then I load it with the --recreation_cache option
>>        In this way I have less errors.
>>
>>        How can I do to load all the files without these errors?
>>        If I have different gff files for the same organism, Is it  
>> possible
>> that these files interact each other in the load process?
>>        Is it possible that the same feature for an organism is  
>> present in
>> different gff files?
>>
>> All the best
>>
>> Dino
>>
>>
>> On May 12, 2010, at 4:38 AM, Scott Cain wrote:
>>
>>> Hi Dino,
>>>
>>> I don't know.  It is unlikely to get worse at any rate.  If you  
>>> wanted
>>> to send an accession, we could try it to, to see what is going  
>>> wrong.
>>>
>>> Scott
>>>
>>>
>>> On Tue, May 11, 2010 at 6:14 PM, Dino Ienco <[hidden email]>  
>>> wrote:
>>>>
>>>> Hi Scott,
>>>>       thanks for the answer.
>>>> I have the Bioperl 1.006 version.
>>>> Is a prokaryotic data but I don't know if it is circular.
>>>> Do you think that If I change the BioPerl version the error  
>>>> disappear?
>>>>
>>>> All the best
>>>>
>>>> Dino
>>>>
>>>>
>>>> On May 11, 2010, at 4:30 PM, Scott Cain wrote:
>>>>
>>>>> Hi Dino,
>>>>>
>>>>> There is a problem with the file you are using and it isn't  
>>>>> generating
>>>>> the parent lines that have ID=acnA and ID=Bmul_6163.  What  
>>>>> version of
>>>>> bioperl are you using?  Can you send a sample of the generated  
>>>>> GFF to
>>>>> the mailing list?  Is this prokaryotic data with a circular  
>>>>> genome?
>>>>> There were some modifications to the genbank2gff3 script a few  
>>>>> month
>>>>> ago that might help.  Try getting an anonymous checkout of
>>>>> bioperl-live:
>>>>>
>>>>>  http://github.com/bioperl/bioperl-live/archives/master
>>>>>
>>>>> Scott
>>>>>
>>>>>
>>>>> On Tue, May 11, 2010 at 10:21 AM, Dino Ienco <[hidden email]>  
>>>>> wrote:
>>>>>>
>>>>>> Hi guys,
>>>>>>      I continue with my error.
>>>>>> When I load gff3 files I have
>>>>>>      no parent error.
>>>>>>
>>>>>> How can I deal with this error?
>>>>>> some of the error are the following:
>>>>>>      no parent acnA;
>>>>>>      no parent Bmul_6163;
>>>>>>
>>>>>>
>>>>>> Is there a way to insert the corresponding gff file?
>>>>>>
>>>>>> Best regards
>>>>>>
>>>>>> Dino
>>>>>>
>>>>>>
>>>>>>
>>>>>> ------------------------------------------------------------------------------
>>>>>>
>>>>>> _______________________________________________
>>>>>> Gmod-schema mailing list
>>>>>> [hidden email]
>>>>>> https://lists.sourceforge.net/lists/listinfo/gmod-schema
>>>>>>
>>>>>
>>>>>
>>>>>
>>>>> --
>>>>> ------------------------------------------------------------------------
>>>>> Scott Cain, Ph. D.                                   scott at  
>>>>> scottcain
>>>>> dot net
>>>>> GMOD Coordinator (http://gmod.org/)                      
>>>>> 216-392-3087
>>>>> Ontario Institute for Cancer Research
>>>>
>>>>
>>>
>>>
>>>
>>> --
>>> ------------------------------------------------------------------------
>>> Scott Cain, Ph. D.                                   scott at  
>>> scottcain
>>> dot net
>>> GMOD Coordinator (http://gmod.org/)                     216-392-3087
>>> Ontario Institute for Cancer Research
>>
>>
>
>
>
> --
> ------------------------------------------------------------------------
> Scott Cain, Ph. D.                                   scott at  
> scottcain dot net
> GMOD Coordinator (http://gmod.org/)                     216-392-3087
> Ontario Institute for Cancer Research


------------------------------------------------------------------------------

_______________________________________________
Gmod-schema mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-schema
Reply | Threaded
Open this post in threaded view
|

Re: [Gmod-schema] no parent error

Robert Buels
Scott Cain wrote:
> It is possible that in that situation that there might be some
> interaction between the data in different GFF files, in fact, I think
> I may have fixed a bug along those lines some time ago.  Are you using

If this was fixed some time ago, was the fix released?

R



------------------------------------------------------------------------------

_______________________________________________
Gmod-schema mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-schema