Can't load Gene Ontology

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Can't load Gene Ontology

Nick Booher
I'm following the guide at http://tripal.info/node/277 and running into issues loading the Gene Ontology. It seems to break when updating the cvtermpath.


----------------------
Updating cvtermpath for biological_process...
WD tripal_chado: Could not fill cvtermpath table: SQLSTATE[54001]: Statement too complex: 7 ERROR:  stack depth limit exceeded                                                                                                                                                                                            [error]
CONTEXT:  SQL statement "SELECT              count(*) FROM cvtermpath WHERE cv_id = cvid AND object_id = origin AND subject_id = child_id AND pathdistance = depth"
PL/pgSQL function _fill_cvtermpath4node(integer,integer,integer,integer,integer) line 18 at PERFORMSQL statement "SELECT _fill_cvtermpath4node(origin, cterm.subject_id, cvid, cterm.type_id, depth+1)"
....
PL/pgSQL function _fill_cvtermpath4root(integer,integer) line 10 at PERFORM
PL/pgSQL function fill_cvtermpath(character varying) line 8 at SQL statement
----------------------


The same error also occurs when updating the cvtermpath for molecular function and cellular_component. This seems to be caused by a cycle in the GO relationships. Swapping the _fill_cvtermpath4root call in fill_cvtermpath for _fill_cvtermpath4root2detect_cycle throws an exception about a cycle between these terms:


----------------------
id: GO:0000045
name: autophagosome assembly
relationship: part_of GO:0016236 ! macroautophagy

id: GO:0016236
name: macroautophagy
relationship: has_part GO:0000045 ! autophagosome assembly
----------------------


Disabling loading of has_part as recommended here (http://gmod.827538.n3.nabble.com/loading-cvterms-from-OBO-file-with-has-part-relationship-td2476548.html) fixes this error and allows the cvtermpath update for biological_process to finish.

However, the cvtermpath updates for molecular_function and cellular_component still fail:


----------------------
Updating cvtermpath for molecular_function...
WD tripal_chado: Could not fill cvtermpath table: SQLSTATE[23505]: Unique violation: 7 ERROR:  duplicate key value violates unique constraint "cvtermpath_c1"                                                                                                                                                             [error]
DETAIL:  Key (subject_id, object_id, type_id, pathdistance)=(17791, 17791, 287, 0) already exists.

Updating cvtermpath for cellular_component...
WD tripal_chado: Could not fill cvtermpath table: SQLSTATE[23505]: Unique violation: 7 ERROR:  duplicate key value violates unique constraint "cvtermpath_c1"                                                                                                                                                             [error]
DETAIL:  Key (subject_id, object_id, type_id, pathdistance)=(38268, 38268, 287, 0) already exists.
----------------------


Has anyone else encountered this issue? Am I doing something wrong?

Thanks,
Nick

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Re: Can't load Gene Ontology

Stephen Ficklin-2
Hi Nick,

That's a new one....  I'm assuming you didn't get the error when loading the sequence ontology? 

Can you try editing your postgresql.conf file and editing the "max_stack_depth" setting.  The default I believe is 4MB.  We've never seen this problem before and haven't needed to recommend this change.   So, I'm interested to know if that will help.  You can find details about the meaning of this setting here:  http://www.postgresql.org/docs/9.4/static/runtime-config-resource.html (scroll down to it).

Stephen

On 2/16/2016 2:39 PM, Nick Booher wrote:
I'm following the guide at http://tripal.info/node/277 and running into issues loading the Gene Ontology. It seems to break when updating the cvtermpath.


----------------------
Updating cvtermpath for biological_process...
WD tripal_chado: Could not fill cvtermpath table: SQLSTATE[54001]: Statement too complex: 7 ERROR:  stack depth limit exceeded                                                                                                                                                                                            [error]
CONTEXT:  SQL statement "SELECT              count(*) FROM cvtermpath WHERE cv_id = cvid AND object_id = origin AND subject_id = child_id AND pathdistance = depth"
PL/pgSQL function _fill_cvtermpath4node(integer,integer,integer,integer,integer) line 18 at PERFORMSQL statement "SELECT _fill_cvtermpath4node(origin, cterm.subject_id, cvid, cterm.type_id, depth+1)"
....
PL/pgSQL function _fill_cvtermpath4root(integer,integer) line 10 at PERFORM
PL/pgSQL function fill_cvtermpath(character varying) line 8 at SQL statement
----------------------


The same error also occurs when updating the cvtermpath for molecular function and cellular_component. This seems to be caused by a cycle in the GO relationships. Swapping the _fill_cvtermpath4root call in fill_cvtermpath for _fill_cvtermpath4root2detect_cycle throws an exception about a cycle between these terms:


----------------------
id: GO:0000045
name: autophagosome assembly
relationship: part_of GO:0016236 ! macroautophagy

id: GO:0016236
name: macroautophagy
relationship: has_part GO:0000045 ! autophagosome assembly
----------------------


Disabling loading of has_part as recommended here (http://gmod.827538.n3.nabble.com/loading-cvterms-from-OBO-file-with-has-part-relationship-td2476548.html) fixes this error and allows the cvtermpath update for biological_process to finish.

However, the cvtermpath updates for molecular_function and cellular_component still fail:


----------------------
Updating cvtermpath for molecular_function...
WD tripal_chado: Could not fill cvtermpath table: SQLSTATE[23505]: Unique violation: 7 ERROR:  duplicate key value violates unique constraint "cvtermpath_c1"                                                                                                                                                             [error]
DETAIL:  Key (subject_id, object_id, type_id, pathdistance)=(17791, 17791, 287, 0) already exists.

Updating cvtermpath for cellular_component...
WD tripal_chado: Could not fill cvtermpath table: SQLSTATE[23505]: Unique violation: 7 ERROR:  duplicate key value violates unique constraint "cvtermpath_c1"                                                                                                                                                             [error]
DETAIL:  Key (subject_id, object_id, type_id, pathdistance)=(38268, 38268, 287, 0) already exists.
----------------------


Has anyone else encountered this issue? Am I doing something wrong?

Thanks,
Nick


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Re: Can't load Gene Ontology

Nick Booher
Hi,

I upped max_stack_depth from to 65MB (seems to be the max supported by OSX) and still get the same error.


----------------------
Updating cvtermpath for biological_process...
WD tripal_chado: Could not fill cvtermpath table: SQLSTATE[54001]: Statement too complex: 7 ERROR:  stack depth limit exceeded                                                                                                                                                                                            [error]
HINT:  Increase the configuration parameter "max_stack_depth" (currently 65020kB), after ensuring the platform's stack depth limit is adequate.
CONTEXT:  SQL statement "SELECT              count(*) FROM cvtermpath WHERE cv_id = cvid AND object_id = origin AND subject_id = child_id AND pathdistance = depth"
PL/pgSQL function _fill_cvtermpath4node(integer,integer,integer,integer,integer) line 13 at SQL statement
SQL statement "SELECT _fill_cvtermpath4node(origin, cterm.subject_id, cvid, cterm.type_id, depth+1)"
----------------------


-Nick

On Tue, Feb 16, 2016 at 10:55 PM, Stephen Ficklin <[hidden email]> wrote:
Hi Nick,

That's a new one....  I'm assuming you didn't get the error when loading the sequence ontology? 

Can you try editing your postgresql.conf file and editing the "max_stack_depth" setting.  The default I believe is 4MB.  We've never seen this problem before and haven't needed to recommend this change.   So, I'm interested to know if that will help.  You can find details about the meaning of this setting here:  http://www.postgresql.org/docs/9.4/static/runtime-config-resource.html (scroll down to it).

Stephen


On 2/16/2016 2:39 PM, Nick Booher wrote:
I'm following the guide at http://tripal.info/node/277 and running into issues loading the Gene Ontology. It seems to break when updating the cvtermpath.


----------------------
Updating cvtermpath for biological_process...
WD tripal_chado: Could not fill cvtermpath table: SQLSTATE[54001]: Statement too complex: 7 ERROR:  stack depth limit exceeded                                                                                                                                                                                            [error]
CONTEXT:  SQL statement "SELECT              count(*) FROM cvtermpath WHERE cv_id = cvid AND object_id = origin AND subject_id = child_id AND pathdistance = depth"
PL/pgSQL function _fill_cvtermpath4node(integer,integer,integer,integer,integer) line 18 at PERFORMSQL statement "SELECT _fill_cvtermpath4node(origin, cterm.subject_id, cvid, cterm.type_id, depth+1)"
....
PL/pgSQL function _fill_cvtermpath4root(integer,integer) line 10 at PERFORM
PL/pgSQL function fill_cvtermpath(character varying) line 8 at SQL statement
----------------------


The same error also occurs when updating the cvtermpath for molecular function and cellular_component. This seems to be caused by a cycle in the GO relationships. Swapping the _fill_cvtermpath4root call in fill_cvtermpath for _fill_cvtermpath4root2detect_cycle throws an exception about a cycle between these terms:


----------------------
id: GO:0000045
name: autophagosome assembly
relationship: part_of GO:0016236 ! macroautophagy

id: GO:0016236
name: macroautophagy
relationship: has_part GO:0000045 ! autophagosome assembly
----------------------


Disabling loading of has_part as recommended here (http://gmod.827538.n3.nabble.com/loading-cvterms-from-OBO-file-with-has-part-relationship-td2476548.html) fixes this error and allows the cvtermpath update for biological_process to finish.

However, the cvtermpath updates for molecular_function and cellular_component still fail:


----------------------
Updating cvtermpath for molecular_function...
WD tripal_chado: Could not fill cvtermpath table: SQLSTATE[23505]: Unique violation: 7 ERROR:  duplicate key value violates unique constraint "cvtermpath_c1"                                                                                                                                                             [error]
DETAIL:  Key (subject_id, object_id, type_id, pathdistance)=(17791, 17791, 287, 0) already exists.

Updating cvtermpath for cellular_component...
WD tripal_chado: Could not fill cvtermpath table: SQLSTATE[23505]: Unique violation: 7 ERROR:  duplicate key value violates unique constraint "cvtermpath_c1"                                                                                                                                                             [error]
DETAIL:  Key (subject_id, object_id, type_id, pathdistance)=(38268, 38268, 287, 0) already exists.
----------------------


Has anyone else encountered this issue? Am I doing something wrong?

Thanks,
Nick


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Re: Can't load Gene Ontology

Nick Booher
I don't get the error when loading the sequence ontology.

-Nick

On Wed, Feb 17, 2016 at 9:04 AM, Nick Booher <[hidden email]> wrote:
Hi,

I upped max_stack_depth from to 65MB (seems to be the max supported by OSX) and still get the same error.


----------------------
Updating cvtermpath for biological_process...
WD tripal_chado: Could not fill cvtermpath table: SQLSTATE[54001]: Statement too complex: 7 ERROR:  stack depth limit exceeded                                                                                                                                                                                            [error]
HINT:  Increase the configuration parameter "max_stack_depth" (currently 65020kB), after ensuring the platform's stack depth limit is adequate.
CONTEXT:  SQL statement "SELECT              count(*) FROM cvtermpath WHERE cv_id = cvid AND object_id = origin AND subject_id = child_id AND pathdistance = depth"
PL/pgSQL function _fill_cvtermpath4node(integer,integer,integer,integer,integer) line 13 at SQL statement
SQL statement "SELECT _fill_cvtermpath4node(origin, cterm.subject_id, cvid, cterm.type_id, depth+1)"
----------------------


-Nick

On Tue, Feb 16, 2016 at 10:55 PM, Stephen Ficklin <[hidden email]> wrote:
Hi Nick,

That's a new one....  I'm assuming you didn't get the error when loading the sequence ontology? 

Can you try editing your postgresql.conf file and editing the "max_stack_depth" setting.  The default I believe is 4MB.  We've never seen this problem before and haven't needed to recommend this change.   So, I'm interested to know if that will help.  You can find details about the meaning of this setting here:  http://www.postgresql.org/docs/9.4/static/runtime-config-resource.html (scroll down to it).

Stephen


On 2/16/2016 2:39 PM, Nick Booher wrote:
I'm following the guide at http://tripal.info/node/277 and running into issues loading the Gene Ontology. It seems to break when updating the cvtermpath.


----------------------
Updating cvtermpath for biological_process...
WD tripal_chado: Could not fill cvtermpath table: SQLSTATE[54001]: Statement too complex: 7 ERROR:  stack depth limit exceeded                                                                                                                                                                                            [error]
CONTEXT:  SQL statement "SELECT              count(*) FROM cvtermpath WHERE cv_id = cvid AND object_id = origin AND subject_id = child_id AND pathdistance = depth"
PL/pgSQL function _fill_cvtermpath4node(integer,integer,integer,integer,integer) line 18 at PERFORMSQL statement "SELECT _fill_cvtermpath4node(origin, cterm.subject_id, cvid, cterm.type_id, depth+1)"
....
PL/pgSQL function _fill_cvtermpath4root(integer,integer) line 10 at PERFORM
PL/pgSQL function fill_cvtermpath(character varying) line 8 at SQL statement
----------------------


The same error also occurs when updating the cvtermpath for molecular function and cellular_component. This seems to be caused by a cycle in the GO relationships. Swapping the _fill_cvtermpath4root call in fill_cvtermpath for _fill_cvtermpath4root2detect_cycle throws an exception about a cycle between these terms:


----------------------
id: GO:0000045
name: autophagosome assembly
relationship: part_of GO:0016236 ! macroautophagy

id: GO:0016236
name: macroautophagy
relationship: has_part GO:0000045 ! autophagosome assembly
----------------------


Disabling loading of has_part as recommended here (http://gmod.827538.n3.nabble.com/loading-cvterms-from-OBO-file-with-has-part-relationship-td2476548.html) fixes this error and allows the cvtermpath update for biological_process to finish.

However, the cvtermpath updates for molecular_function and cellular_component still fail:


----------------------
Updating cvtermpath for molecular_function...
WD tripal_chado: Could not fill cvtermpath table: SQLSTATE[23505]: Unique violation: 7 ERROR:  duplicate key value violates unique constraint "cvtermpath_c1"                                                                                                                                                             [error]
DETAIL:  Key (subject_id, object_id, type_id, pathdistance)=(17791, 17791, 287, 0) already exists.

Updating cvtermpath for cellular_component...
WD tripal_chado: Could not fill cvtermpath table: SQLSTATE[23505]: Unique violation: 7 ERROR:  duplicate key value violates unique constraint "cvtermpath_c1"                                                                                                                                                             [error]
DETAIL:  Key (subject_id, object_id, type_id, pathdistance)=(38268, 38268, 287, 0) already exists.
----------------------


Has anyone else encountered this issue? Am I doing something wrong?

Thanks,
Nick


------------------------------------------------------------------------------
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Re: Can't load Gene Ontology

Stephen Ficklin-2
In reply to this post by Nick Booher
Hi Nick,

I too am now getting this error on the GO vocabularies:  cellular_component, biological_process and molecular_function.  This did not happen previously so I've got to dig a bit deeper to see if I can determine the cause.    It takes a while to test because it takes so long to load.  But, I'm working on it.

Stephen

On 2/17/2016 7:04 AM, Nick Booher wrote:
Hi,

I upped max_stack_depth from to 65MB (seems to be the max supported by OSX) and still get the same error.


----------------------
Updating cvtermpath for biological_process...
WD tripal_chado: Could not fill cvtermpath table: SQLSTATE[54001]: Statement too complex: 7 ERROR:  stack depth limit exceeded                                                                                                                                                                                            [error]
HINT:  Increase the configuration parameter "max_stack_depth" (currently 65020kB), after ensuring the platform's stack depth limit is adequate.
CONTEXT:  SQL statement "SELECT              count(*) FROM cvtermpath WHERE cv_id = cvid AND object_id = origin AND subject_id = child_id AND pathdistance = depth"
PL/pgSQL function _fill_cvtermpath4node(integer,integer,integer,integer,integer) line 13 at SQL statement
SQL statement "SELECT _fill_cvtermpath4node(origin, cterm.subject_id, cvid, cterm.type_id, depth+1)"
----------------------


-Nick

On Tue, Feb 16, 2016 at 10:55 PM, Stephen Ficklin <[hidden email]> wrote:
Hi Nick,

That's a new one....  I'm assuming you didn't get the error when loading the sequence ontology? 

Can you try editing your postgresql.conf file and editing the "max_stack_depth" setting.  The default I believe is 4MB.  We've never seen this problem before and haven't needed to recommend this change.   So, I'm interested to know if that will help.  You can find details about the meaning of this setting here:  http://www.postgresql.org/docs/9.4/static/runtime-config-resource.html (scroll down to it).

Stephen


On 2/16/2016 2:39 PM, Nick Booher wrote:
I'm following the guide at http://tripal.info/node/277 and running into issues loading the Gene Ontology. It seems to break when updating the cvtermpath.


----------------------
Updating cvtermpath for biological_process...
WD tripal_chado: Could not fill cvtermpath table: SQLSTATE[54001]: Statement too complex: 7 ERROR:  stack depth limit exceeded                                                                                                                                                                                            [error]
CONTEXT:  SQL statement "SELECT              count(*) FROM cvtermpath WHERE cv_id = cvid AND object_id = origin AND subject_id = child_id AND pathdistance = depth"
PL/pgSQL function _fill_cvtermpath4node(integer,integer,integer,integer,integer) line 18 at PERFORMSQL statement "SELECT _fill_cvtermpath4node(origin, cterm.subject_id, cvid, cterm.type_id, depth+1)"
....
PL/pgSQL function _fill_cvtermpath4root(integer,integer) line 10 at PERFORM
PL/pgSQL function fill_cvtermpath(character varying) line 8 at SQL statement
----------------------


The same error also occurs when updating the cvtermpath for molecular function and cellular_component. This seems to be caused by a cycle in the GO relationships. Swapping the _fill_cvtermpath4root call in fill_cvtermpath for _fill_cvtermpath4root2detect_cycle throws an exception about a cycle between these terms:


----------------------
id: GO:0000045
name: autophagosome assembly
relationship: part_of GO:0016236 ! macroautophagy

id: GO:0016236
name: macroautophagy
relationship: has_part GO:0000045 ! autophagosome assembly
----------------------


Disabling loading of has_part as recommended here (http://gmod.827538.n3.nabble.com/loading-cvterms-from-OBO-file-with-has-part-relationship-td2476548.html) fixes this error and allows the cvtermpath update for biological_process to finish.

However, the cvtermpath updates for molecular_function and cellular_component still fail:


----------------------
Updating cvtermpath for molecular_function...
WD tripal_chado: Could not fill cvtermpath table: SQLSTATE[23505]: Unique violation: 7 ERROR:  duplicate key value violates unique constraint "cvtermpath_c1"                                                                                                                                                             [error]
DETAIL:  Key (subject_id, object_id, type_id, pathdistance)=(17791, 17791, 287, 0) already exists.

Updating cvtermpath for cellular_component...
WD tripal_chado: Could not fill cvtermpath table: SQLSTATE[23505]: Unique violation: 7 ERROR:  duplicate key value violates unique constraint "cvtermpath_c1"                                                                                                                                                             [error]
DETAIL:  Key (subject_id, object_id, type_id, pathdistance)=(38268, 38268, 287, 0) already exists.
----------------------


Has anyone else encountered this issue? Am I doing something wrong?

Thanks,
Nick


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Re: Can't load Gene Ontology

Nick Booher
Any updates on this?

Thanks,
Nick

On Wed, Feb 17, 2016 at 8:14 PM, Stephen Ficklin <[hidden email]> wrote:
Hi Nick,

I too am now getting this error on the GO vocabularies:  cellular_component, biological_process and molecular_function.  This did not happen previously so I've got to dig a bit deeper to see if I can determine the cause.    It takes a while to test because it takes so long to load.  But, I'm working on it.

Stephen


On 2/17/2016 7:04 AM, Nick Booher wrote:
Hi,

I upped max_stack_depth from to 65MB (seems to be the max supported by OSX) and still get the same error.


----------------------
Updating cvtermpath for biological_process...
WD tripal_chado: Could not fill cvtermpath table: SQLSTATE[54001]: Statement too complex: 7 ERROR:  stack depth limit exceeded                                                                                                                                                                                            [error]
HINT:  Increase the configuration parameter "max_stack_depth" (currently 65020kB), after ensuring the platform's stack depth limit is adequate.
CONTEXT:  SQL statement "SELECT              count(*) FROM cvtermpath WHERE cv_id = cvid AND object_id = origin AND subject_id = child_id AND pathdistance = depth"
PL/pgSQL function _fill_cvtermpath4node(integer,integer,integer,integer,integer) line 13 at SQL statement
SQL statement "SELECT _fill_cvtermpath4node(origin, cterm.subject_id, cvid, cterm.type_id, depth+1)"
----------------------


-Nick

On Tue, Feb 16, 2016 at 10:55 PM, Stephen Ficklin <[hidden email]> wrote:
Hi Nick,

That's a new one....  I'm assuming you didn't get the error when loading the sequence ontology? 

Can you try editing your postgresql.conf file and editing the "max_stack_depth" setting.  The default I believe is 4MB.  We've never seen this problem before and haven't needed to recommend this change.   So, I'm interested to know if that will help.  You can find details about the meaning of this setting here:  http://www.postgresql.org/docs/9.4/static/runtime-config-resource.html (scroll down to it).

Stephen


On 2/16/2016 2:39 PM, Nick Booher wrote:
I'm following the guide at http://tripal.info/node/277 and running into issues loading the Gene Ontology. It seems to break when updating the cvtermpath.


----------------------
Updating cvtermpath for biological_process...
WD tripal_chado: Could not fill cvtermpath table: SQLSTATE[54001]: Statement too complex: 7 ERROR:  stack depth limit exceeded                                                                                                                                                                                            [error]
CONTEXT:  SQL statement "SELECT              count(*) FROM cvtermpath WHERE cv_id = cvid AND object_id = origin AND subject_id = child_id AND pathdistance = depth"
PL/pgSQL function _fill_cvtermpath4node(integer,integer,integer,integer,integer) line 18 at PERFORMSQL statement "SELECT _fill_cvtermpath4node(origin, cterm.subject_id, cvid, cterm.type_id, depth+1)"
....
PL/pgSQL function _fill_cvtermpath4root(integer,integer) line 10 at PERFORM
PL/pgSQL function fill_cvtermpath(character varying) line 8 at SQL statement
----------------------


The same error also occurs when updating the cvtermpath for molecular function and cellular_component. This seems to be caused by a cycle in the GO relationships. Swapping the _fill_cvtermpath4root call in fill_cvtermpath for _fill_cvtermpath4root2detect_cycle throws an exception about a cycle between these terms:


----------------------
id: GO:0000045
name: autophagosome assembly
relationship: part_of GO:0016236 ! macroautophagy

id: GO:0016236
name: macroautophagy
relationship: has_part GO:0000045 ! autophagosome assembly
----------------------


Disabling loading of has_part as recommended here (http://gmod.827538.n3.nabble.com/loading-cvterms-from-OBO-file-with-has-part-relationship-td2476548.html) fixes this error and allows the cvtermpath update for biological_process to finish.

However, the cvtermpath updates for molecular_function and cellular_component still fail:


----------------------
Updating cvtermpath for molecular_function...
WD tripal_chado: Could not fill cvtermpath table: SQLSTATE[23505]: Unique violation: 7 ERROR:  duplicate key value violates unique constraint "cvtermpath_c1"                                                                                                                                                             [error]
DETAIL:  Key (subject_id, object_id, type_id, pathdistance)=(17791, 17791, 287, 0) already exists.

Updating cvtermpath for cellular_component...
WD tripal_chado: Could not fill cvtermpath table: SQLSTATE[23505]: Unique violation: 7 ERROR:  duplicate key value violates unique constraint "cvtermpath_c1"                                                                                                                                                             [error]
DETAIL:  Key (subject_id, object_id, type_id, pathdistance)=(38268, 38268, 287, 0) already exists.
----------------------


Has anyone else encountered this issue? Am I doing something wrong?

Thanks,
Nick


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