Re: [Gmod-schema] Trying to load my first database

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Re: [Gmod-schema] Trying to load my first database

Scott Cain
Hi Daniel,

I'm cc'ing the MAKER and BioPerl lists, since this bug is germane to both lists.

Of course, the file you sent me would be the same file you sent me
yesterday; sorry for my poor memory :-)

This file uncovered a bug in BioPerl in the FeatureIO module.  While
fixing the bug may be difficult, working around it might not be too
bad.  Additionally, I'm not sure we should fix it right now, as this
is an effort underway to rework this section of BioPerl anyway.  The
good news is that the work around is fairly simple.

In the GFF that MAKER created, when parsing prodigal output, it
generates GFF lines like this:

Contig125       pred_gff:prodigal_v2.00 match   104     1723    157.5
 +       .
ID=Contig125:hit:75;Name=pred_gff_Prodigal_v2.00-Contig125-abinit-gene-0.0-mRNA-1;_AED=0.25;cscore=151.05;partial=00;rbs_motif=AGGA;rbs_spacer=5-10bp;rscore=3.57;score=157.5,157.53;sscore=6.48;tscore=3.50;type=ATG;uscore=-0.59;

The tricky part is this tag/value in the ninth column: type=ATG.  The
tag "type" is (semi) reserved in Bio::FeatureIO::gff to mean what is
in the third column, so when it is parsing this line of GFF, it tries
to reassign the feature type to something that isn't valid.  The work
around is pretty easy: since "type" is a problematic tag, and it
appears that the type tag here is defining the start type, I would
suggest doing a global search and replace on the file to replace
"type=" with "start_type=".  I did that and the file loaded fine.  I
don't know if it is MAKER that creates this tag or the BioPerl parser
for prodigal, but changing this at the source might be nice (of
course, it might also break somebody else's code :-/  I'll enter a bug
for this in the BioPerl bug tracker.

Scott


On Fri, May 21, 2010 at 1:40 PM, Daniel Quest <[hidden email]> wrote:

> Hi Scott,
>
> I used Maker to generate the attached file.
>
> -Daniel
>
> On Fri, May 21, 2010 at 10:34 AM, Scott Cain <[hidden email]> wrote:
>> Hi Daniel,
>>
>> Please keep the schema mailing list cc'ed in so the responses can be
>> archived and more eyes than just mine can try to solve the problem.
>>
>> Can you send a sample of the GFF that is causing the problem?  Any
>> ontology term that is in Chado should be "legal."  If there's
>> something causing a problem, we need to figure out what it is.
>>
>> Scott
>>
>>
>> On Fri, May 21, 2010 at 1:24 PM, Daniel Quest <[hidden email]> wrote:
>>> Hi Scott,
>>>
>>> I am using the same image as we used in class.  I was able to load
>>> each of the examples in the GMOD course (Pythium) and on the Chado
>>> website (yeast).
>>>
>>> On another note, is there an easy way to navigate the ontology terms
>>> that are legal and standard in both GFF3 and in Chado.  I am having
>>> trouble understanding how to convert from an arbitrary analysis (e.g.
>>> Blasting KEGG) into a format that works.
>>>
>>> Thanks so much!
>>> -Daniel
>>>
>>> On Fri, May 21, 2010 at 9:41 AM, Scott Cain <[hidden email]> wrote:
>>>> Hi Daniel,
>>>>
>>>> That error message looks like one that would come from an older
>>>> version of BioPerl.  What version do you have?
>>>>
>>>> Scott
>>>>
>>>>
>>>> On Fri, May 21, 2010 at 11:51 AM, Daniel Quest <[hidden email]> wrote:
>>>>> Hi Scott,
>>>>>
>>>>> Thanks for the reply.  Sorry, I should have been able to track down
>>>>> that error.  Could you tell me what the following error means?
>>>>>
>>>>> gmod@ubuntu:~/Cthe/ProdigalONLYcthe.maker.output/cthe_datastore/Contig125$
>>>>> gmod_bulk_load_gff3.pl --organism Cthe -a -g
>>>>> /home/gmod/Cthe/ProdigalONLYcthe.maker.output/cthe_datastore/Contig125/Contig125.gff
>>>>> --noexon --recreate_cache
>>>>> (Re)creating the uniquename cache in the database...
>>>>> Creating table...
>>>>> Populating table...
>>>>> Creating indexes...
>>>>> Adjusting the primary key sequences (if necessary)...Done.
>>>>> Preparing data for inserting into the chado database
>>>>> (This may take a while ...)
>>>>>
>>>>> ------------- EXCEPTION: Bio::Root::Exception -------------
>>>>> MSG: Object Bio::Annotation::SimpleValue=HASH(0xa858ac8) was not valid
>>>>> with key type. If you were adding new keys in, perhaps you want to
>>>>> make use
>>>>> of the archetype method to allow registration to a more basic type
>>>>> STACK: Error::throw
>>>>> STACK: Bio::Root::Root::throw /usr/local/share/perl/5.10.0/Bio/Root/Root.pm:368
>>>>> STACK: Bio::Annotation::Collection::add_Annotation
>>>>> /usr/local/share/perl/5.10.0/Bio/Annotation/Collection.pm:361
>>>>> STACK: Bio::SeqFeature::Annotated::add_Annotation
>>>>> /usr/local/share/perl/5.10.0/Bio/SeqFeature/Annotated.pm:609
>>>>> STACK: Bio::FeatureIO::gff::_handle_non_reserved_tag
>>>>> /usr/local/share/perl/5.10.0/Bio/FeatureIO/gff.pm:797
>>>>> STACK: Bio::FeatureIO::gff::_handle_feature
>>>>> /usr/local/share/perl/5.10.0/Bio/FeatureIO/gff.pm:752
>>>>> STACK: Bio::FeatureIO::gff::next_feature
>>>>> /usr/local/share/perl/5.10.0/Bio/FeatureIO/gff.pm:172
>>>>> STACK: /usr/local/bin/gmod_bulk_load_gff3.pl:775
>>>>> -----------------------------------------------------------
>>>>>
>>>>> Abnormal termination, trying to clean up...
>>>>>
>>>>> Attempting to clean up the loader temp table (so that --recreate_cache
>>>>> won't be needed)...
>>>>> Trying to remove the run lock (so that --remove_lock won't be needed)...
>>>>> Exiting...
>>>>>
>>>>>
>>>>> Thanks so much!
>>>>> -Daniel
>>>>>
>>>>> On Thu, May 20, 2010 at 6:20 PM, Scott Cain <[hidden email]> wrote:
>>>>>> Hi Daniel,
>>>>>>
>>>>>> The error message you got said that the GFF file that you are trying
>>>>>> to load couldn't be found; are you sure the path was correct?  The
>>>>>> file itself looks OK.
>>>>>>
>>>>>> Scott
>>>>>>
>>>>>>
>>>>>> On Thu, May 20, 2010 at 5:06 PM, Daniel Quest <[hidden email]> wrote:
>>>>>>> Hello All,
>>>>>>>
>>>>>>> I am trying to load my first genome from maker.  Not sure what the
>>>>>>> problem is... any help is awesome!  I am attaching at least part of
>>>>>>> the dataset.
>>>>>>>
>>>>>>> -Daniel
>>>>>>>
>>>>>>>
>>>>>>> gmod@ubuntu:~/Cthe/cthe.maker.output/cthe_datastore/Contig125$
>>>>>>> gmod_bulk_load_gff3.pl --organism Cthe -a -g
>>>>>>> /home/gmod/Cthe/cthe.maker.output/cthe_datastore/Contig125.gff3
>>>>>>> --noexon
>>>>>>>
>>>>>>> ------------- EXCEPTION: Bio::Root::Exception -------------
>>>>>>> MSG: Could not open
>>>>>>> /home/gmod/Cthe/cthe.maker.output/cthe_datastore/Contig125.gff3: No
>>>>>>> such file or directory
>>>>>>> STACK: Error::throw
>>>>>>> STACK: Bio::Root::Root::throw /usr/local/share/perl/5.10.0/Bio/Root/Root.pm:368
>>>>>>> STACK: Bio::Root::IO::_initialize_io
>>>>>>> /usr/local/share/perl/5.10.0/Bio/Root/IO.pm:341
>>>>>>> STACK: Bio::FeatureIO::_initialize
>>>>>>> /usr/local/share/perl/5.10.0/Bio/FeatureIO.pm:353
>>>>>>> STACK: Bio::FeatureIO::gff::_initialize
>>>>>>> /usr/local/share/perl/5.10.0/Bio/FeatureIO/gff.pm:102
>>>>>>> STACK: Bio::FeatureIO::new /usr/local/share/perl/5.10.0/Bio/FeatureIO.pm:276
>>>>>>> STACK: Bio::FeatureIO::new /usr/local/share/perl/5.10.0/Bio/FeatureIO.pm:296
>>>>>>> STACK: /usr/local/bin/gmod_bulk_load_gff3.pl:720
>>>>>>> -----------------------------------------------------------
>>>>>>>
>>>>>>> Abnormal termination, trying to clean up...
>>>>>>>
>>>>>>> Trying to remove the run lock (so that --remove_lock won't be needed)...
>>>>>>> Exiting...
>>>>>>> gmod@ubuntu:~/Cthe/cthe.maker.output/cthe_datastore/Contig125$
>>>>>>>
>>>>>>> ------------------------------------------------------------------------------
>>>>>>>
>>>>>>>
>>>>>>> _______________________________________________
>>>>>>> Gmod-schema mailing list
>>>>>>> [hidden email]
>>>>>>> https://lists.sourceforge.net/lists/listinfo/gmod-schema
>>>>>>>
>>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>> --
>>>>>> ------------------------------------------------------------------------
>>>>>> Scott Cain, Ph. D.                                   scott at scottcain dot net
>>>>>> GMOD Coordinator (http://gmod.org/)                     216-392-3087
>>>>>> Ontario Institute for Cancer Research
>>>>>>
>>>>>
>>>>
>>>>
>>>>
>>>> --
>>>> ------------------------------------------------------------------------
>>>> Scott Cain, Ph. D.                                   scott at scottcain dot net
>>>> GMOD Coordinator (http://gmod.org/)                     216-392-3087
>>>> Ontario Institute for Cancer Research
>>>>
>>>
>>
>>
>>
>> --
>> ------------------------------------------------------------------------
>> Scott Cain, Ph. D.                                   scott at scottcain dot net
>> GMOD Coordinator (http://gmod.org/)                     216-392-3087
>> Ontario Institute for Cancer Research
>>
>



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

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Re: [Gmod-schema] Trying to load my first database

Daniel Quest
Hey Scott,

Thanks so much for the work on this.  I have CC'ed Doug Hyatt, the
developer of Prodigal so that he is aware of this problem.  I am
thinking that Maker just passed the Prodigal tags through and then the
conflict happened on the Chado load.  From my POV it is probably
easiest to make small changes to the Prodigal GFF3 output to sync up
with the Chado schema.

Thanks so much
-Daniel

On Fri, May 21, 2010 at 11:15 AM, Scott Cain <[hidden email]> wrote:

> Hi Daniel,
>
> I'm cc'ing the MAKER and BioPerl lists, since this bug is germane to both lists.
>
> Of course, the file you sent me would be the same file you sent me
> yesterday; sorry for my poor memory :-)
>
> This file uncovered a bug in BioPerl in the FeatureIO module.  While
> fixing the bug may be difficult, working around it might not be too
> bad.  Additionally, I'm not sure we should fix it right now, as this
> is an effort underway to rework this section of BioPerl anyway.  The
> good news is that the work around is fairly simple.
>
> In the GFF that MAKER created, when parsing prodigal output, it
> generates GFF lines like this:
>
> Contig125       pred_gff:prodigal_v2.00 match   104     1723    157.5
>  +       .
> ID=Contig125:hit:75;Name=pred_gff_Prodigal_v2.00-Contig125-abinit-gene-0.0-mRNA-1;_AED=0.25;cscore=151.05;partial=00;rbs_motif=AGGA;rbs_spacer=5-10bp;rscore=3.57;score=157.5,157.53;sscore=6.48;tscore=3.50;type=ATG;uscore=-0.59;
>
> The tricky part is this tag/value in the ninth column: type=ATG.  The
> tag "type" is (semi) reserved in Bio::FeatureIO::gff to mean what is
> in the third column, so when it is parsing this line of GFF, it tries
> to reassign the feature type to something that isn't valid.  The work
> around is pretty easy: since "type" is a problematic tag, and it
> appears that the type tag here is defining the start type, I would
> suggest doing a global search and replace on the file to replace
> "type=" with "start_type=".  I did that and the file loaded fine.  I
> don't know if it is MAKER that creates this tag or the BioPerl parser
> for prodigal, but changing this at the source might be nice (of
> course, it might also break somebody else's code :-/  I'll enter a bug
> for this in the BioPerl bug tracker.
>
> Scott
>
>
> On Fri, May 21, 2010 at 1:40 PM, Daniel Quest <[hidden email]> wrote:
>> Hi Scott,
>>
>> I used Maker to generate the attached file.
>>
>> -Daniel
>>
>> On Fri, May 21, 2010 at 10:34 AM, Scott Cain <[hidden email]> wrote:
>>> Hi Daniel,
>>>
>>> Please keep the schema mailing list cc'ed in so the responses can be
>>> archived and more eyes than just mine can try to solve the problem.
>>>
>>> Can you send a sample of the GFF that is causing the problem?  Any
>>> ontology term that is in Chado should be "legal."  If there's
>>> something causing a problem, we need to figure out what it is.
>>>
>>> Scott
>>>
>>>
>>> On Fri, May 21, 2010 at 1:24 PM, Daniel Quest <[hidden email]> wrote:
>>>> Hi Scott,
>>>>
>>>> I am using the same image as we used in class.  I was able to load
>>>> each of the examples in the GMOD course (Pythium) and on the Chado
>>>> website (yeast).
>>>>
>>>> On another note, is there an easy way to navigate the ontology terms
>>>> that are legal and standard in both GFF3 and in Chado.  I am having
>>>> trouble understanding how to convert from an arbitrary analysis (e.g.
>>>> Blasting KEGG) into a format that works.
>>>>
>>>> Thanks so much!
>>>> -Daniel
>>>>
>>>> On Fri, May 21, 2010 at 9:41 AM, Scott Cain <[hidden email]> wrote:
>>>>> Hi Daniel,
>>>>>
>>>>> That error message looks like one that would come from an older
>>>>> version of BioPerl.  What version do you have?
>>>>>
>>>>> Scott
>>>>>
>>>>>
>>>>> On Fri, May 21, 2010 at 11:51 AM, Daniel Quest <[hidden email]> wrote:
>>>>>> Hi Scott,
>>>>>>
>>>>>> Thanks for the reply.  Sorry, I should have been able to track down
>>>>>> that error.  Could you tell me what the following error means?
>>>>>>
>>>>>> gmod@ubuntu:~/Cthe/ProdigalONLYcthe.maker.output/cthe_datastore/Contig125$
>>>>>> gmod_bulk_load_gff3.pl --organism Cthe -a -g
>>>>>> /home/gmod/Cthe/ProdigalONLYcthe.maker.output/cthe_datastore/Contig125/Contig125.gff
>>>>>> --noexon --recreate_cache
>>>>>> (Re)creating the uniquename cache in the database...
>>>>>> Creating table...
>>>>>> Populating table...
>>>>>> Creating indexes...
>>>>>> Adjusting the primary key sequences (if necessary)...Done.
>>>>>> Preparing data for inserting into the chado database
>>>>>> (This may take a while ...)
>>>>>>
>>>>>> ------------- EXCEPTION: Bio::Root::Exception -------------
>>>>>> MSG: Object Bio::Annotation::SimpleValue=HASH(0xa858ac8) was not valid
>>>>>> with key type. If you were adding new keys in, perhaps you want to
>>>>>> make use
>>>>>> of the archetype method to allow registration to a more basic type
>>>>>> STACK: Error::throw
>>>>>> STACK: Bio::Root::Root::throw /usr/local/share/perl/5.10.0/Bio/Root/Root.pm:368
>>>>>> STACK: Bio::Annotation::Collection::add_Annotation
>>>>>> /usr/local/share/perl/5.10.0/Bio/Annotation/Collection.pm:361
>>>>>> STACK: Bio::SeqFeature::Annotated::add_Annotation
>>>>>> /usr/local/share/perl/5.10.0/Bio/SeqFeature/Annotated.pm:609
>>>>>> STACK: Bio::FeatureIO::gff::_handle_non_reserved_tag
>>>>>> /usr/local/share/perl/5.10.0/Bio/FeatureIO/gff.pm:797
>>>>>> STACK: Bio::FeatureIO::gff::_handle_feature
>>>>>> /usr/local/share/perl/5.10.0/Bio/FeatureIO/gff.pm:752
>>>>>> STACK: Bio::FeatureIO::gff::next_feature
>>>>>> /usr/local/share/perl/5.10.0/Bio/FeatureIO/gff.pm:172
>>>>>> STACK: /usr/local/bin/gmod_bulk_load_gff3.pl:775
>>>>>> -----------------------------------------------------------
>>>>>>
>>>>>> Abnormal termination, trying to clean up...
>>>>>>
>>>>>> Attempting to clean up the loader temp table (so that --recreate_cache
>>>>>> won't be needed)...
>>>>>> Trying to remove the run lock (so that --remove_lock won't be needed)...
>>>>>> Exiting...
>>>>>>
>>>>>>
>>>>>> Thanks so much!
>>>>>> -Daniel
>>>>>>
>>>>>> On Thu, May 20, 2010 at 6:20 PM, Scott Cain <[hidden email]> wrote:
>>>>>>> Hi Daniel,
>>>>>>>
>>>>>>> The error message you got said that the GFF file that you are trying
>>>>>>> to load couldn't be found; are you sure the path was correct?  The
>>>>>>> file itself looks OK.
>>>>>>>
>>>>>>> Scott
>>>>>>>
>>>>>>>
>>>>>>> On Thu, May 20, 2010 at 5:06 PM, Daniel Quest <[hidden email]> wrote:
>>>>>>>> Hello All,
>>>>>>>>
>>>>>>>> I am trying to load my first genome from maker.  Not sure what the
>>>>>>>> problem is... any help is awesome!  I am attaching at least part of
>>>>>>>> the dataset.
>>>>>>>>
>>>>>>>> -Daniel
>>>>>>>>
>>>>>>>>
>>>>>>>> gmod@ubuntu:~/Cthe/cthe.maker.output/cthe_datastore/Contig125$
>>>>>>>> gmod_bulk_load_gff3.pl --organism Cthe -a -g
>>>>>>>> /home/gmod/Cthe/cthe.maker.output/cthe_datastore/Contig125.gff3
>>>>>>>> --noexon
>>>>>>>>
>>>>>>>> ------------- EXCEPTION: Bio::Root::Exception -------------
>>>>>>>> MSG: Could not open
>>>>>>>> /home/gmod/Cthe/cthe.maker.output/cthe_datastore/Contig125.gff3: No
>>>>>>>> such file or directory
>>>>>>>> STACK: Error::throw
>>>>>>>> STACK: Bio::Root::Root::throw /usr/local/share/perl/5.10.0/Bio/Root/Root.pm:368
>>>>>>>> STACK: Bio::Root::IO::_initialize_io
>>>>>>>> /usr/local/share/perl/5.10.0/Bio/Root/IO.pm:341
>>>>>>>> STACK: Bio::FeatureIO::_initialize
>>>>>>>> /usr/local/share/perl/5.10.0/Bio/FeatureIO.pm:353
>>>>>>>> STACK: Bio::FeatureIO::gff::_initialize
>>>>>>>> /usr/local/share/perl/5.10.0/Bio/FeatureIO/gff.pm:102
>>>>>>>> STACK: Bio::FeatureIO::new /usr/local/share/perl/5.10.0/Bio/FeatureIO.pm:276
>>>>>>>> STACK: Bio::FeatureIO::new /usr/local/share/perl/5.10.0/Bio/FeatureIO.pm:296
>>>>>>>> STACK: /usr/local/bin/gmod_bulk_load_gff3.pl:720
>>>>>>>> -----------------------------------------------------------
>>>>>>>>
>>>>>>>> Abnormal termination, trying to clean up...
>>>>>>>>
>>>>>>>> Trying to remove the run lock (so that --remove_lock won't be needed)...
>>>>>>>> Exiting...
>>>>>>>> gmod@ubuntu:~/Cthe/cthe.maker.output/cthe_datastore/Contig125$
>>>>>>>>
>>>>>>>> ------------------------------------------------------------------------------
>>>>>>>>
>>>>>>>>
>>>>>>>> _______________________________________________
>>>>>>>> Gmod-schema mailing list
>>>>>>>> [hidden email]
>>>>>>>> https://lists.sourceforge.net/lists/listinfo/gmod-schema
>>>>>>>>
>>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> --
>>>>>>> ------------------------------------------------------------------------
>>>>>>> Scott Cain, Ph. D.                                   scott at scottcain dot net
>>>>>>> GMOD Coordinator (http://gmod.org/)                     216-392-3087
>>>>>>> Ontario Institute for Cancer Research
>>>>>>>
>>>>>>
>>>>>
>>>>>
>>>>>
>>>>> --
>>>>> ------------------------------------------------------------------------
>>>>> Scott Cain, Ph. D.                                   scott at scottcain dot net
>>>>> GMOD Coordinator (http://gmod.org/)                     216-392-3087
>>>>> Ontario Institute for Cancer Research
>>>>>
>>>>
>>>
>>>
>>>
>>> --
>>> ------------------------------------------------------------------------
>>> Scott Cain, Ph. D.                                   scott at scottcain dot net
>>> GMOD Coordinator (http://gmod.org/)                     216-392-3087
>>> Ontario Institute for Cancer Research
>>>
>>
>
>
>
> --
> ------------------------------------------------------------------------
> Scott Cain, Ph. D.                                   scott at scottcain dot net
> GMOD Coordinator (http://gmod.org/)                     216-392-3087
> Ontario Institute for Cancer Research
>

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Re: [Gmod-schema] Trying to load my first database

Carson Hinton Holt
Re: [maker-devel] [Gmod-schema] Trying to load my first database That is correct.  MAKER will just pass user defined GFF3 tags through rather than trying to make sense of them or trimming them off.

Carson


On 5/21/10 1:34 PM, "Daniel Quest" <daniel.quest@...> wrote:

Hey Scott,

Thanks so much for the work on this.  I have CC'ed Doug Hyatt, the
developer of Prodigal so that he is aware of this problem.  I am
thinking that Maker just passed the Prodigal tags through and then the
conflict happened on the Chado load.  From my POV it is probably
easiest to make small changes to the Prodigal GFF3 output to sync up
with the Chado schema.

Thanks so much
-Daniel

On Fri, May 21, 2010 at 11:15 AM, Scott Cain <scott@...> wrote:
> Hi Daniel,
>
> I'm cc'ing the MAKER and BioPerl lists, since this bug is germane to both lists.
>
> Of course, the file you sent me would be the same file you sent me
> yesterday; sorry for my poor memory :-)
>
> This file uncovered a bug in BioPerl in the FeatureIO module.  While
> fixing the bug may be difficult, working around it might not be too
> bad.  Additionally, I'm not sure we should fix it right now, as this
> is an effort underway to rework this section of BioPerl anyway.  The
> good news is that the work around is fairly simple.
>
> In the GFF that MAKER created, when parsing prodigal output, it
> generates GFF lines like this:
>
> Contig125       pred_gff:prodigal_v2.00 match   104     1723    157.5
>  +       .
> ID=Contig125:hit:75;Name=pred_gff_Prodigal_v2.00-Contig125-abinit-gene-0.0-mRNA-1;_AED=0.25;cscore=151.05;partial=00;rbs_motif=AGGA;rbs_spacer=5-10bp;rscore=3.57;score=157.5,157.53;sscore=6.48;tscore=3.50;type=ATG;uscore=-0.59;
>
> The tricky part is this tag/value in the ninth column: type=ATG.  The
> tag "type" is (semi) reserved in Bio::FeatureIO::gff to mean what is
> in the third column, so when it is parsing this line of GFF, it tries
> to reassign the feature type to something that isn't valid.  The work
> around is pretty easy: since "type" is a problematic tag, and it
> appears that the type tag here is defining the start type, I would
> suggest doing a global search and replace on the file to replace
> "type=" with "start_type=".  I did that and the file loaded fine.  I
> don't know if it is MAKER that creates this tag or the BioPerl parser
> for prodigal, but changing this at the source might be nice (of
> course, it might also break somebody else's code :-/  I'll enter a bug
> for this in the BioPerl bug tracker.
>
> Scott
>
>
> On Fri, May 21, 2010 at 1:40 PM, Daniel Quest <daniel.quest@...> wrote:
>> Hi Scott,
>>
>> I used Maker to generate the attached file.
>>
>> -Daniel
>>
>> On Fri, May 21, 2010 at 10:34 AM, Scott Cain <scott@...> wrote:
>>> Hi Daniel,
>>>
>>> Please keep the schema mailing list cc'ed in so the responses can be
>>> archived and more eyes than just mine can try to solve the problem.
>>>
>>> Can you send a sample of the GFF that is causing the problem?  Any
>>> ontology term that is in Chado should be "legal."  If there's
>>> something causing a problem, we need to figure out what it is.
>>>
>>> Scott
>>>
>>>
>>> On Fri, May 21, 2010 at 1:24 PM, Daniel Quest <daniel.quest@...> wrote:
>>>> Hi Scott,
>>>>
>>>> I am using the same image as we used in class.  I was able to load
>>>> each of the examples in the GMOD course (Pythium) and on the Chado
>>>> website (yeast).
>>>>
>>>> On another note, is there an easy way to navigate the ontology terms
>>>> that are legal and standard in both GFF3 and in Chado.  I am having
>>>> trouble understanding how to convert from an arbitrary analysis (e.g.
>>>> Blasting KEGG) into a format that works.
>>>>
>>>> Thanks so much!
>>>> -Daniel
>>>>
>>>> On Fri, May 21, 2010 at 9:41 AM, Scott Cain <scott@...> wrote:
>>>>> Hi Daniel,
>>>>>
>>>>> That error message looks like one that would come from an older
>>>>> version of BioPerl.  What version do you have?
>>>>>
>>>>> Scott
>>>>>
>>>>>
>>>>> On Fri, May 21, 2010 at 11:51 AM, Daniel Quest <daniel.quest@...> wrote:
>>>>>> Hi Scott,
>>>>>>
>>>>>> Thanks for the reply.  Sorry, I should have been able to track down
>>>>>> that error.  Could you tell me what the following error means?
>>>>>>
>>>>>> gmod@ubuntu:~/Cthe/ProdigalONLYcthe.maker.output/cthe_datastore/Contig125$
>>>>>> gmod_bulk_load_gff3.pl --organism Cthe -a -g
>>>>>> /home/gmod/Cthe/ProdigalONLYcthe.maker.output/cthe_datastore/Contig125/Contig125.gff
>>>>>> --noexon --recreate_cache
>>>>>> (Re)creating the uniquename cache in the database...
>>>>>> Creating table...
>>>>>> Populating table...
>>>>>> Creating indexes...
>>>>>> Adjusting the primary key sequences (if necessary)...Done.
>>>>>> Preparing data for inserting into the chado database
>>>>>> (This may take a while ...)
>>>>>>
>>>>>> ------------- EXCEPTION: Bio::Root::Exception -------------
>>>>>> MSG: Object Bio::Annotation::SimpleValue=HASH(0xa858ac8) was not valid
>>>>>> with key type. If you were adding new keys in, perhaps you want to
>>>>>> make use
>>>>>> of the archetype method to allow registration to a more basic type
>>>>>> STACK: Error::throw
>>>>>> STACK: Bio::Root::Root::throw /usr/local/share/perl/5.10.0/Bio/Root/Root.pm:368
>>>>>> STACK: Bio::Annotation::Collection::add_Annotation
>>>>>> /usr/local/share/perl/5.10.0/Bio/Annotation/Collection.pm:361
>>>>>> STACK: Bio::SeqFeature::Annotated::add_Annotation
>>>>>> /usr/local/share/perl/5.10.0/Bio/SeqFeature/Annotated.pm:609
>>>>>> STACK: Bio::FeatureIO::gff::_handle_non_reserved_tag
>>>>>> /usr/local/share/perl/5.10.0/Bio/FeatureIO/gff.pm:797
>>>>>> STACK: Bio::FeatureIO::gff::_handle_feature
>>>>>> /usr/local/share/perl/5.10.0/Bio/FeatureIO/gff.pm:752
>>>>>> STACK: Bio::FeatureIO::gff::next_feature
>>>>>> /usr/local/share/perl/5.10.0/Bio/FeatureIO/gff.pm:172
>>>>>> STACK: /usr/local/bin/gmod_bulk_load_gff3.pl:775
>>>>>> -----------------------------------------------------------
>>>>>>
>>>>>> Abnormal termination, trying to clean up...
>>>>>>
>>>>>> Attempting to clean up the loader temp table (so that --recreate_cache
>>>>>> won't be needed)...
>>>>>> Trying to remove the run lock (so that --remove_lock won't be needed)...
>>>>>> Exiting...
>>>>>>
>>>>>>
>>>>>> Thanks so much!
>>>>>> -Daniel
>>>>>>
>>>>>> On Thu, May 20, 2010 at 6:20 PM, Scott Cain <scott@...> wrote:
>>>>>>> Hi Daniel,
>>>>>>>
>>>>>>> The error message you got said that the GFF file that you are trying
>>>>>>> to load couldn't be found; are you sure the path was correct?  The
>>>>>>> file itself looks OK.
>>>>>>>
>>>>>>> Scott
>>>>>>>
>>>>>>>
>>>>>>> On Thu, May 20, 2010 at 5:06 PM, Daniel Quest <daniel.quest@...> wrote:
>>>>>>>> Hello All,
>>>>>>>>
>>>>>>>> I am trying to load my first genome from maker.  Not sure what the
>>>>>>>> problem is... any help is awesome!  I am attaching at least part of
>>>>>>>> the dataset.
>>>>>>>>
>>>>>>>> -Daniel
>>>>>>>>
>>>>>>>>
>>>>>>>> gmod@ubuntu:~/Cthe/cthe.maker.output/cthe_datastore/Contig125$
>>>>>>>> gmod_bulk_load_gff3.pl --organism Cthe -a -g
>>>>>>>> /home/gmod/Cthe/cthe.maker.output/cthe_datastore/Contig125.gff3
>>>>>>>> --noexon
>>>>>>>>
>>>>>>>> ------------- EXCEPTION: Bio::Root::Exception -------------
>>>>>>>> MSG: Could not open
>>>>>>>> /home/gmod/Cthe/cthe.maker.output/cthe_datastore/Contig125.gff3: No
>>>>>>>> such file or directory
>>>>>>>> STACK: Error::throw
>>>>>>>> STACK: Bio::Root::Root::throw /usr/local/share/perl/5.10.0/Bio/Root/Root.pm:368
>>>>>>>> STACK: Bio::Root::IO::_initialize_io
>>>>>>>> /usr/local/share/perl/5.10.0/Bio/Root/IO.pm:341
>>>>>>>> STACK: Bio::FeatureIO::_initialize
>>>>>>>> /usr/local/share/perl/5.10.0/Bio/FeatureIO.pm:353
>>>>>>>> STACK: Bio::FeatureIO::gff::_initialize
>>>>>>>> /usr/local/share/perl/5.10.0/Bio/FeatureIO/gff.pm:102
>>>>>>>> STACK: Bio::FeatureIO::new /usr/local/share/perl/5.10.0/Bio/FeatureIO.pm:276
>>>>>>>> STACK: Bio::FeatureIO::new /usr/local/share/perl/5.10.0/Bio/FeatureIO.pm:296
>>>>>>>> STACK: /usr/local/bin/gmod_bulk_load_gff3.pl:720
>>>>>>>> -----------------------------------------------------------
>>>>>>>>
>>>>>>>> Abnormal termination, trying to clean up...
>>>>>>>>
>>>>>>>> Trying to remove the run lock (so that --remove_lock won't be needed)...
>>>>>>>> Exiting...
>>>>>>>> gmod@ubuntu:~/Cthe/cthe.maker.output/cthe_datastore/Contig125$
>>>>>>>>
>>>>>>>> ------------------------------------------------------------------------------
>>>>>>>>
>>>>>>>>
>>>>>>>> _______________________________________________
>>>>>>>> Gmod-schema mailing list
>>>>>>>> Gmod-schema@...
>>>>>>>> https://lists.sourceforge.net/lists/listinfo/gmod-schema
>>>>>>>>
>>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>> --
>>>>>>> ------------------------------------------------------------------------
>>>>>>> Scott Cain, Ph. D.                                   scott at scottcain dot net
>>>>>>> GMOD Coordinator (http://gmod.org/)                     216-392-3087
>>>>>>> Ontario Institute for Cancer Research
>>>>>>>
>>>>>>
>>>>>
>>>>>
>>>>>
>>>>> --
>>>>> ------------------------------------------------------------------------
>>>>> Scott Cain, Ph. D.                                   scott at scottcain dot net
>>>>> GMOD Coordinator (http://gmod.org/)                     216-392-3087
>>>>> Ontario Institute for Cancer Research
>>>>>
>>>>
>>>
>>>
>>>
>>> --
>>> ------------------------------------------------------------------------
>>> Scott Cain, Ph. D.                                   scott at scottcain dot net
>>> GMOD Coordinator (http://gmod.org/)                     216-392-3087
>>> Ontario Institute for Cancer Research
>>>
>>
>
>
>
> --
> ------------------------------------------------------------------------
> Scott Cain, Ph. D.                                   scott at scottcain dot net
> GMOD Coordinator (http://gmod.org/)                     216-392-3087
> Ontario Institute for Cancer Research
>

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