Object method "get_Annotations" error

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Object method "get_Annotations" error

Francisco García Atienza
Hello,

I'm trying to use the Chado adapter from WebApollo but I get some errors, I've instantiated Chado following your guide at http://gmod.org/wiki/Chado and when I try to load some example in the Chado database doing this:

gmod_bulk_load_gff3.pl --organism yeast  --gfffile saccharomyces_cerevisiae.gff.sorted

(These are my parameters)
GMOD_ROOT=/usr/local/gmod
PERL5LIB=$PERL5LIB:/usr/local/bioperl/bioperl-live
CHADO_DB_NAME=webapollochado
CHADO_DB_USER=web_apollo_users_admin 
CHADO_DB_HOST=localhost
CHADO_DB_PORT=5432

 I get this error 

"WARNING:
Unable to find a 'part_of' term in the relationship ontology;
It's absence indicates that there is something really wrong with the database.
Consider stopping and checking the state of your cvterm table.


Preparing data for inserting into the webapollochado database
(This may take a while ...)
Can't locate object method "get_Annotations" via package "Bio::SeqFeature::Annotated" at /usr/local/share/perl/5.14.2/Bio/SeqFeature/Annotated.pm line 287, <GEN0> line 2.

Abnormal termination, trying to clean up...

Trying to remove the run lock (so that --remove_lock won't be needed)...
Exiting..."


Any ideas what could be wrong? Thank you.

Regards, 

/Francisco.

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Re: Object method "get_Annotations" error

Scott Cain
Resenting to the mailing list (how did I manage to misspell it?)

Sent from my iPad

On Jan 21, 2014, at 9:05 AM, Scott Cain <[hidden email]> wrote:

Hi Francisco,

Please keep the schema mailing list cc'ed (if I'm the one that forgot, sorry). 

So you're sure that part_of term is gone?  (Ie, rerunning that query only gives you one row?)

Also, this is unrelated to your current problem, but the fact that it completed a load and put data in the feature table is going to cause you problems. To clean up, delete everything from the feature table (assuming there's nothing there you want) and use the --recreate_cache option with the bulk loader. Until you get the part of thing straightened out, you should kill the loader when it gives you that message ("consider stopping..."). To delete everything from the feature table, do this:

  DELETE FROM feature;

Scott




Sent from my iPad

On Jan 21, 2014, at 1:59 AM, Francisco García Atienza <[hidden email]> wrote:

Hi Scott,

I've deleted the PO's ontology but I got the same warning:

./gmod_bulk_load_gff3.pl --dbname webapollochado --dbuser web_apollo_users_admin --dbpass web_apollo_users_admin --organism yeast --gfffile /home/francisco/webapollo/webapollo_sample/saccharomyces_cerevisiae.gff.sorted

"WARNING:
Unable to find a 'part_of' term in the relationship ontology;
It's absense indicates that there is something really wrong with the database.
Consider stopping and checking the state of your cvterm table.


Preparing data for inserting into the webapollochado database
(This may take a while ...)
couldn't find GO:0010551 's cvterm_id in cvterm table
couldn't find GO:0010551 's cvterm_id in cvterm table
Unable to find srcfeature chr01 in the database.
Perhaps you need to rerun your data load with the '--recreate_cache' option. at /usr/local/share/perl/5.14.2/Bio/GMOD/DB/Adapter.pm line 4603, <GEN0> line 4283.
Bio::GMOD::DB::Adapter::src_second_chance(Bio::GMOD::DB::Adapter=HASH(0x242ee38), Bio::SeqFeature::Annotated=HASH(0x4260078)) called at ./gmod_bulk_load_gff3.pl line 851

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..."


With a few lines from the gff3 file (Populus trichocarpa) that I want to load to the chado database I got load the data, I had to change a bit the file to the form 

Potri.001G000100 phytozome8_0 gene 1660 2502 . - . ID=Potri.001G000100;Name=Potri.001G000100

Before I had this

Chr01 phytozome8_0 gene 1660 2502 . - . ID=Potri.001G000100;Name=Potri.001G000100

and I got the error "Unable to find srcfeature Chr01 in the database", but still the same problem with ontologies: 

"WARNING:
Unable to find a 'part_of' term in the relationship ontology;
It's absense indicates that there is something really wrong with the database.
Consider stopping and checking the state of your cvterm table.


Preparing data for inserting into the webapollochado database
(This may take a while ...)
Skipping organism table since the load file is empty...
Skipping analysis table since the load file is empty...
Skipping db table since the load file is empty...
Skipping dbxref table since the load file is empty...
Skipping cv table since the load file is empty...
Skipping cvterm table since the load file is empty...
Loading data into feature table ...
Skipping featureloc table since the load file is empty...
Skipping feature_relationship table since the load file is empty...
Skipping featureprop table since the load file is empty...
Skipping feature_cvterm table since the load file is empty...
Loading data into synonym table ...
Loading data into feature_synonym table ...
Loading data into feature_dbxref table ...
Skipping analysisfeature table since the load file is empty...
Adding cvtermprop=MapReferenceType for 'gene' ...
Loading sequences (if any) ...

Done."

What do you think? 

/Francisco


2014/1/20 Scott Cain <[hidden email]>
Hi Francisco,

Ah, then I think we can blame the plant_ontology (well, to be fair, you can blame me, since I failed to anticipate that an ontology would provide their own "part_of").  The fix, as ugly as it is, is to remove PO's part_of:

  DELETE FROM cvterm WHERE cvterm_id = 95;

While you're at it, you should also check the derives_from term, as it will cause a similar problem.

Scott



On Mon, Jan 20, 2014 at 1:16 AM, Francisco García Atienza <[hidden email]> wrote:
Hi Scott,

Thank you for your answer. Yes, I loaded the Relationship Ontolgy and this is my result with the SQL query 

Select cvterm.*,cv.name from cvterm join cv using (cv_id) where cvterm.name = 'part_of'; 

cvterm_id cv_id name definition dbxref_id is_obsolete is_relationshiptype name








37 7 part_of
39 0 1 relationship
95 18 part_of
121 0 1 plant_ontology

/Francisco


2014/1/8 Scott Cain <[hidden email]>
Hi Francisco,

The message about not finding part_of is pretty important. Did you load the Relationship Ontology?  If so, what happens when you execute this command:

  Select cvterm.*,cv.name from cvterm join cv using cv_id where cvterm.name = 'part_of';

(I think that SQL is right, but I'm writing it on an iPad without a database to test against, but hopefully you get the idea.)

Scott


Sent from Mailbox for iPad


On Wed, Jan 8, 2014 at 10:42 AM, Francisco García Atienza <[hidden email]> wrote:

Hello,

I'm trying to use the Chado adapter from WebApollo but I get some errors, I've instantiated Chado following your guide at http://gmod.org/wiki/Chado and when I try to load some example in the Chado database doing this:

gmod_bulk_load_gff3.pl --organism yeast  --gfffile saccharomyces_cerevisiae.gff.sorted

(These are my parameters)
GMOD_ROOT=/usr/local/gmod
PERL5LIB=$PERL5LIB:/usr/local/bioperl/bioperl-live
CHADO_DB_NAME=webapollochado
CHADO_DB_USER=web_apollo_users_admin 
CHADO_DB_HOST=localhost
CHADO_DB_PORT=5432

 I get this error 

"WARNING:
Unable to find a 'part_of' term in the relationship ontology;
It's absence indicates that there is something really wrong with the database.
Consider stopping and checking the state of your cvterm table.


Preparing data for inserting into the webapollochado database
(This may take a while ...)
Can't locate object method "get_Annotations" via package "Bio::SeqFeature::Annotated" at /usr/local/share/perl/5.14.2/Bio/SeqFeature/Annotated.pm line 287, <GEN0> line 2.

Abnormal termination, trying to clean up...

Trying to remove the run lock (so that --remove_lock won't be needed)...
Exiting..."


Any ideas what could be wrong? Thank you.

Regards, 

/Francisco.





--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     <a href="tel:216-392-3087" value="+12163923087" target="_blank">216-392-3087
Ontario Institute for Cancer Research


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Re: Object method "get_Annotations" error

Francisco García Atienza
Hi Scott,

Sorry to say but I still have the same problem with only one part_of row (relationship ontology's). I don't know what can cause this warning.

My apologies for my ignorance but is there any instance of chado already created to which I can add my organism? 

Regards,

/Francisco.




2014/1/21 Scott Cain <[hidden email]>
Resenting to the mailing list (how did I manage to misspell it?)

Sent from my iPad

On Jan 21, 2014, at 9:05 AM, Scott Cain <[hidden email]> wrote:

Hi Francisco,

Please keep the schema mailing list cc'ed (if I'm the one that forgot, sorry). 

So you're sure that part_of term is gone?  (Ie, rerunning that query only gives you one row?)

Also, this is unrelated to your current problem, but the fact that it completed a load and put data in the feature table is going to cause you problems. To clean up, delete everything from the feature table (assuming there's nothing there you want) and use the --recreate_cache option with the bulk loader. Until you get the part of thing straightened out, you should kill the loader when it gives you that message ("consider stopping..."). To delete everything from the feature table, do this:

  DELETE FROM feature;

Scott




Sent from my iPad

On Jan 21, 2014, at 1:59 AM, Francisco García Atienza <[hidden email]> wrote:

Hi Scott,

I've deleted the PO's ontology but I got the same warning:

./gmod_bulk_load_gff3.pl --dbname webapollochado --dbuser web_apollo_users_admin --dbpass web_apollo_users_admin --organism yeast --gfffile /home/francisco/webapollo/webapollo_sample/saccharomyces_cerevisiae.gff.sorted

"WARNING:
Unable to find a 'part_of' term in the relationship ontology;
It's absense indicates that there is something really wrong with the database.
Consider stopping and checking the state of your cvterm table.


Preparing data for inserting into the webapollochado database
(This may take a while ...)
couldn't find GO:0010551 's cvterm_id in cvterm table
couldn't find GO:0010551 's cvterm_id in cvterm table
Unable to find srcfeature chr01 in the database.
Perhaps you need to rerun your data load with the '--recreate_cache' option. at /usr/local/share/perl/5.14.2/Bio/GMOD/DB/Adapter.pm line 4603, <GEN0> line 4283.
Bio::GMOD::DB::Adapter::src_second_chance(Bio::GMOD::DB::Adapter=HASH(0x242ee38), Bio::SeqFeature::Annotated=HASH(0x4260078)) called at ./gmod_bulk_load_gff3.pl line 851

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..."


With a few lines from the gff3 file (Populus trichocarpa) that I want to load to the chado database I got load the data, I had to change a bit the file to the form 

Potri.001G000100 phytozome8_0 gene 1660 2502 . - . ID=Potri.001G000100;Name=Potri.001G000100

Before I had this

Chr01 phytozome8_0 gene 1660 2502 . - . ID=Potri.001G000100;Name=Potri.001G000100

and I got the error "Unable to find srcfeature Chr01 in the database", but still the same problem with ontologies: 

"WARNING:
Unable to find a 'part_of' term in the relationship ontology;
It's absense indicates that there is something really wrong with the database.
Consider stopping and checking the state of your cvterm table.


Preparing data for inserting into the webapollochado database
(This may take a while ...)
Skipping organism table since the load file is empty...
Skipping analysis table since the load file is empty...
Skipping db table since the load file is empty...
Skipping dbxref table since the load file is empty...
Skipping cv table since the load file is empty...
Skipping cvterm table since the load file is empty...
Loading data into feature table ...
Skipping featureloc table since the load file is empty...
Skipping feature_relationship table since the load file is empty...
Skipping featureprop table since the load file is empty...
Skipping feature_cvterm table since the load file is empty...
Loading data into synonym table ...
Loading data into feature_synonym table ...
Loading data into feature_dbxref table ...
Skipping analysisfeature table since the load file is empty...
Adding cvtermprop=MapReferenceType for 'gene' ...
Loading sequences (if any) ...

Done."

What do you think? 

/Francisco


2014/1/20 Scott Cain <[hidden email]>
Hi Francisco,

Ah, then I think we can blame the plant_ontology (well, to be fair, you can blame me, since I failed to anticipate that an ontology would provide their own "part_of").  The fix, as ugly as it is, is to remove PO's part_of:

  DELETE FROM cvterm WHERE cvterm_id = 95;

While you're at it, you should also check the derives_from term, as it will cause a similar problem.

Scott



On Mon, Jan 20, 2014 at 1:16 AM, Francisco García Atienza <[hidden email]> wrote:
Hi Scott,

Thank you for your answer. Yes, I loaded the Relationship Ontolgy and this is my result with the SQL query 

Select cvterm.*,cv.name from cvterm join cv using (cv_id) where cvterm.name = 'part_of'; 

cvterm_id cv_id name definition dbxref_id is_obsolete is_relationshiptype name








37 7 part_of
39 0 1 relationship
95 18 part_of
121 0 1 plant_ontology

/Francisco


2014/1/8 Scott Cain <[hidden email]>
Hi Francisco,

The message about not finding part_of is pretty important. Did you load the Relationship Ontology?  If so, what happens when you execute this command:

  Select cvterm.*,cv.name from cvterm join cv using cv_id where cvterm.name = 'part_of';

(I think that SQL is right, but I'm writing it on an iPad without a database to test against, but hopefully you get the idea.)

Scott


Sent from Mailbox for iPad


On Wed, Jan 8, 2014 at 10:42 AM, Francisco García Atienza <[hidden email]> wrote:

Hello,

I'm trying to use the Chado adapter from WebApollo but I get some errors, I've instantiated Chado following your guide at http://gmod.org/wiki/Chado and when I try to load some example in the Chado database doing this:

gmod_bulk_load_gff3.pl --organism yeast  --gfffile saccharomyces_cerevisiae.gff.sorted

(These are my parameters)
GMOD_ROOT=/usr/local/gmod
PERL5LIB=$PERL5LIB:/usr/local/bioperl/bioperl-live
CHADO_DB_NAME=webapollochado
CHADO_DB_USER=web_apollo_users_admin 
CHADO_DB_HOST=localhost
CHADO_DB_PORT=5432

 I get this error 

"WARNING:
Unable to find a 'part_of' term in the relationship ontology;
It's absence indicates that there is something really wrong with the database.
Consider stopping and checking the state of your cvterm table.


Preparing data for inserting into the webapollochado database
(This may take a while ...)
Can't locate object method "get_Annotations" via package "Bio::SeqFeature::Annotated" at /usr/local/share/perl/5.14.2/Bio/SeqFeature/Annotated.pm line 287, <GEN0> line 2.

Abnormal termination, trying to clean up...

Trying to remove the run lock (so that --remove_lock won't be needed)...
Exiting..."


Any ideas what could be wrong? Thank you.

Regards, 

/Francisco.





--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     <a href="tel:216-392-3087" value="+12163923087" target="_blank">216-392-3087
Ontario Institute for Cancer Research



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Re: Object method "get_Annotations" error

Scott Cain
Hi Francisco,

Perhaps there is a data problem and I can recreate what you're doing. Could you make a small GFF file that causes this to happen and send it me?

The other thing I just want to make sure of because I do it occasionally: do you have more than one chado database, and if you have more than one, are you sure you're loading the one where you deleted the part_of and derives_from?

Scott

Sent from my iPhone

On Jan 22, 2014, at 1:37 AM, Francisco García Atienza <[hidden email]> wrote:

Hi Scott,

Sorry to say but I still have the same problem with only one part_of row (relationship ontology's). I don't know what can cause this warning.

My apologies for my ignorance but is there any instance of chado already created to which I can add my organism? 

Regards,

/Francisco.




2014/1/21 Scott Cain <[hidden email]>
Resenting to the mailing list (how did I manage to misspell it?)

Sent from my iPad

On Jan 21, 2014, at 9:05 AM, Scott Cain <[hidden email]> wrote:

Hi Francisco,

Please keep the schema mailing list cc'ed (if I'm the one that forgot, sorry). 

So you're sure that part_of term is gone?  (Ie, rerunning that query only gives you one row?)

Also, this is unrelated to your current problem, but the fact that it completed a load and put data in the feature table is going to cause you problems. To clean up, delete everything from the feature table (assuming there's nothing there you want) and use the --recreate_cache option with the bulk loader. Until you get the part of thing straightened out, you should kill the loader when it gives you that message ("consider stopping..."). To delete everything from the feature table, do this:

  DELETE FROM feature;

Scott




Sent from my iPad

On Jan 21, 2014, at 1:59 AM, Francisco García Atienza <[hidden email]> wrote:

Hi Scott,

I've deleted the PO's ontology but I got the same warning:

./gmod_bulk_load_gff3.pl --dbname webapollochado --dbuser web_apollo_users_admin --dbpass web_apollo_users_admin --organism yeast --gfffile /home/francisco/webapollo/webapollo_sample/saccharomyces_cerevisiae.gff.sorted

"WARNING:
Unable to find a 'part_of' term in the relationship ontology;
It's absense indicates that there is something really wrong with the database.
Consider stopping and checking the state of your cvterm table.


Preparing data for inserting into the webapollochado database
(This may take a while ...)
couldn't find GO:0010551 's cvterm_id in cvterm table
couldn't find GO:0010551 's cvterm_id in cvterm table
Unable to find srcfeature chr01 in the database.
Perhaps you need to rerun your data load with the '--recreate_cache' option. at /usr/local/share/perl/5.14.2/Bio/GMOD/DB/Adapter.pm line 4603, <GEN0> line 4283.
Bio::GMOD::DB::Adapter::src_second_chance(Bio::GMOD::DB::Adapter=HASH(0x242ee38), Bio::SeqFeature::Annotated=HASH(0x4260078)) called at ./gmod_bulk_load_gff3.pl line 851

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..."


With a few lines from the gff3 file (Populus trichocarpa) that I want to load to the chado database I got load the data, I had to change a bit the file to the form 

Potri.001G000100 phytozome8_0 gene 1660 2502 . - . ID=Potri.001G000100;Name=Potri.001G000100

Before I had this

Chr01 phytozome8_0 gene 1660 2502 . - . ID=Potri.001G000100;Name=Potri.001G000100

and I got the error "Unable to find srcfeature Chr01 in the database", but still the same problem with ontologies: 

"WARNING:
Unable to find a 'part_of' term in the relationship ontology;
It's absense indicates that there is something really wrong with the database.
Consider stopping and checking the state of your cvterm table.


Preparing data for inserting into the webapollochado database
(This may take a while ...)
Skipping organism table since the load file is empty...
Skipping analysis table since the load file is empty...
Skipping db table since the load file is empty...
Skipping dbxref table since the load file is empty...
Skipping cv table since the load file is empty...
Skipping cvterm table since the load file is empty...
Loading data into feature table ...
Skipping featureloc table since the load file is empty...
Skipping feature_relationship table since the load file is empty...
Skipping featureprop table since the load file is empty...
Skipping feature_cvterm table since the load file is empty...
Loading data into synonym table ...
Loading data into feature_synonym table ...
Loading data into feature_dbxref table ...
Skipping analysisfeature table since the load file is empty...
Adding cvtermprop=MapReferenceType for 'gene' ...
Loading sequences (if any) ...

Done."

What do you think? 

/Francisco


2014/1/20 Scott Cain <[hidden email]>
Hi Francisco,

Ah, then I think we can blame the plant_ontology (well, to be fair, you can blame me, since I failed to anticipate that an ontology would provide their own "part_of").  The fix, as ugly as it is, is to remove PO's part_of:

  DELETE FROM cvterm WHERE cvterm_id = 95;

While you're at it, you should also check the derives_from term, as it will cause a similar problem.

Scott



On Mon, Jan 20, 2014 at 1:16 AM, Francisco García Atienza <[hidden email]> wrote:
Hi Scott,

Thank you for your answer. Yes, I loaded the Relationship Ontolgy and this is my result with the SQL query 

Select cvterm.*,cv.name from cvterm join cv using (cv_id) where cvterm.name = 'part_of'; 

cvterm_id cv_id name definition dbxref_id is_obsolete is_relationshiptype name








37 7 part_of
39 0 1 relationship
95 18 part_of
121 0 1 plant_ontology

/Francisco


2014/1/8 Scott Cain <[hidden email]>
Hi Francisco,

The message about not finding part_of is pretty important. Did you load the Relationship Ontology?  If so, what happens when you execute this command:

  Select cvterm.*,cv.name from cvterm join cv using cv_id where cvterm.name = 'part_of';

(I think that SQL is right, but I'm writing it on an iPad without a database to test against, but hopefully you get the idea.)

Scott


Sent from Mailbox for iPad


On Wed, Jan 8, 2014 at 10:42 AM, Francisco García Atienza <[hidden email]> wrote:

Hello,

I'm trying to use the Chado adapter from WebApollo but I get some errors, I've instantiated Chado following your guide at http://gmod.org/wiki/Chado and when I try to load some example in the Chado database doing this:

gmod_bulk_load_gff3.pl --organism yeast  --gfffile saccharomyces_cerevisiae.gff.sorted

(These are my parameters)
GMOD_ROOT=/usr/local/gmod
PERL5LIB=$PERL5LIB:/usr/local/bioperl/bioperl-live
CHADO_DB_NAME=webapollochado
CHADO_DB_USER=web_apollo_users_admin 
CHADO_DB_HOST=localhost
CHADO_DB_PORT=5432

 I get this error 

"WARNING:
Unable to find a 'part_of' term in the relationship ontology;
It's absence indicates that there is something really wrong with the database.
Consider stopping and checking the state of your cvterm table.


Preparing data for inserting into the webapollochado database
(This may take a while ...)
Can't locate object method "get_Annotations" via package "Bio::SeqFeature::Annotated" at /usr/local/share/perl/5.14.2/Bio/SeqFeature/Annotated.pm line 287, <GEN0> line 2.

Abnormal termination, trying to clean up...

Trying to remove the run lock (so that --remove_lock won't be needed)...
Exiting..."


Any ideas what could be wrong? Thank you.

Regards, 

/Francisco.





--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     <a href="tel:216-392-3087" value="+12163923087" target="_blank">216-392-3087
Ontario Institute for Cancer Research



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Learn Why More Businesses Are Choosing CenturyLink Cloud For
Critical Workloads, Development Environments & Everything In Between.
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http://pubads.g.doubleclick.net/gampad/clk?id=119420431&iu=/4140/ostg.clktrk
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Re: Object method "get_Annotations" error

Scott Cain
In reply to this post by Francisco García Atienza
Hi Francisco,

The other thing the would be good if you can do it is a database dump with pg_dump; that might make it easier to replicate what is happening. 

Thanks,
Scott


Sent from my iPhone

On Jan 22, 2014, at 1:37 AM, Francisco García Atienza <[hidden email]> wrote:

Hi Scott,

Sorry to say but I still have the same problem with only one part_of row (relationship ontology's). I don't know what can cause this warning.

My apologies for my ignorance but is there any instance of chado already created to which I can add my organism? 

Regards,

/Francisco.




2014/1/21 Scott Cain <[hidden email]>
Resenting to the mailing list (how did I manage to misspell it?)

Sent from my iPad

On Jan 21, 2014, at 9:05 AM, Scott Cain <[hidden email]> wrote:

Hi Francisco,

Please keep the schema mailing list cc'ed (if I'm the one that forgot, sorry). 

So you're sure that part_of term is gone?  (Ie, rerunning that query only gives you one row?)

Also, this is unrelated to your current problem, but the fact that it completed a load and put data in the feature table is going to cause you problems. To clean up, delete everything from the feature table (assuming there's nothing there you want) and use the --recreate_cache option with the bulk loader. Until you get the part of thing straightened out, you should kill the loader when it gives you that message ("consider stopping..."). To delete everything from the feature table, do this:

  DELETE FROM feature;

Scott




Sent from my iPad

On Jan 21, 2014, at 1:59 AM, Francisco García Atienza <[hidden email]> wrote:

Hi Scott,

I've deleted the PO's ontology but I got the same warning:

./gmod_bulk_load_gff3.pl --dbname webapollochado --dbuser web_apollo_users_admin --dbpass web_apollo_users_admin --organism yeast --gfffile /home/francisco/webapollo/webapollo_sample/saccharomyces_cerevisiae.gff.sorted

"WARNING:
Unable to find a 'part_of' term in the relationship ontology;
It's absense indicates that there is something really wrong with the database.
Consider stopping and checking the state of your cvterm table.


Preparing data for inserting into the webapollochado database
(This may take a while ...)
couldn't find GO:0010551 's cvterm_id in cvterm table
couldn't find GO:0010551 's cvterm_id in cvterm table
Unable to find srcfeature chr01 in the database.
Perhaps you need to rerun your data load with the '--recreate_cache' option. at /usr/local/share/perl/5.14.2/Bio/GMOD/DB/Adapter.pm line 4603, <GEN0> line 4283.
Bio::GMOD::DB::Adapter::src_second_chance(Bio::GMOD::DB::Adapter=HASH(0x242ee38), Bio::SeqFeature::Annotated=HASH(0x4260078)) called at ./gmod_bulk_load_gff3.pl line 851

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..."


With a few lines from the gff3 file (Populus trichocarpa) that I want to load to the chado database I got load the data, I had to change a bit the file to the form 

Potri.001G000100 phytozome8_0 gene 1660 2502 . - . ID=Potri.001G000100;Name=Potri.001G000100

Before I had this

Chr01 phytozome8_0 gene 1660 2502 . - . ID=Potri.001G000100;Name=Potri.001G000100

and I got the error "Unable to find srcfeature Chr01 in the database", but still the same problem with ontologies: 

"WARNING:
Unable to find a 'part_of' term in the relationship ontology;
It's absense indicates that there is something really wrong with the database.
Consider stopping and checking the state of your cvterm table.


Preparing data for inserting into the webapollochado database
(This may take a while ...)
Skipping organism table since the load file is empty...
Skipping analysis table since the load file is empty...
Skipping db table since the load file is empty...
Skipping dbxref table since the load file is empty...
Skipping cv table since the load file is empty...
Skipping cvterm table since the load file is empty...
Loading data into feature table ...
Skipping featureloc table since the load file is empty...
Skipping feature_relationship table since the load file is empty...
Skipping featureprop table since the load file is empty...
Skipping feature_cvterm table since the load file is empty...
Loading data into synonym table ...
Loading data into feature_synonym table ...
Loading data into feature_dbxref table ...
Skipping analysisfeature table since the load file is empty...
Adding cvtermprop=MapReferenceType for 'gene' ...
Loading sequences (if any) ...

Done."

What do you think? 

/Francisco


2014/1/20 Scott Cain <[hidden email]>
Hi Francisco,

Ah, then I think we can blame the plant_ontology (well, to be fair, you can blame me, since I failed to anticipate that an ontology would provide their own "part_of").  The fix, as ugly as it is, is to remove PO's part_of:

  DELETE FROM cvterm WHERE cvterm_id = 95;

While you're at it, you should also check the derives_from term, as it will cause a similar problem.

Scott



On Mon, Jan 20, 2014 at 1:16 AM, Francisco García Atienza <[hidden email]> wrote:
Hi Scott,

Thank you for your answer. Yes, I loaded the Relationship Ontolgy and this is my result with the SQL query 

Select cvterm.*,cv.name from cvterm join cv using (cv_id) where cvterm.name = 'part_of'; 

cvterm_id cv_id name definition dbxref_id is_obsolete is_relationshiptype name








37 7 part_of
39 0 1 relationship
95 18 part_of
121 0 1 plant_ontology

/Francisco


2014/1/8 Scott Cain <[hidden email]>
Hi Francisco,

The message about not finding part_of is pretty important. Did you load the Relationship Ontology?  If so, what happens when you execute this command:

  Select cvterm.*,cv.name from cvterm join cv using cv_id where cvterm.name = 'part_of';

(I think that SQL is right, but I'm writing it on an iPad without a database to test against, but hopefully you get the idea.)

Scott


Sent from Mailbox for iPad


On Wed, Jan 8, 2014 at 10:42 AM, Francisco García Atienza <[hidden email]> wrote:

Hello,

I'm trying to use the Chado adapter from WebApollo but I get some errors, I've instantiated Chado following your guide at http://gmod.org/wiki/Chado and when I try to load some example in the Chado database doing this:

gmod_bulk_load_gff3.pl --organism yeast  --gfffile saccharomyces_cerevisiae.gff.sorted

(These are my parameters)
GMOD_ROOT=/usr/local/gmod
PERL5LIB=$PERL5LIB:/usr/local/bioperl/bioperl-live
CHADO_DB_NAME=webapollochado
CHADO_DB_USER=web_apollo_users_admin 
CHADO_DB_HOST=localhost
CHADO_DB_PORT=5432

 I get this error 

"WARNING:
Unable to find a 'part_of' term in the relationship ontology;
It's absence indicates that there is something really wrong with the database.
Consider stopping and checking the state of your cvterm table.


Preparing data for inserting into the webapollochado database
(This may take a while ...)
Can't locate object method "get_Annotations" via package "Bio::SeqFeature::Annotated" at /usr/local/share/perl/5.14.2/Bio/SeqFeature/Annotated.pm line 287, <GEN0> line 2.

Abnormal termination, trying to clean up...

Trying to remove the run lock (so that --remove_lock won't be needed)...
Exiting..."


Any ideas what could be wrong? Thank you.

Regards, 

/Francisco.





--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     <a href="tel:216-392-3087" value="+12163923087" target="_blank">216-392-3087
Ontario Institute for Cancer Research



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Re: Object method "get_Annotations" error

Francisco García Atienza
Hi Scott,

Yes, I have more than one chado database but I'm pretty sure I'm loading the one I've deleted the part_of and derives_from and that this is the default chado db.

You can get the files I'm using in:


I've created a dump (test_dump.sql) and the gff3 files are example.gff3 or scf1117875582023.gff, both gives me the same warning message.

I'm also using these commands:

./gmod_bulk_load_gff3.pl --noexon --analysis -g /home/francisco/webapollo/webapollo_sample/pyu_data/scf1117875582023.gff
./gmod_bulk_load_gff3.pl --noexon --recreate_cache --organism poplar --gfffile /home/francisco/webapollo/webapollo_sample/example.gff3

Maybe, like you said, the problem is that there is some conflict with a previous chado instance related to Gbrowse, I don't know.

We are at the same point, I get load the data (I've tried last time with scf1117875582023.gff) but I get also the warning message. 

I hope you can help me to find the mistake. Thank you.

/Francisco. 


2014-01-23 Scott Cain <[hidden email]>
Hi Francisco,

The other thing the would be good if you can do it is a database dump with pg_dump; that might make it easier to replicate what is happening. 

Thanks,
Scott


Sent from my iPhone

On Jan 22, 2014, at 1:37 AM, Francisco García Atienza <[hidden email]> wrote:

Hi Scott,

Sorry to say but I still have the same problem with only one part_of row (relationship ontology's). I don't know what can cause this warning.

My apologies for my ignorance but is there any instance of chado already created to which I can add my organism? 

Regards,

/Francisco.




2014/1/21 Scott Cain <[hidden email]>
Resenting to the mailing list (how did I manage to misspell it?)

Sent from my iPad

On Jan 21, 2014, at 9:05 AM, Scott Cain <[hidden email]> wrote:

Hi Francisco,

Please keep the schema mailing list cc'ed (if I'm the one that forgot, sorry). 

So you're sure that part_of term is gone?  (Ie, rerunning that query only gives you one row?)

Also, this is unrelated to your current problem, but the fact that it completed a load and put data in the feature table is going to cause you problems. To clean up, delete everything from the feature table (assuming there's nothing there you want) and use the --recreate_cache option with the bulk loader. Until you get the part of thing straightened out, you should kill the loader when it gives you that message ("consider stopping..."). To delete everything from the feature table, do this:

  DELETE FROM feature;

Scott




Sent from my iPad

On Jan 21, 2014, at 1:59 AM, Francisco García Atienza <[hidden email]> wrote:

Hi Scott,

I've deleted the PO's ontology but I got the same warning:

./gmod_bulk_load_gff3.pl --dbname webapollochado --dbuser web_apollo_users_admin --dbpass web_apollo_users_admin --organism yeast --gfffile /home/francisco/webapollo/webapollo_sample/saccharomyces_cerevisiae.gff.sorted

"WARNING:
Unable to find a 'part_of' term in the relationship ontology;
It's absense indicates that there is something really wrong with the database.
Consider stopping and checking the state of your cvterm table.


Preparing data for inserting into the webapollochado database
(This may take a while ...)
couldn't find GO:0010551 's cvterm_id in cvterm table
couldn't find GO:0010551 's cvterm_id in cvterm table
Unable to find srcfeature chr01 in the database.
Perhaps you need to rerun your data load with the '--recreate_cache' option. at /usr/local/share/perl/5.14.2/Bio/GMOD/DB/Adapter.pm line 4603, <GEN0> line 4283.
Bio::GMOD::DB::Adapter::src_second_chance(Bio::GMOD::DB::Adapter=HASH(0x242ee38), Bio::SeqFeature::Annotated=HASH(0x4260078)) called at ./gmod_bulk_load_gff3.pl line 851

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..."


With a few lines from the gff3 file (Populus trichocarpa) that I want to load to the chado database I got load the data, I had to change a bit the file to the form 

Potri.001G000100 phytozome8_0 gene 1660 2502 . - . ID=Potri.001G000100;Name=Potri.001G000100

Before I had this

Chr01 phytozome8_0 gene 1660 2502 . - . ID=Potri.001G000100;Name=Potri.001G000100

and I got the error "Unable to find srcfeature Chr01 in the database", but still the same problem with ontologies: 

"WARNING:
Unable to find a 'part_of' term in the relationship ontology;
It's absense indicates that there is something really wrong with the database.
Consider stopping and checking the state of your cvterm table.


Preparing data for inserting into the webapollochado database
(This may take a while ...)
Skipping organism table since the load file is empty...
Skipping analysis table since the load file is empty...
Skipping db table since the load file is empty...
Skipping dbxref table since the load file is empty...
Skipping cv table since the load file is empty...
Skipping cvterm table since the load file is empty...
Loading data into feature table ...
Skipping featureloc table since the load file is empty...
Skipping feature_relationship table since the load file is empty...
Skipping featureprop table since the load file is empty...
Skipping feature_cvterm table since the load file is empty...
Loading data into synonym table ...
Loading data into feature_synonym table ...
Loading data into feature_dbxref table ...
Skipping analysisfeature table since the load file is empty...
Adding cvtermprop=MapReferenceType for 'gene' ...
Loading sequences (if any) ...

Done."

What do you think? 

/Francisco


2014/1/20 Scott Cain <[hidden email]>
Hi Francisco,

Ah, then I think we can blame the plant_ontology (well, to be fair, you can blame me, since I failed to anticipate that an ontology would provide their own "part_of").  The fix, as ugly as it is, is to remove PO's part_of:

  DELETE FROM cvterm WHERE cvterm_id = 95;

While you're at it, you should also check the derives_from term, as it will cause a similar problem.

Scott



On Mon, Jan 20, 2014 at 1:16 AM, Francisco García Atienza <[hidden email]> wrote:
Hi Scott,

Thank you for your answer. Yes, I loaded the Relationship Ontolgy and this is my result with the SQL query 

Select cvterm.*,cv.name from cvterm join cv using (cv_id) where cvterm.name = 'part_of'; 

cvterm_id cv_id name definition dbxref_id is_obsolete is_relationshiptype name








37 7 part_of
39 0 1 relationship
95 18 part_of
121 0 1 plant_ontology

/Francisco


2014/1/8 Scott Cain <[hidden email]>
Hi Francisco,

The message about not finding part_of is pretty important. Did you load the Relationship Ontology?  If so, what happens when you execute this command:

  Select cvterm.*,cv.name from cvterm join cv using cv_id where cvterm.name = 'part_of';

(I think that SQL is right, but I'm writing it on an iPad without a database to test against, but hopefully you get the idea.)

Scott


Sent from Mailbox for iPad


On Wed, Jan 8, 2014 at 10:42 AM, Francisco García Atienza <[hidden email]> wrote:

Hello,

I'm trying to use the Chado adapter from WebApollo but I get some errors, I've instantiated Chado following your guide at http://gmod.org/wiki/Chado and when I try to load some example in the Chado database doing this:

gmod_bulk_load_gff3.pl --organism yeast  --gfffile saccharomyces_cerevisiae.gff.sorted

(These are my parameters)
GMOD_ROOT=/usr/local/gmod
PERL5LIB=$PERL5LIB:/usr/local/bioperl/bioperl-live
CHADO_DB_NAME=webapollochado
CHADO_DB_USER=web_apollo_users_admin 
CHADO_DB_HOST=localhost
CHADO_DB_PORT=5432

 I get this error 

"WARNING:
Unable to find a 'part_of' term in the relationship ontology;
It's absence indicates that there is something really wrong with the database.
Consider stopping and checking the state of your cvterm table.


Preparing data for inserting into the webapollochado database
(This may take a while ...)
Can't locate object method "get_Annotations" via package "Bio::SeqFeature::Annotated" at /usr/local/share/perl/5.14.2/Bio/SeqFeature/Annotated.pm line 287, <GEN0> line 2.

Abnormal termination, trying to clean up...

Trying to remove the run lock (so that --remove_lock won't be needed)...
Exiting..."


Any ideas what could be wrong? Thank you.

Regards, 

/Francisco.





--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     <a href="tel:216-392-3087" value="+12163923087" target="_blank">216-392-3087
Ontario Institute for Cancer Research




------------------------------------------------------------------------------
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Learn Why More Businesses Are Choosing CenturyLink Cloud For
Critical Workloads, Development Environments & Everything In Between.
Get a Quote or Start a Free Trial Today.
http://pubads.g.doubleclick.net/gampad/clk?id=119420431&iu=/4140/ostg.clktrk
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Re: Object method "get_Annotations" error

Francisco García Atienza
Hi Scott,

I am also sending you the steps I've follow to install Chado. 

 
CHADO INSTALLATION
------------------------------------


PREREQUISITES

* PostgreSQL version 9.1

* Postgres user with create/delete db permissions (francisco)

* pg_hba.conf -- configured

* bioperl-live -- version 1.6.923 installed in /usr/local/bioperl

* go-perl installed with CPAN

* ant installed in /usr/bin/ant

* Perl modules installed via CPAN

INSTALL THE CHADO SCHEMA

- Exporting environment variables in .bashrc

GMOD_ROOT=/usr/local/gmod 

CHADO_DB_NAME=webapollochado 

CHADO_DB_USERNAME=francisco 

CHADO_DB_PASSWORD=xxxxxx 

CHADO_DB_HOST=localhost 

CHADO_DB_PORT=5432 

- Create the Makefile and other configuration files 

$ perl Makefile.PL 

*   What database server will you be using? [PostgreSQL]

*   What is the Chado database name? [webapollochado]

*   What is the database username? [francisco]

*   What is the password for 'francisco'?

*   What is the database host? [localhost]

*   What is your database port? [5432]

*   Where shall downloaded ontologies go? [./tmp]

*   What is the default organism (common name, or "none")? poplar

*   Do you want to make this the default chado instance? [y]

- Make the schema and Install the scripts and modules

$ make

$ sudo make install

- Install the schema

$ make load_schema

        - Insert baseline data

$ make prepdb

- Load ontologies

$ make ontologies

[Relationship Ontology, Sequence Ontology, Gene Ontology, and Chado Features loaded.]


BACKUP

$ pg_dump webapollochado  >  webapollochado_dump.sql


LOADING DATA

./gmod_bulk_load_gff3.pl --organism poplar --gfffile example.gff3


#############################################################################

All the configuration steps seems to be all right but I still have the same message warning me that something is really wrong with the database. It is a hard thing that Chado schema!

I hope you can help me, now that I've sent you the dump, to find what can cause this problem.


Regards.

/Francisco




















2014-01-27 Francisco García Atienza <[hidden email]>:
Hi Scott,

Yes, I have more than one chado database but I'm pretty sure I'm loading the one I've deleted the part_of and derives_from and that this is the default chado db.

You can get the files I'm using in:


I've created a dump (test_dump.sql) and the gff3 files are example.gff3 or scf1117875582023.gff, both gives me the same warning message.

I'm also using these commands:

./gmod_bulk_load_gff3.pl --noexon --analysis -g /home/francisco/webapollo/webapollo_sample/pyu_data/scf1117875582023.gff
./gmod_bulk_load_gff3.pl --noexon --recreate_cache --organism poplar --gfffile /home/francisco/webapollo/webapollo_sample/example.gff3

Maybe, like you said, the problem is that there is some conflict with a previous chado instance related to Gbrowse, I don't know.

We are at the same point, I get load the data (I've tried last time with scf1117875582023.gff) but I get also the warning message. 

I hope you can help me to find the mistake. Thank you.

/Francisco. 


2014-01-23 Scott Cain <[hidden email]>

Hi Francisco,

The other thing the would be good if you can do it is a database dump with pg_dump; that might make it easier to replicate what is happening. 

Thanks,
Scott


Sent from my iPhone

On Jan 22, 2014, at 1:37 AM, Francisco García Atienza <[hidden email]> wrote:

Hi Scott,

Sorry to say but I still have the same problem with only one part_of row (relationship ontology's). I don't know what can cause this warning.

My apologies for my ignorance but is there any instance of chado already created to which I can add my organism? 

Regards,

/Francisco.




2014/1/21 Scott Cain <[hidden email]>
Resenting to the mailing list (how did I manage to misspell it?)

Sent from my iPad

On Jan 21, 2014, at 9:05 AM, Scott Cain <[hidden email]> wrote:

Hi Francisco,

Please keep the schema mailing list cc'ed (if I'm the one that forgot, sorry). 

So you're sure that part_of term is gone?  (Ie, rerunning that query only gives you one row?)

Also, this is unrelated to your current problem, but the fact that it completed a load and put data in the feature table is going to cause you problems. To clean up, delete everything from the feature table (assuming there's nothing there you want) and use the --recreate_cache option with the bulk loader. Until you get the part of thing straightened out, you should kill the loader when it gives you that message ("consider stopping..."). To delete everything from the feature table, do this:

  DELETE FROM feature;

Scott




Sent from my iPad

On Jan 21, 2014, at 1:59 AM, Francisco García Atienza <[hidden email]> wrote:

Hi Scott,

I've deleted the PO's ontology but I got the same warning:

./gmod_bulk_load_gff3.pl --dbname webapollochado --dbuser web_apollo_users_admin --dbpass web_apollo_users_admin --organism yeast --gfffile /home/francisco/webapollo/webapollo_sample/saccharomyces_cerevisiae.gff.sorted

"WARNING:
Unable to find a 'part_of' term in the relationship ontology;
It's absense indicates that there is something really wrong with the database.
Consider stopping and checking the state of your cvterm table.


Preparing data for inserting into the webapollochado database
(This may take a while ...)
couldn't find GO:0010551 's cvterm_id in cvterm table
couldn't find GO:0010551 's cvterm_id in cvterm table
Unable to find srcfeature chr01 in the database.
Perhaps you need to rerun your data load with the '--recreate_cache' option. at /usr/local/share/perl/5.14.2/Bio/GMOD/DB/Adapter.pm line 4603, <GEN0> line 4283.
Bio::GMOD::DB::Adapter::src_second_chance(Bio::GMOD::DB::Adapter=HASH(0x242ee38), Bio::SeqFeature::Annotated=HASH(0x4260078)) called at ./gmod_bulk_load_gff3.pl line 851

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..."


With a few lines from the gff3 file (Populus trichocarpa) that I want to load to the chado database I got load the data, I had to change a bit the file to the form 

Potri.001G000100 phytozome8_0 gene 1660 2502 . - . ID=Potri.001G000100;Name=Potri.001G000100

Before I had this

Chr01 phytozome8_0 gene 1660 2502 . - . ID=Potri.001G000100;Name=Potri.001G000100

and I got the error "Unable to find srcfeature Chr01 in the database", but still the same problem with ontologies: 

"WARNING:
Unable to find a 'part_of' term in the relationship ontology;
It's absense indicates that there is something really wrong with the database.
Consider stopping and checking the state of your cvterm table.


Preparing data for inserting into the webapollochado database
(This may take a while ...)
Skipping organism table since the load file is empty...
Skipping analysis table since the load file is empty...
Skipping db table since the load file is empty...
Skipping dbxref table since the load file is empty...
Skipping cv table since the load file is empty...
Skipping cvterm table since the load file is empty...
Loading data into feature table ...
Skipping featureloc table since the load file is empty...
Skipping feature_relationship table since the load file is empty...
Skipping featureprop table since the load file is empty...
Skipping feature_cvterm table since the load file is empty...
Loading data into synonym table ...
Loading data into feature_synonym table ...
Loading data into feature_dbxref table ...
Skipping analysisfeature table since the load file is empty...
Adding cvtermprop=MapReferenceType for 'gene' ...
Loading sequences (if any) ...

Done."

What do you think? 

/Francisco


2014/1/20 Scott Cain <[hidden email]>
Hi Francisco,

Ah, then I think we can blame the plant_ontology (well, to be fair, you can blame me, since I failed to anticipate that an ontology would provide their own "part_of").  The fix, as ugly as it is, is to remove PO's part_of:

  DELETE FROM cvterm WHERE cvterm_id = 95;

While you're at it, you should also check the derives_from term, as it will cause a similar problem.

Scott



On Mon, Jan 20, 2014 at 1:16 AM, Francisco García Atienza <[hidden email]> wrote:
Hi Scott,

Thank you for your answer. Yes, I loaded the Relationship Ontolgy and this is my result with the SQL query 

Select cvterm.*,cv.name from cvterm join cv using (cv_id) where cvterm.name = 'part_of'; 

cvterm_id cv_id name definition dbxref_id is_obsolete is_relationshiptype name








37 7 part_of
39 0 1 relationship
95 18 part_of
121 0 1 plant_ontology

/Francisco


2014/1/8 Scott Cain <[hidden email]>
Hi Francisco,

The message about not finding part_of is pretty important. Did you load the Relationship Ontology?  If so, what happens when you execute this command:

  Select cvterm.*,cv.name from cvterm join cv using cv_id where cvterm.name = 'part_of';

(I think that SQL is right, but I'm writing it on an iPad without a database to test against, but hopefully you get the idea.)

Scott


Sent from Mailbox for iPad


On Wed, Jan 8, 2014 at 10:42 AM, Francisco García Atienza <[hidden email]> wrote:

Hello,

I'm trying to use the Chado adapter from WebApollo but I get some errors, I've instantiated Chado following your guide at http://gmod.org/wiki/Chado and when I try to load some example in the Chado database doing this:

gmod_bulk_load_gff3.pl --organism yeast  --gfffile saccharomyces_cerevisiae.gff.sorted

(These are my parameters)
GMOD_ROOT=/usr/local/gmod
PERL5LIB=$PERL5LIB:/usr/local/bioperl/bioperl-live
CHADO_DB_NAME=webapollochado
CHADO_DB_USER=web_apollo_users_admin 
CHADO_DB_HOST=localhost
CHADO_DB_PORT=5432

 I get this error 

"WARNING:
Unable to find a 'part_of' term in the relationship ontology;
It's absence indicates that there is something really wrong with the database.
Consider stopping and checking the state of your cvterm table.


Preparing data for inserting into the webapollochado database
(This may take a while ...)
Can't locate object method "get_Annotations" via package "Bio::SeqFeature::Annotated" at /usr/local/share/perl/5.14.2/Bio/SeqFeature/Annotated.pm line 287, <GEN0> line 2.

Abnormal termination, trying to clean up...

Trying to remove the run lock (so that --remove_lock won't be needed)...
Exiting..."


Any ideas what could be wrong? Thank you.

Regards, 

/Francisco.





--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     <a href="tel:216-392-3087" value="+12163923087" target="_blank">216-392-3087
Ontario Institute for Cancer Research





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Re: Object method "get_Annotations" error

Scott Cain
Hi Francisco,

I've been traveling the last few days, but I will take a look at this over the weekend.

Scott



On Fri, Jan 31, 2014 at 7:08 AM, Francisco García Atienza <[hidden email]> wrote:
Hi Scott,

I am also sending you the steps I've follow to install Chado. 

 
CHADO INSTALLATION
------------------------------------


PREREQUISITES

* PostgreSQL version 9.1

* Postgres user with create/delete db permissions (francisco)

* pg_hba.conf -- configured

* bioperl-live -- version 1.6.923 installed in /usr/local/bioperl

* go-perl installed with CPAN

* ant installed in /usr/bin/ant

* Perl modules installed via CPAN

INSTALL THE CHADO SCHEMA

- Exporting environment variables in .bashrc

GMOD_ROOT=/usr/local/gmod 

CHADO_DB_NAME=webapollochado 

CHADO_DB_USERNAME=francisco 

CHADO_DB_PASSWORD=xxxxxx 

CHADO_DB_HOST=localhost 

CHADO_DB_PORT=5432 

- Create the Makefile and other configuration files 

$ perl Makefile.PL 

*   What database server will you be using? [PostgreSQL]

*   What is the Chado database name? [webapollochado]

*   What is the database username? [francisco]

*   What is the password for 'francisco'?

*   What is the database host? [localhost]

*   What is your database port? [5432]

*   Where shall downloaded ontologies go? [./tmp]

*   What is the default organism (common name, or "none")? poplar

*   Do you want to make this the default chado instance? [y]

- Make the schema and Install the scripts and modules

$ make

$ sudo make install

- Install the schema

$ make load_schema

        - Insert baseline data

$ make prepdb

- Load ontologies

$ make ontologies

[Relationship Ontology, Sequence Ontology, Gene Ontology, and Chado Features loaded.]


BACKUP

$ pg_dump webapollochado  >  webapollochado_dump.sql


LOADING DATA

./gmod_bulk_load_gff3.pl --organism poplar --gfffile example.gff3


#############################################################################

All the configuration steps seems to be all right but I still have the same message warning me that something is really wrong with the database. It is a hard thing that Chado schema!

I hope you can help me, now that I've sent you the dump, to find what can cause this problem.


Regards.

/Francisco




















2014-01-27 Francisco García Atienza <[hidden email]>:

Hi Scott,

Yes, I have more than one chado database but I'm pretty sure I'm loading the one I've deleted the part_of and derives_from and that this is the default chado db.

You can get the files I'm using in:


I've created a dump (test_dump.sql) and the gff3 files are example.gff3 or scf1117875582023.gff, both gives me the same warning message.

I'm also using these commands:

./gmod_bulk_load_gff3.pl --noexon --analysis -g /home/francisco/webapollo/webapollo_sample/pyu_data/scf1117875582023.gff
./gmod_bulk_load_gff3.pl --noexon --recreate_cache --organism poplar --gfffile /home/francisco/webapollo/webapollo_sample/example.gff3

Maybe, like you said, the problem is that there is some conflict with a previous chado instance related to Gbrowse, I don't know.

We are at the same point, I get load the data (I've tried last time with scf1117875582023.gff) but I get also the warning message. 

I hope you can help me to find the mistake. Thank you.

/Francisco. 


2014-01-23 Scott Cain <[hidden email]>

Hi Francisco,

The other thing the would be good if you can do it is a database dump with pg_dump; that might make it easier to replicate what is happening. 

Thanks,
Scott


Sent from my iPhone

On Jan 22, 2014, at 1:37 AM, Francisco García Atienza <[hidden email]> wrote:

Hi Scott,

Sorry to say but I still have the same problem with only one part_of row (relationship ontology's). I don't know what can cause this warning.

My apologies for my ignorance but is there any instance of chado already created to which I can add my organism? 

Regards,

/Francisco.




2014/1/21 Scott Cain <[hidden email]>
Resenting to the mailing list (how did I manage to misspell it?)

Sent from my iPad

On Jan 21, 2014, at 9:05 AM, Scott Cain <[hidden email]> wrote:

Hi Francisco,

Please keep the schema mailing list cc'ed (if I'm the one that forgot, sorry). 

So you're sure that part_of term is gone?  (Ie, rerunning that query only gives you one row?)

Also, this is unrelated to your current problem, but the fact that it completed a load and put data in the feature table is going to cause you problems. To clean up, delete everything from the feature table (assuming there's nothing there you want) and use the --recreate_cache option with the bulk loader. Until you get the part of thing straightened out, you should kill the loader when it gives you that message ("consider stopping..."). To delete everything from the feature table, do this:

  DELETE FROM feature;

Scott




Sent from my iPad

On Jan 21, 2014, at 1:59 AM, Francisco García Atienza <[hidden email]> wrote:

Hi Scott,

I've deleted the PO's ontology but I got the same warning:

./gmod_bulk_load_gff3.pl --dbname webapollochado --dbuser web_apollo_users_admin --dbpass web_apollo_users_admin --organism yeast --gfffile /home/francisco/webapollo/webapollo_sample/saccharomyces_cerevisiae.gff.sorted

"WARNING:
Unable to find a 'part_of' term in the relationship ontology;
It's absense indicates that there is something really wrong with the database.
Consider stopping and checking the state of your cvterm table.


Preparing data for inserting into the webapollochado database
(This may take a while ...)
couldn't find GO:0010551 's cvterm_id in cvterm table
couldn't find GO:0010551 's cvterm_id in cvterm table
Unable to find srcfeature chr01 in the database.
Perhaps you need to rerun your data load with the '--recreate_cache' option. at /usr/local/share/perl/5.14.2/Bio/GMOD/DB/Adapter.pm line 4603, <GEN0> line 4283.
Bio::GMOD::DB::Adapter::src_second_chance(Bio::GMOD::DB::Adapter=HASH(0x242ee38), Bio::SeqFeature::Annotated=HASH(0x4260078)) called at ./gmod_bulk_load_gff3.pl line 851

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..."


With a few lines from the gff3 file (Populus trichocarpa) that I want to load to the chado database I got load the data, I had to change a bit the file to the form 

Potri.001G000100 phytozome8_0 gene 1660 2502 . - . ID=Potri.001G000100;Name=Potri.001G000100

Before I had this

Chr01 phytozome8_0 gene 1660 2502 . - . ID=Potri.001G000100;Name=Potri.001G000100

and I got the error "Unable to find srcfeature Chr01 in the database", but still the same problem with ontologies: 

"WARNING:
Unable to find a 'part_of' term in the relationship ontology;
It's absense indicates that there is something really wrong with the database.
Consider stopping and checking the state of your cvterm table.


Preparing data for inserting into the webapollochado database
(This may take a while ...)
Skipping organism table since the load file is empty...
Skipping analysis table since the load file is empty...
Skipping db table since the load file is empty...
Skipping dbxref table since the load file is empty...
Skipping cv table since the load file is empty...
Skipping cvterm table since the load file is empty...
Loading data into feature table ...
Skipping featureloc table since the load file is empty...
Skipping feature_relationship table since the load file is empty...
Skipping featureprop table since the load file is empty...
Skipping feature_cvterm table since the load file is empty...
Loading data into synonym table ...
Loading data into feature_synonym table ...
Loading data into feature_dbxref table ...
Skipping analysisfeature table since the load file is empty...
Adding cvtermprop=MapReferenceType for 'gene' ...
Loading sequences (if any) ...

Done."

What do you think? 

/Francisco


2014/1/20 Scott Cain <[hidden email]>
Hi Francisco,

Ah, then I think we can blame the plant_ontology (well, to be fair, you can blame me, since I failed to anticipate that an ontology would provide their own "part_of").  The fix, as ugly as it is, is to remove PO's part_of:

  DELETE FROM cvterm WHERE cvterm_id = 95;

While you're at it, you should also check the derives_from term, as it will cause a similar problem.

Scott



On Mon, Jan 20, 2014 at 1:16 AM, Francisco García Atienza <[hidden email]> wrote:
Hi Scott,

Thank you for your answer. Yes, I loaded the Relationship Ontolgy and this is my result with the SQL query 

Select cvterm.*,cv.name from cvterm join cv using (cv_id) where cvterm.name = 'part_of'; 

cvterm_id cv_id name definition dbxref_id is_obsolete is_relationshiptype name








37 7 part_of
39 0 1 relationship
95 18 part_of
121 0 1 plant_ontology

/Francisco


2014/1/8 Scott Cain <[hidden email]>
Hi Francisco,

The message about not finding part_of is pretty important. Did you load the Relationship Ontology?  If so, what happens when you execute this command:

  Select cvterm.*,cv.name from cvterm join cv using cv_id where cvterm.name = 'part_of';

(I think that SQL is right, but I'm writing it on an iPad without a database to test against, but hopefully you get the idea.)

Scott


Sent from Mailbox for iPad


On Wed, Jan 8, 2014 at 10:42 AM, Francisco García Atienza <[hidden email]> wrote:

Hello,

I'm trying to use the Chado adapter from WebApollo but I get some errors, I've instantiated Chado following your guide at http://gmod.org/wiki/Chado and when I try to load some example in the Chado database doing this:

gmod_bulk_load_gff3.pl --organism yeast  --gfffile saccharomyces_cerevisiae.gff.sorted

(These are my parameters)
GMOD_ROOT=/usr/local/gmod
PERL5LIB=$PERL5LIB:/usr/local/bioperl/bioperl-live
CHADO_DB_NAME=webapollochado
CHADO_DB_USER=web_apollo_users_admin 
CHADO_DB_HOST=localhost
CHADO_DB_PORT=5432

 I get this error 

"WARNING:
Unable to find a 'part_of' term in the relationship ontology;
It's absence indicates that there is something really wrong with the database.
Consider stopping and checking the state of your cvterm table.


Preparing data for inserting into the webapollochado database
(This may take a while ...)
Can't locate object method "get_Annotations" via package "Bio::SeqFeature::Annotated" at /usr/local/share/perl/5.14.2/Bio/SeqFeature/Annotated.pm line 287, <GEN0> line 2.

Abnormal termination, trying to clean up...

Trying to remove the run lock (so that --remove_lock won't be needed)...
Exiting..."


Any ideas what could be wrong? Thank you.

Regards, 

/Francisco.





--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     <a href="tel:216-392-3087" value="+12163923087" target="_blank">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

------------------------------------------------------------------------------
WatchGuard Dimension instantly turns raw network data into actionable
security intelligence. It gives you real-time visual feedback on key
security issues and trends.  Skip the complicated setup - simply import
a virtual appliance and go from zero to informed in seconds.
http://pubads.g.doubleclick.net/gampad/clk?id=123612991&iu=/4140/ostg.clktrk
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Re: Object method "get_Annotations" error

Francisco García Atienza
Hi Scott,

I'm glad to say that I've fixed the problem, like I told you I have several Chado instances and I tried to put the last one (webapollo) as not default and I don't get now the warning message.

Anyway, I'd like to ask you about another error. I'm trying to load this gff3 file 


 (First line...)

Chr01 phytozome8_0 gene 1660 2502 . - . ID=Potri.001G000100;Name=Potri.001G000100

but I get this error "Unable to find srcfeature Chr01 in the database".

I've read that this is because you need to indentify on what sequence/feature the features in the GFF file 
reside. I changed the gff3 file to this:

Potri.001G000100 phytozome8_0 gene 1660 2502 . - . ID=Potri.001G000100;Name=Potri.001G000100

But now I get this error "Unable to find srcfeature Potri.001G000100.1 in the database"

Potri.001G000100.1 phytozome8_0 mRNA 1660 2502 . - . ID=PAC:27043735;Name=Potri.001G000100.1;pacid=27043735;longest=1;Parent=Potri.001G000100

What would be the correct form to load the mRNA? Thank you.

Regards,

/Francisco






2014-01-31 Scott Cain <[hidden email]>:
Hi Francisco,

I've been traveling the last few days, but I will take a look at this over the weekend.

Scott



On Fri, Jan 31, 2014 at 7:08 AM, Francisco García Atienza <[hidden email]> wrote:
Hi Scott,

I am also sending you the steps I've follow to install Chado. 

 
CHADO INSTALLATION
------------------------------------


PREREQUISITES

* PostgreSQL version 9.1

* Postgres user with create/delete db permissions (francisco)

* pg_hba.conf -- configured

* bioperl-live -- version 1.6.923 installed in /usr/local/bioperl

* go-perl installed with CPAN

* ant installed in /usr/bin/ant

* Perl modules installed via CPAN

INSTALL THE CHADO SCHEMA

- Exporting environment variables in .bashrc

GMOD_ROOT=/usr/local/gmod 

CHADO_DB_NAME=webapollochado 

CHADO_DB_USERNAME=francisco 

CHADO_DB_PASSWORD=xxxxxx 

CHADO_DB_HOST=localhost 

CHADO_DB_PORT=5432 

- Create the Makefile and other configuration files 

$ perl Makefile.PL 

*   What database server will you be using? [PostgreSQL]

*   What is the Chado database name? [webapollochado]

*   What is the database username? [francisco]

*   What is the password for 'francisco'?

*   What is the database host? [localhost]

*   What is your database port? [5432]

*   Where shall downloaded ontologies go? [./tmp]

*   What is the default organism (common name, or "none")? poplar

*   Do you want to make this the default chado instance? [y]

- Make the schema and Install the scripts and modules

$ make

$ sudo make install

- Install the schema

$ make load_schema

        - Insert baseline data

$ make prepdb

- Load ontologies

$ make ontologies

[Relationship Ontology, Sequence Ontology, Gene Ontology, and Chado Features loaded.]


BACKUP

$ pg_dump webapollochado  >  webapollochado_dump.sql


LOADING DATA

./gmod_bulk_load_gff3.pl --organism poplar --gfffile example.gff3


#############################################################################

All the configuration steps seems to be all right but I still have the same message warning me that something is really wrong with the database. It is a hard thing that Chado schema!

I hope you can help me, now that I've sent you the dump, to find what can cause this problem.


Regards.

/Francisco




















2014-01-27 Francisco García Atienza <[hidden email]>:

Hi Scott,

Yes, I have more than one chado database but I'm pretty sure I'm loading the one I've deleted the part_of and derives_from and that this is the default chado db.

You can get the files I'm using in:


I've created a dump (test_dump.sql) and the gff3 files are example.gff3 or scf1117875582023.gff, both gives me the same warning message.

I'm also using these commands:

./gmod_bulk_load_gff3.pl --noexon --analysis -g /home/francisco/webapollo/webapollo_sample/pyu_data/scf1117875582023.gff
./gmod_bulk_load_gff3.pl --noexon --recreate_cache --organism poplar --gfffile /home/francisco/webapollo/webapollo_sample/example.gff3

Maybe, like you said, the problem is that there is some conflict with a previous chado instance related to Gbrowse, I don't know.

We are at the same point, I get load the data (I've tried last time with scf1117875582023.gff) but I get also the warning message. 

I hope you can help me to find the mistake. Thank you.

/Francisco. 


2014-01-23 Scott Cain <[hidden email]>

Hi Francisco,

The other thing the would be good if you can do it is a database dump with pg_dump; that might make it easier to replicate what is happening. 

Thanks,
Scott


Sent from my iPhone

On Jan 22, 2014, at 1:37 AM, Francisco García Atienza <[hidden email]> wrote:

Hi Scott,

Sorry to say but I still have the same problem with only one part_of row (relationship ontology's). I don't know what can cause this warning.

My apologies for my ignorance but is there any instance of chado already created to which I can add my organism? 

Regards,

/Francisco.




2014/1/21 Scott Cain <[hidden email]>
Resenting to the mailing list (how did I manage to misspell it?)

Sent from my iPad

On Jan 21, 2014, at 9:05 AM, Scott Cain <[hidden email]> wrote:

Hi Francisco,

Please keep the schema mailing list cc'ed (if I'm the one that forgot, sorry). 

So you're sure that part_of term is gone?  (Ie, rerunning that query only gives you one row?)

Also, this is unrelated to your current problem, but the fact that it completed a load and put data in the feature table is going to cause you problems. To clean up, delete everything from the feature table (assuming there's nothing there you want) and use the --recreate_cache option with the bulk loader. Until you get the part of thing straightened out, you should kill the loader when it gives you that message ("consider stopping..."). To delete everything from the feature table, do this:

  DELETE FROM feature;

Scott




Sent from my iPad

On Jan 21, 2014, at 1:59 AM, Francisco García Atienza <[hidden email]> wrote:

Hi Scott,

I've deleted the PO's ontology but I got the same warning:

./gmod_bulk_load_gff3.pl --dbname webapollochado --dbuser web_apollo_users_admin --dbpass web_apollo_users_admin --organism yeast --gfffile /home/francisco/webapollo/webapollo_sample/saccharomyces_cerevisiae.gff.sorted

"WARNING:
Unable to find a 'part_of' term in the relationship ontology;
It's absense indicates that there is something really wrong with the database.
Consider stopping and checking the state of your cvterm table.


Preparing data for inserting into the webapollochado database
(This may take a while ...)
couldn't find GO:0010551 's cvterm_id in cvterm table
couldn't find GO:0010551 's cvterm_id in cvterm table
Unable to find srcfeature chr01 in the database.
Perhaps you need to rerun your data load with the '--recreate_cache' option. at /usr/local/share/perl/5.14.2/Bio/GMOD/DB/Adapter.pm line 4603, <GEN0> line 4283.
Bio::GMOD::DB::Adapter::src_second_chance(Bio::GMOD::DB::Adapter=HASH(0x242ee38), Bio::SeqFeature::Annotated=HASH(0x4260078)) called at ./gmod_bulk_load_gff3.pl line 851

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..."


With a few lines from the gff3 file (Populus trichocarpa) that I want to load to the chado database I got load the data, I had to change a bit the file to the form 

Potri.001G000100 phytozome8_0 gene 1660 2502 . - . ID=Potri.001G000100;Name=Potri.001G000100

Before I had this

Chr01 phytozome8_0 gene 1660 2502 . - . ID=Potri.001G000100;Name=Potri.001G000100

and I got the error "Unable to find srcfeature Chr01 in the database", but still the same problem with ontologies: 

"WARNING:
Unable to find a 'part_of' term in the relationship ontology;
It's absense indicates that there is something really wrong with the database.
Consider stopping and checking the state of your cvterm table.


Preparing data for inserting into the webapollochado database
(This may take a while ...)
Skipping organism table since the load file is empty...
Skipping analysis table since the load file is empty...
Skipping db table since the load file is empty...
Skipping dbxref table since the load file is empty...
Skipping cv table since the load file is empty...
Skipping cvterm table since the load file is empty...
Loading data into feature table ...
Skipping featureloc table since the load file is empty...
Skipping feature_relationship table since the load file is empty...
Skipping featureprop table since the load file is empty...
Skipping feature_cvterm table since the load file is empty...
Loading data into synonym table ...
Loading data into feature_synonym table ...
Loading data into feature_dbxref table ...
Skipping analysisfeature table since the load file is empty...
Adding cvtermprop=MapReferenceType for 'gene' ...
Loading sequences (if any) ...

Done."

What do you think? 

/Francisco


2014/1/20 Scott Cain <[hidden email]>
Hi Francisco,

Ah, then I think we can blame the plant_ontology (well, to be fair, you can blame me, since I failed to anticipate that an ontology would provide their own "part_of").  The fix, as ugly as it is, is to remove PO's part_of:

  DELETE FROM cvterm WHERE cvterm_id = 95;

While you're at it, you should also check the derives_from term, as it will cause a similar problem.

Scott



On Mon, Jan 20, 2014 at 1:16 AM, Francisco García Atienza <[hidden email]> wrote:
Hi Scott,

Thank you for your answer. Yes, I loaded the Relationship Ontolgy and this is my result with the SQL query 

Select cvterm.*,cv.name from cvterm join cv using (cv_id) where cvterm.name = 'part_of'; 

cvterm_id cv_id name definition dbxref_id is_obsolete is_relationshiptype name








37 7 part_of
39 0 1 relationship
95 18 part_of
121 0 1 plant_ontology

/Francisco


2014/1/8 Scott Cain <[hidden email]>
Hi Francisco,

The message about not finding part_of is pretty important. Did you load the Relationship Ontology?  If so, what happens when you execute this command:

  Select cvterm.*,cv.name from cvterm join cv using cv_id where cvterm.name = 'part_of';

(I think that SQL is right, but I'm writing it on an iPad without a database to test against, but hopefully you get the idea.)

Scott


Sent from Mailbox for iPad


On Wed, Jan 8, 2014 at 10:42 AM, Francisco García Atienza <[hidden email]> wrote:

Hello,

I'm trying to use the Chado adapter from WebApollo but I get some errors, I've instantiated Chado following your guide at http://gmod.org/wiki/Chado and when I try to load some example in the Chado database doing this:

gmod_bulk_load_gff3.pl --organism yeast  --gfffile saccharomyces_cerevisiae.gff.sorted

(These are my parameters)
GMOD_ROOT=/usr/local/gmod
PERL5LIB=$PERL5LIB:/usr/local/bioperl/bioperl-live
CHADO_DB_NAME=webapollochado
CHADO_DB_USER=web_apollo_users_admin 
CHADO_DB_HOST=localhost
CHADO_DB_PORT=5432

 I get this error 

"WARNING:
Unable to find a 'part_of' term in the relationship ontology;
It's absence indicates that there is something really wrong with the database.
Consider stopping and checking the state of your cvterm table.


Preparing data for inserting into the webapollochado database
(This may take a while ...)
Can't locate object method "get_Annotations" via package "Bio::SeqFeature::Annotated" at /usr/local/share/perl/5.14.2/Bio/SeqFeature/Annotated.pm line 287, <GEN0> line 2.

Abnormal termination, trying to clean up...

Trying to remove the run lock (so that --remove_lock won't be needed)...
Exiting..."


Any ideas what could be wrong? Thank you.

Regards, 

/Francisco.





--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     <a href="tel:216-392-3087" value="+12163923087" target="_blank">216-392-3087
Ontario Institute for Cancer Research







--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     <a href="tel:216-392-3087" value="+12163923087" target="_blank">216-392-3087
Ontario Institute for Cancer Research


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Re: Object method "get_Annotations" error

Scott Cain
Hi Francisco,

I'm glad you sorted out the database issues. The problem with the GFF is that you need to identify on what feature the coordinates refer.  For example, your first GFF line of the gene has start and end coordinates of 1660 and 2502.  The question Chado needs answered is, on what?  Presumably it's Chr01, so you need a GFF line that looks something like this:

Chr01   .    chromosome    1    1234567     .    .    .    ID=Chr01;Name=Chr01

where "1234567" is the length of the chromosome.  Of course, it doesn't have to be a chromosome, it could be a contig or something else, you just have to identify it.

Scott



On Mon, Feb 3, 2014 at 5:24 AM, Francisco García Atienza <[hidden email]> wrote:
Hi Scott,

I'm glad to say that I've fixed the problem, like I told you I have several Chado instances and I tried to put the last one (webapollo) as not default and I don't get now the warning message.

Anyway, I'd like to ask you about another error. I'm trying to load this gff3 file 


 (First line...)

Chr01 phytozome8_0 gene 1660 2502 . - . ID=Potri.001G000100;Name=Potri.001G000100

but I get this error "Unable to find srcfeature Chr01 in the database".

I've read that this is because you need to indentify on what sequence/feature the features in the GFF file 
reside. I changed the gff3 file to this:

Potri.001G000100 phytozome8_0 gene 1660 2502 . - . ID=Potri.001G000100;Name=Potri.001G000100

But now I get this error "Unable to find srcfeature Potri.001G000100.1 in the database"

Potri.001G000100.1 phytozome8_0 mRNA 1660 2502 . - . ID=PAC:27043735;Name=Potri.001G000100.1;pacid=27043735;longest=1;Parent=Potri.001G000100

What would be the correct form to load the mRNA? Thank you.

Regards,

/Francisco






2014-01-31 Scott Cain <[hidden email]>:

Hi Francisco,

I've been traveling the last few days, but I will take a look at this over the weekend.

Scott



On Fri, Jan 31, 2014 at 7:08 AM, Francisco García Atienza <[hidden email]> wrote:
Hi Scott,

I am also sending you the steps I've follow to install Chado. 

 
CHADO INSTALLATION
------------------------------------


PREREQUISITES

* PostgreSQL version 9.1

* Postgres user with create/delete db permissions (francisco)

* pg_hba.conf -- configured

* bioperl-live -- version 1.6.923 installed in /usr/local/bioperl

* go-perl installed with CPAN

* ant installed in /usr/bin/ant

* Perl modules installed via CPAN

INSTALL THE CHADO SCHEMA

- Exporting environment variables in .bashrc

GMOD_ROOT=/usr/local/gmod 

CHADO_DB_NAME=webapollochado 

CHADO_DB_USERNAME=francisco 

CHADO_DB_PASSWORD=xxxxxx 

CHADO_DB_HOST=localhost 

CHADO_DB_PORT=5432 

- Create the Makefile and other configuration files 

$ perl Makefile.PL 

*   What database server will you be using? [PostgreSQL]

*   What is the Chado database name? [webapollochado]

*   What is the database username? [francisco]

*   What is the password for 'francisco'?

*   What is the database host? [localhost]

*   What is your database port? [5432]

*   Where shall downloaded ontologies go? [./tmp]

*   What is the default organism (common name, or "none")? poplar

*   Do you want to make this the default chado instance? [y]

- Make the schema and Install the scripts and modules

$ make

$ sudo make install

- Install the schema

$ make load_schema

        - Insert baseline data

$ make prepdb

- Load ontologies

$ make ontologies

[Relationship Ontology, Sequence Ontology, Gene Ontology, and Chado Features loaded.]


BACKUP

$ pg_dump webapollochado  >  webapollochado_dump.sql


LOADING DATA

./gmod_bulk_load_gff3.pl --organism poplar --gfffile example.gff3


#############################################################################

All the configuration steps seems to be all right but I still have the same message warning me that something is really wrong with the database. It is a hard thing that Chado schema!

I hope you can help me, now that I've sent you the dump, to find what can cause this problem.


Regards.

/Francisco




















2014-01-27 Francisco García Atienza <[hidden email]>:

Hi Scott,

Yes, I have more than one chado database but I'm pretty sure I'm loading the one I've deleted the part_of and derives_from and that this is the default chado db.

You can get the files I'm using in:


I've created a dump (test_dump.sql) and the gff3 files are example.gff3 or scf1117875582023.gff, both gives me the same warning message.

I'm also using these commands:

./gmod_bulk_load_gff3.pl --noexon --analysis -g /home/francisco/webapollo/webapollo_sample/pyu_data/scf1117875582023.gff
./gmod_bulk_load_gff3.pl --noexon --recreate_cache --organism poplar --gfffile /home/francisco/webapollo/webapollo_sample/example.gff3

Maybe, like you said, the problem is that there is some conflict with a previous chado instance related to Gbrowse, I don't know.

We are at the same point, I get load the data (I've tried last time with scf1117875582023.gff) but I get also the warning message. 

I hope you can help me to find the mistake. Thank you.

/Francisco. 


2014-01-23 Scott Cain <[hidden email]>

Hi Francisco,

The other thing the would be good if you can do it is a database dump with pg_dump; that might make it easier to replicate what is happening. 

Thanks,
Scott


Sent from my iPhone

On Jan 22, 2014, at 1:37 AM, Francisco García Atienza <[hidden email]> wrote:

Hi Scott,

Sorry to say but I still have the same problem with only one part_of row (relationship ontology's). I don't know what can cause this warning.

My apologies for my ignorance but is there any instance of chado already created to which I can add my organism? 

Regards,

/Francisco.




2014/1/21 Scott Cain <[hidden email]>
Resenting to the mailing list (how did I manage to misspell it?)

Sent from my iPad

On Jan 21, 2014, at 9:05 AM, Scott Cain <[hidden email]> wrote:

Hi Francisco,

Please keep the schema mailing list cc'ed (if I'm the one that forgot, sorry). 

So you're sure that part_of term is gone?  (Ie, rerunning that query only gives you one row?)

Also, this is unrelated to your current problem, but the fact that it completed a load and put data in the feature table is going to cause you problems. To clean up, delete everything from the feature table (assuming there's nothing there you want) and use the --recreate_cache option with the bulk loader. Until you get the part of thing straightened out, you should kill the loader when it gives you that message ("consider stopping..."). To delete everything from the feature table, do this:

  DELETE FROM feature;

Scott




Sent from my iPad

On Jan 21, 2014, at 1:59 AM, Francisco García Atienza <[hidden email]> wrote:

Hi Scott,

I've deleted the PO's ontology but I got the same warning:

./gmod_bulk_load_gff3.pl --dbname webapollochado --dbuser web_apollo_users_admin --dbpass web_apollo_users_admin --organism yeast --gfffile /home/francisco/webapollo/webapollo_sample/saccharomyces_cerevisiae.gff.sorted

"WARNING:
Unable to find a 'part_of' term in the relationship ontology;
It's absense indicates that there is something really wrong with the database.
Consider stopping and checking the state of your cvterm table.


Preparing data for inserting into the webapollochado database
(This may take a while ...)
couldn't find GO:0010551 's cvterm_id in cvterm table
couldn't find GO:0010551 's cvterm_id in cvterm table
Unable to find srcfeature chr01 in the database.
Perhaps you need to rerun your data load with the '--recreate_cache' option. at /usr/local/share/perl/5.14.2/Bio/GMOD/DB/Adapter.pm line 4603, <GEN0> line 4283.
Bio::GMOD::DB::Adapter::src_second_chance(Bio::GMOD::DB::Adapter=HASH(0x242ee38), Bio::SeqFeature::Annotated=HASH(0x4260078)) called at ./gmod_bulk_load_gff3.pl line 851

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..."


With a few lines from the gff3 file (Populus trichocarpa) that I want to load to the chado database I got load the data, I had to change a bit the file to the form 

Potri.001G000100 phytozome8_0 gene 1660 2502 . - . ID=Potri.001G000100;Name=Potri.001G000100

Before I had this

Chr01 phytozome8_0 gene 1660 2502 . - . ID=Potri.001G000100;Name=Potri.001G000100

and I got the error "Unable to find srcfeature Chr01 in the database", but still the same problem with ontologies: 

"WARNING:
Unable to find a 'part_of' term in the relationship ontology;
It's absense indicates that there is something really wrong with the database.
Consider stopping and checking the state of your cvterm table.


Preparing data for inserting into the webapollochado database
(This may take a while ...)
Skipping organism table since the load file is empty...
Skipping analysis table since the load file is empty...
Skipping db table since the load file is empty...
Skipping dbxref table since the load file is empty...
Skipping cv table since the load file is empty...
Skipping cvterm table since the load file is empty...
Loading data into feature table ...
Skipping featureloc table since the load file is empty...
Skipping feature_relationship table since the load file is empty...
Skipping featureprop table since the load file is empty...
Skipping feature_cvterm table since the load file is empty...
Loading data into synonym table ...
Loading data into feature_synonym table ...
Loading data into feature_dbxref table ...
Skipping analysisfeature table since the load file is empty...
Adding cvtermprop=MapReferenceType for 'gene' ...
Loading sequences (if any) ...

Done."

What do you think? 

/Francisco


2014/1/20 Scott Cain <[hidden email]>
Hi Francisco,

Ah, then I think we can blame the plant_ontology (well, to be fair, you can blame me, since I failed to anticipate that an ontology would provide their own "part_of").  The fix, as ugly as it is, is to remove PO's part_of:

  DELETE FROM cvterm WHERE cvterm_id = 95;

While you're at it, you should also check the derives_from term, as it will cause a similar problem.

Scott



On Mon, Jan 20, 2014 at 1:16 AM, Francisco García Atienza <[hidden email]> wrote:
Hi Scott,

Thank you for your answer. Yes, I loaded the Relationship Ontolgy and this is my result with the SQL query 

Select cvterm.*,cv.name from cvterm join cv using (cv_id) where cvterm.name = 'part_of'; 

cvterm_id cv_id name definition dbxref_id is_obsolete is_relationshiptype name








37 7 part_of
39 0 1 relationship
95 18 part_of
121 0 1 plant_ontology

/Francisco


2014/1/8 Scott Cain <[hidden email]>
Hi Francisco,

The message about not finding part_of is pretty important. Did you load the Relationship Ontology?  If so, what happens when you execute this command:

  Select cvterm.*,cv.name from cvterm join cv using cv_id where cvterm.name = 'part_of';

(I think that SQL is right, but I'm writing it on an iPad without a database to test against, but hopefully you get the idea.)

Scott


Sent from Mailbox for iPad


On Wed, Jan 8, 2014 at 10:42 AM, Francisco García Atienza <[hidden email]> wrote:

Hello,

I'm trying to use the Chado adapter from WebApollo but I get some errors, I've instantiated Chado following your guide at http://gmod.org/wiki/Chado and when I try to load some example in the Chado database doing this:

gmod_bulk_load_gff3.pl --organism yeast  --gfffile saccharomyces_cerevisiae.gff.sorted

(These are my parameters)
GMOD_ROOT=/usr/local/gmod
PERL5LIB=$PERL5LIB:/usr/local/bioperl/bioperl-live
CHADO_DB_NAME=webapollochado
CHADO_DB_USER=web_apollo_users_admin 
CHADO_DB_HOST=localhost
CHADO_DB_PORT=5432

 I get this error 

"WARNING:
Unable to find a 'part_of' term in the relationship ontology;
It's absence indicates that there is something really wrong with the database.
Consider stopping and checking the state of your cvterm table.


Preparing data for inserting into the webapollochado database
(This may take a while ...)
Can't locate object method "get_Annotations" via package "Bio::SeqFeature::Annotated" at /usr/local/share/perl/5.14.2/Bio/SeqFeature/Annotated.pm line 287, <GEN0> line 2.

Abnormal termination, trying to clean up...

Trying to remove the run lock (so that --remove_lock won't be needed)...
Exiting..."


Any ideas what could be wrong? Thank you.

Regards, 

/Francisco.





--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     <a href="tel:216-392-3087" value="+12163923087" target="_blank">216-392-3087
Ontario Institute for Cancer Research







--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     <a href="tel:216-392-3087" value="+12163923087" target="_blank">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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