GFF Bulk Uploader error(s)

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GFF Bulk Uploader error(s)

Shane McCoy
Hello! Tried uploading multiple GFF files tonight and got these errors. 
I did read on GMOD mailing list archives about 'Warning' part_of issue here:
though i'm not sure still what to do. (the schema is set in 'public' fyi)
Thanks for looking!
Shane M.


gmod_bulk_load_gff3.pl --noexon --analysis --organism striped bass --gfffile SBDraft_Pt1.all.gff SBDraft_Pt2.all.gff SBDraft_Pt3.all.gff SBDraft_Pt4.all.gff SBDraft_Pt5.all.gff

defined(@array) is deprecated at /home/bjreadin/perl5/perlbrew/perls/perl-5.20.1/lib/site_perl/5.20.1/Bio/GMOD/DB/Adapter.pm line 498.

(Maybe you should just omit the defined()?)

defined(@array) is deprecated at /home/bjreadin/perl5/perlbrew/perls/perl-5.20.1/lib/site_perl/5.20.1/Bio/GMOD/DB/Adapter.pm line 1078.

(Maybe you should just omit the defined()?)

defined(@array) is deprecated at /home/bjreadin/perl5/perlbrew/perls/perl-5.20.1/lib/site_perl/5.20.1/Bio/GMOD/DB/Adapter.pm line 1111.

(Maybe you should just omit the defined()?)

defined(@array) is deprecated at /home/bjreadin/perl5/perlbrew/perls/perl-5.20.1/lib/site_perl/5.20.1/Bio/GMOD/DB/Adapter.pm line 1144.

(Maybe you should just omit the defined()?)

defined(@array) is deprecated at /home/bjreadin/perl5/perlbrew/perls/perl-5.20.1/lib/site_perl/5.20.1/Bio/GMOD/DB/Adapter.pm line 1469.

(Maybe you should just omit the defined()?)

defined(@array) is deprecated at /home/bjreadin/perl5/perlbrew/perls/perl-5.20.1/lib/site_perl/5.20.1/Bio/GMOD/DB/Adapter.pm line 1664.

(Maybe you should just omit the defined()?)

defined(@array) is deprecated at /home/bjreadin/perl5/perlbrew/perls/perl-5.20.1/lib/site_perl/5.20.1/Bio/GMOD/DB/Adapter.pm line 1696.

(Maybe you should just omit the defined()?)

defined(@array) is deprecated at /home/bjreadin/perl5/perlbrew/perls/perl-5.20.1/lib/site_perl/5.20.1/Bio/GMOD/DB/Adapter.pm line 1728.

(Maybe you should just omit the defined()?)

defined(@array) is deprecated at /home/bjreadin/perl5/perlbrew/perls/perl-5.20.1/lib/site_perl/5.20.1/Bio/GMOD/DB/Adapter.pm line 1760.

(Maybe you should just omit the defined()?)

defined(@array) is deprecated at /home/bjreadin/perl5/perlbrew/perls/perl-5.20.1/lib/site_perl/5.20.1/Bio/GMOD/DB/Adapter.pm line 1977.

(Maybe you should just omit the defined()?)

defined(@array) is deprecated at /home/bjreadin/perl5/perlbrew/perls/perl-5.20.1/lib/site_perl/5.20.1/Bio/GMOD/DB/Adapter.pm line 2007.

(Maybe you should just omit the defined()?)

defined(@array) is deprecated at /home/bjreadin/perl5/perlbrew/perls/perl-5.20.1/lib/site_perl/5.20.1/Bio/GMOD/DB/Adapter.pm line 2037.

(Maybe you should just omit the defined()?)

defined(@array) is deprecated at /home/bjreadin/perl5/perlbrew/perls/perl-5.20.1/lib/site_perl/5.20.1/Bio/GMOD/DB/Adapter.pm line 2067.

(Maybe you should just omit the defined()?)

defined(@array) is deprecated at /home/bjreadin/perl5/perlbrew/perls/perl-5.20.1/lib/site_perl/5.20.1/Bio/GMOD/DB/Adapter.pm line 2099.

(Maybe you should just omit the defined()?)

defined(@array) is deprecated at /home/bjreadin/perl5/perlbrew/perls/perl-5.20.1/lib/site_perl/5.20.1/Bio/GMOD/DB/Adapter.pm line 2284.

(Maybe you should just omit the defined()?)

defined(@array) is deprecated at /home/bjreadin/perl5/perlbrew/perls/perl-5.20.1/lib/site_perl/5.20.1/Bio/GMOD/DB/Adapter.pm line 2313.

(Maybe you should just omit the defined()?)

defined(@array) is deprecated at /home/bjreadin/perl5/perlbrew/perls/perl-5.20.1/lib/site_perl/5.20.1/Bio/GMOD/DB/Adapter.pm line 2345.

(Maybe you should just omit the defined()?)

defined(@array) is deprecated at /home/bjreadin/perl5/perlbrew/perls/perl-5.20.1/lib/site_perl/5.20.1/Bio/GMOD/DB/Adapter.pm line 2376.

(Maybe you should just omit the defined()?)

defined(@array) is deprecated at /home/bjreadin/perl5/perlbrew/perls/perl-5.20.1/lib/site_perl/5.20.1/Bio/GMOD/DB/Adapter.pm line 2409.

(Maybe you should just omit the defined()?)

defined(@array) is deprecated at /home/bjreadin/perl5/perlbrew/perls/perl-5.20.1/lib/site_perl/5.20.1/Bio/GMOD/DB/Adapter.pm line 2443.

(Maybe you should just omit the defined()?)

defined(@array) is deprecated at /home/bjreadin/perl5/perlbrew/perls/perl-5.20.1/lib/site_perl/5.20.1/Bio/GMOD/DB/Adapter.pm line 2474.

(Maybe you should just omit the defined()?)

defined(@array) is deprecated at /home/bjreadin/perl5/perlbrew/perls/perl-5.20.1/lib/site_perl/5.20.1/Bio/GMOD/DB/Adapter.pm line 2504.

(Maybe you should just omit the defined()?)

defined(@array) is deprecated at /home/bjreadin/perl5/perlbrew/perls/perl-5.20.1/lib/site_perl/5.20.1/Bio/GMOD/DB/Adapter.pm line 4872.

(Maybe you should just omit the defined()?)

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.

(Re)creating the uniquename cache in the database...
Creating table...
Populating table...
Creating indexes...
Adjusting the primary key sequences (if necessary)...Done.
Creating gff_meta table...
Preparing data for inserting into the sbass_ncsu database
(This may take a while ...)

DBD::Pg::st fetchrow_array failed: no statement executing at /home/bjreadin/perl5/perlbrew/perls/perl-5.20.1/lib/site_perl/5.20.1/Bio/GMOD/DB/Adapter.pm line 1209, <GEN0> line 2.

striped organism not found in the database at /home/bjreadin/perl5/perlbrew/perls/perl-5.20.1/bin/gmod_bulk_load_gff3.pl line 749, <GEN0> line 2.

Abnormal termination, trying to clean up...
Trying to remove the run lock (so that --remove_lock won't be needed)...
Exiting...

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Re: GFF Bulk Uploader error(s)

Andrew Farmer
Hi Shane-
from this error:
On 12/8/14 7:30 PM, Shane McCoy wrote:
striped organism not found in the database at /home/bjreadin/perl5/perlbrew/perls/perl-5.20.1/bin/gmod_bulk_load_gff3.pl line 749, <GEN0> line 2.
I'd guess you simply need to use quotes around the parameter supplied to --organism (ie --organism "striped bass")
so that the shell will recognize it as a single value to be passed in rather than two separate cmdline tokens.

hope that helps

Andrew


-- 
...all concepts in which an entire process is semiotically concentrated
elude definition; only that which has no history is definable.

Friedrich Nietzsche

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Re: GFF Bulk Uploader error(s)

Scott Cain
Hi Shane,

In addition, I'm worried about the missing 'part_of'; where there any issues, warnings or errors when you loaded your ontologies?  What happens if you execute this query:

SELECT cvterm.*,cv.name FROM cvterm JOIN cv ON (cvterm.cv_id=cv.cv_id) WHERE cvterm.name = 'part_of';

Scott


On Tue, Dec 9, 2014 at 10:30 AM, Andrew Farmer <[hidden email]> wrote:
Hi Shane-
from this error:
On 12/8/14 7:30 PM, Shane McCoy wrote:
striped organism not found in the database at /home/bjreadin/perl5/perlbrew/perls/perl-5.20.1/bin/gmod_bulk_load_gff3.pl line 749, <GEN0> line 2.
I'd guess you simply need to use quotes around the parameter supplied to --organism (ie --organism "striped bass")
so that the shell will recognize it as a single value to be passed in rather than two separate cmdline tokens.

hope that helps

Andrew


-- 
...all concepts in which an entire process is semiotically concentrated
elude definition; only that which has no history is definable.

Friedrich Nietzsche

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GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research

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Re: GFF Bulk Uploader error(s)

Shane McCoy
Hi Scott, thanks for getting back!

heres the query: 

 cvterm_id | cv_id |  name   | definition | dbxref_id | is_obsolete | is_relationshiptype |     name     

-----------+-------+---------+------------+-----------+-------------+---------------------+--------------

        37 |     7 | part_of |            |        39 |           0 |                   1 | relationship

        95 |    15 | part_of |            |       121 |           0 |                   1 | external

(2 rows)


not sure where the external is coming from?? i don't see that on other posts of peoples results. 

thanks!

shane


On Tue, Dec 9, 2014 at 12:04 PM, Scott Cain <[hidden email]> wrote:
Hi Shane,

In addition, I'm worried about the missing 'part_of'; where there any issues, warnings or errors when you loaded your ontologies?  What happens if you execute this query:

SELECT cvterm.*,cv.name FROM cvterm JOIN cv ON (cvterm.cv_id=cv.cv_id) WHERE cvterm.name = 'part_of';

Scott


On Tue, Dec 9, 2014 at 10:30 AM, Andrew Farmer <[hidden email]> wrote:
Hi Shane-
from this error:
On 12/8/14 7:30 PM, Shane McCoy wrote:
striped organism not found in the database at /home/bjreadin/perl5/perlbrew/perls/perl-5.20.1/bin/gmod_bulk_load_gff3.pl line 749, <GEN0> line 2.
I'd guess you simply need to use quotes around the parameter supplied to --organism (ie --organism "striped bass")
so that the shell will recognize it as a single value to be passed in rather than two separate cmdline tokens.

hope that helps

Andrew


-- 
...all concepts in which an entire process is semiotically concentrated
elude definition; only that which has no history is definable.

Friedrich Nietzsche

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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: GFF Bulk Uploader error(s)

Scott Cain
I don't know where that would have come from either, and the database adaptor should ignore it but maybe it isn't.  If you try to delete it (ie, DELETE FROM cvterm WHERE cvterm_id=95) does it delete or fail because it is being used as a foreign key somewhere?  If you do delete it, does that fix the problem?


On Tue, Dec 9, 2014 at 12:16 PM, Shane McCoy <[hidden email]> wrote:
Hi Scott, thanks for getting back!

heres the query: 

 cvterm_id | cv_id |  name   | definition | dbxref_id | is_obsolete | is_relationshiptype |     name     

-----------+-------+---------+------------+-----------+-------------+---------------------+--------------

        37 |     7 | part_of |            |        39 |           0 |                   1 | relationship

        95 |    15 | part_of |            |       121 |           0 |                   1 | external

(2 rows)


not sure where the external is coming from?? i don't see that on other posts of peoples results. 

thanks!

shane


On Tue, Dec 9, 2014 at 12:04 PM, Scott Cain <[hidden email]> wrote:
Hi Shane,

In addition, I'm worried about the missing 'part_of'; where there any issues, warnings or errors when you loaded your ontologies?  What happens if you execute this query:

SELECT cvterm.*,cv.name FROM cvterm JOIN cv ON (cvterm.cv_id=cv.cv_id) WHERE cvterm.name = 'part_of';

Scott


On Tue, Dec 9, 2014 at 10:30 AM, Andrew Farmer <[hidden email]> wrote:
Hi Shane-
from this error:
On 12/8/14 7:30 PM, Shane McCoy wrote:
striped organism not found in the database at /home/bjreadin/perl5/perlbrew/perls/perl-5.20.1/bin/gmod_bulk_load_gff3.pl line 749, <GEN0> line 2.
I'd guess you simply need to use quotes around the parameter supplied to --organism (ie --organism "striped bass")
so that the shell will recognize it as a single value to be passed in rather than two separate cmdline tokens.

hope that helps

Andrew


-- 
...all concepts in which an entire process is semiotically concentrated
elude definition; only that which has no history is definable.

Friedrich Nietzsche

------------------------------------------------------------------------------
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--
------------------------------------------------------------------------
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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Re: GFF Bulk Uploader error(s)

Shane McCoy
I tried deleting it using the script, and received error when checking but second attempt shows results w/ external still there. 

sbass_ncsu=> DELETE FROM cvterm WHERE cvterm_id=95

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

ERROR:  syntax error at or near "Select"

LINE 2: Select cvterm.*,cv.name from cvterm join cv using (cv_id) wh...

        ^

sbass_ncsu=> 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 |    15 | part_of |            |       121 |           0 |                   1 | external

(2 rows)


Thanks,

Shane


On Tue, Dec 9, 2014 at 12:33 PM, Scott Cain <[hidden email]> wrote:
I don't know where that would have come from either, and the database adaptor should ignore it but maybe it isn't.  If you try to delete it (ie, DELETE FROM cvterm WHERE cvterm_id=95) does it delete or fail because it is being used as a foreign key somewhere?  If you do delete it, does that fix the problem?


On Tue, Dec 9, 2014 at 12:16 PM, Shane McCoy <[hidden email]> wrote:
Hi Scott, thanks for getting back!

heres the query: 

 cvterm_id | cv_id |  name   | definition | dbxref_id | is_obsolete | is_relationshiptype |     name     

-----------+-------+---------+------------+-----------+-------------+---------------------+--------------

        37 |     7 | part_of |            |        39 |           0 |                   1 | relationship

        95 |    15 | part_of |            |       121 |           0 |                   1 | external

(2 rows)


not sure where the external is coming from?? i don't see that on other posts of peoples results. 

thanks!

shane


On Tue, Dec 9, 2014 at 12:04 PM, Scott Cain <[hidden email]> wrote:
Hi Shane,

In addition, I'm worried about the missing 'part_of'; where there any issues, warnings or errors when you loaded your ontologies?  What happens if you execute this query:

SELECT cvterm.*,cv.name FROM cvterm JOIN cv ON (cvterm.cv_id=cv.cv_id) WHERE cvterm.name = 'part_of';

Scott


On Tue, Dec 9, 2014 at 10:30 AM, Andrew Farmer <[hidden email]> wrote:
Hi Shane-
from this error:
On 12/8/14 7:30 PM, Shane McCoy wrote:
striped organism not found in the database at /home/bjreadin/perl5/perlbrew/perls/perl-5.20.1/bin/gmod_bulk_load_gff3.pl line 749, <GEN0> line 2.
I'd guess you simply need to use quotes around the parameter supplied to --organism (ie --organism "striped bass")
so that the shell will recognize it as a single value to be passed in rather than two separate cmdline tokens.

hope that helps

Andrew


-- 
...all concepts in which an entire process is semiotically concentrated
elude definition; only that which has no history is definable.

Friedrich Nietzsche

------------------------------------------------------------------------------
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with Interactivity, Sharing, Native Excel Exports, App Integration & more
Get technology previously reserved for billion-dollar corporations, FREE
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_______________________________________________
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--
------------------------------------------------------------------------
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: GFF Bulk Uploader error(s)

Shane McCoy
Hey Scott, 
i missed answering your question earlier, i did not have any errors during loading the ontologies. GO took 3hrs but other than that seemed fine. 
thanks!
Shane

On Tue, Dec 9, 2014 at 12:39 PM, Shane McCoy <[hidden email]> wrote:
I tried deleting it using the script, and received error when checking but second attempt shows results w/ external still there. 

sbass_ncsu=> DELETE FROM cvterm WHERE cvterm_id=95

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

ERROR:  syntax error at or near "Select"

LINE 2: Select cvterm.*,cv.name from cvterm join cv using (cv_id) wh...

        ^

sbass_ncsu=> 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 |    15 | part_of |            |       121 |           0 |                   1 | external

(2 rows)


Thanks,

Shane


On Tue, Dec 9, 2014 at 12:33 PM, Scott Cain <[hidden email]> wrote:
I don't know where that would have come from either, and the database adaptor should ignore it but maybe it isn't.  If you try to delete it (ie, DELETE FROM cvterm WHERE cvterm_id=95) does it delete or fail because it is being used as a foreign key somewhere?  If you do delete it, does that fix the problem?


On Tue, Dec 9, 2014 at 12:16 PM, Shane McCoy <[hidden email]> wrote:
Hi Scott, thanks for getting back!

heres the query: 

 cvterm_id | cv_id |  name   | definition | dbxref_id | is_obsolete | is_relationshiptype |     name     

-----------+-------+---------+------------+-----------+-------------+---------------------+--------------

        37 |     7 | part_of |            |        39 |           0 |                   1 | relationship

        95 |    15 | part_of |            |       121 |           0 |                   1 | external

(2 rows)


not sure where the external is coming from?? i don't see that on other posts of peoples results. 

thanks!

shane


On Tue, Dec 9, 2014 at 12:04 PM, Scott Cain <[hidden email]> wrote:
Hi Shane,

In addition, I'm worried about the missing 'part_of'; where there any issues, warnings or errors when you loaded your ontologies?  What happens if you execute this query:

SELECT cvterm.*,cv.name FROM cvterm JOIN cv ON (cvterm.cv_id=cv.cv_id) WHERE cvterm.name = 'part_of';

Scott


On Tue, Dec 9, 2014 at 10:30 AM, Andrew Farmer <[hidden email]> wrote:
Hi Shane-
from this error:
On 12/8/14 7:30 PM, Shane McCoy wrote:
striped organism not found in the database at /home/bjreadin/perl5/perlbrew/perls/perl-5.20.1/bin/gmod_bulk_load_gff3.pl line 749, <GEN0> line 2.
I'd guess you simply need to use quotes around the parameter supplied to --organism (ie --organism "striped bass")
so that the shell will recognize it as a single value to be passed in rather than two separate cmdline tokens.

hope that helps

Andrew


-- 
...all concepts in which an entire process is semiotically concentrated
elude definition; only that which has no history is definable.

Friedrich Nietzsche

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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: GFF Bulk Uploader error(s)

Scott Cain
In reply to this post by Shane McCoy
Hi Shane,

I just left the semicolon off the end of the delete query; try this:

DELETE FROM cvterm WHERE cvterm_id=95;

Scott


On Tue, Dec 9, 2014 at 12:39 PM, Shane McCoy <[hidden email]> wrote:
I tried deleting it using the script, and received error when checking but second attempt shows results w/ external still there. 

sbass_ncsu=> DELETE FROM cvterm WHERE cvterm_id=95

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

ERROR:  syntax error at or near "Select"

LINE 2: Select cvterm.*,cv.name from cvterm join cv using (cv_id) wh...

        ^

sbass_ncsu=> 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 |    15 | part_of |            |       121 |           0 |                   1 | external

(2 rows)


Thanks,

Shane


On Tue, Dec 9, 2014 at 12:33 PM, Scott Cain <[hidden email]> wrote:
I don't know where that would have come from either, and the database adaptor should ignore it but maybe it isn't.  If you try to delete it (ie, DELETE FROM cvterm WHERE cvterm_id=95) does it delete or fail because it is being used as a foreign key somewhere?  If you do delete it, does that fix the problem?


On Tue, Dec 9, 2014 at 12:16 PM, Shane McCoy <[hidden email]> wrote:
Hi Scott, thanks for getting back!

heres the query: 

 cvterm_id | cv_id |  name   | definition | dbxref_id | is_obsolete | is_relationshiptype |     name     

-----------+-------+---------+------------+-----------+-------------+---------------------+--------------

        37 |     7 | part_of |            |        39 |           0 |                   1 | relationship

        95 |    15 | part_of |            |       121 |           0 |                   1 | external

(2 rows)


not sure where the external is coming from?? i don't see that on other posts of peoples results. 

thanks!

shane


On Tue, Dec 9, 2014 at 12:04 PM, Scott Cain <[hidden email]> wrote:
Hi Shane,

In addition, I'm worried about the missing 'part_of'; where there any issues, warnings or errors when you loaded your ontologies?  What happens if you execute this query:

SELECT cvterm.*,cv.name FROM cvterm JOIN cv ON (cvterm.cv_id=cv.cv_id) WHERE cvterm.name = 'part_of';

Scott


On Tue, Dec 9, 2014 at 10:30 AM, Andrew Farmer <[hidden email]> wrote:
Hi Shane-
from this error:
On 12/8/14 7:30 PM, Shane McCoy wrote:
striped organism not found in the database at /home/bjreadin/perl5/perlbrew/perls/perl-5.20.1/bin/gmod_bulk_load_gff3.pl line 749, <GEN0> line 2.
I'd guess you simply need to use quotes around the parameter supplied to --organism (ie --organism "striped bass")
so that the shell will recognize it as a single value to be passed in rather than two separate cmdline tokens.

hope that helps

Andrew


-- 
...all concepts in which an entire process is semiotically concentrated
elude definition; only that which has no history is definable.

Friedrich Nietzsche

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--
------------------------------------------------------------------------
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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Re: GFF Bulk Uploader error(s)

Shane McCoy
Ha! yeah, i missed that. It has deleted it. 
I'll go ahead and try loading gff again and get back to you. 
Thanks again!
Shane M.

On Tue, Dec 9, 2014 at 1:03 PM, Scott Cain <[hidden email]> wrote:
Hi Shane,

I just left the semicolon off the end of the delete query; try this:

DELETE FROM cvterm WHERE cvterm_id=95;

Scott


On Tue, Dec 9, 2014 at 12:39 PM, Shane McCoy <[hidden email]> wrote:
I tried deleting it using the script, and received error when checking but second attempt shows results w/ external still there. 

sbass_ncsu=> DELETE FROM cvterm WHERE cvterm_id=95

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

ERROR:  syntax error at or near "Select"

LINE 2: Select cvterm.*,cv.name from cvterm join cv using (cv_id) wh...

        ^

sbass_ncsu=> 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 |    15 | part_of |            |       121 |           0 |                   1 | external

(2 rows)


Thanks,

Shane


On Tue, Dec 9, 2014 at 12:33 PM, Scott Cain <[hidden email]> wrote:
I don't know where that would have come from either, and the database adaptor should ignore it but maybe it isn't.  If you try to delete it (ie, DELETE FROM cvterm WHERE cvterm_id=95) does it delete or fail because it is being used as a foreign key somewhere?  If you do delete it, does that fix the problem?


On Tue, Dec 9, 2014 at 12:16 PM, Shane McCoy <[hidden email]> wrote:
Hi Scott, thanks for getting back!

heres the query: 

 cvterm_id | cv_id |  name   | definition | dbxref_id | is_obsolete | is_relationshiptype |     name     

-----------+-------+---------+------------+-----------+-------------+---------------------+--------------

        37 |     7 | part_of |            |        39 |           0 |                   1 | relationship

        95 |    15 | part_of |            |       121 |           0 |                   1 | external

(2 rows)


not sure where the external is coming from?? i don't see that on other posts of peoples results. 

thanks!

shane


On Tue, Dec 9, 2014 at 12:04 PM, Scott Cain <[hidden email]> wrote:
Hi Shane,

In addition, I'm worried about the missing 'part_of'; where there any issues, warnings or errors when you loaded your ontologies?  What happens if you execute this query:

SELECT cvterm.*,cv.name FROM cvterm JOIN cv ON (cvterm.cv_id=cv.cv_id) WHERE cvterm.name = 'part_of';

Scott


On Tue, Dec 9, 2014 at 10:30 AM, Andrew Farmer <[hidden email]> wrote:
Hi Shane-
from this error:
On 12/8/14 7:30 PM, Shane McCoy wrote:
striped organism not found in the database at /home/bjreadin/perl5/perlbrew/perls/perl-5.20.1/bin/gmod_bulk_load_gff3.pl line 749, <GEN0> line 2.
I'd guess you simply need to use quotes around the parameter supplied to --organism (ie --organism "striped bass")
so that the shell will recognize it as a single value to be passed in rather than two separate cmdline tokens.

hope that helps

Andrew


-- 
...all concepts in which an entire process is semiotically concentrated
elude definition; only that which has no history is definable.

Friedrich Nietzsche

------------------------------------------------------------------------------
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--
------------------------------------------------------------------------
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/)                     <a href="tel:216-392-3087" value="+12163923087" target="_blank">216-392-3087
Ontario Institute for Cancer Research


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Get technology previously reserved for billion-dollar corporations, FREE
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Re: GFF Bulk Uploader error(s)

Shane McCoy
Well, that was quicker than expected - the part_of warning still appears and now i have many 'skipping  load file is empty' errors. I'll start looking into that but wanted to let you know the part of error is still appearing.
Thanks!
Shane M. 

bjreadin@nc:~/SB_Genome/GFF_files$ gmod_bulk_load_gff3.pl --noexon --analysis --organism stripedbass --gfffile SBDraft_Pt1.all.gff SBDraft_Pt2.all.gff SBDraft_Pt3.all.gff SBDraft_Pt4.all.gff SBDraft_Pt5.all.gff

defined(@array) is deprecated at /home/bjreadin/perl5/perlbrew/perls/perl-5.20.1/lib/site_perl/5.20.1/Bio/GMOD/DB/Adapter.pm line 498.

(Maybe you should just omit the defined()?)

defined(@array) is deprecated at /home/bjreadin/perl5/perlbrew/perls/perl-5.20.1/lib/site_perl/5.20.1/Bio/GMOD/DB/Adapter.pm line 1078.

(Maybe you should just omit the defined()?)

defined(@array) is deprecated at /home/bjreadin/perl5/perlbrew/perls/perl-5.20.1/lib/site_perl/5.20.1/Bio/GMOD/DB/Adapter.pm line 1111.

(Maybe you should just omit the defined()?)

defined(@array) is deprecated at /home/bjreadin/perl5/perlbrew/perls/perl-5.20.1/lib/site_perl/5.20.1/Bio/GMOD/DB/Adapter.pm line 1144.

(Maybe you should just omit the defined()?)

defined(@array) is deprecated at /home/bjreadin/perl5/perlbrew/perls/perl-5.20.1/lib/site_perl/5.20.1/Bio/GMOD/DB/Adapter.pm line 1469.

(Maybe you should just omit the defined()?)

defined(@array) is deprecated at /home/bjreadin/perl5/perlbrew/perls/perl-5.20.1/lib/site_perl/5.20.1/Bio/GMOD/DB/Adapter.pm line 1664.

(Maybe you should just omit the defined()?)

defined(@array) is deprecated at /home/bjreadin/perl5/perlbrew/perls/perl-5.20.1/lib/site_perl/5.20.1/Bio/GMOD/DB/Adapter.pm line 1696.

(Maybe you should just omit the defined()?)

defined(@array) is deprecated at /home/bjreadin/perl5/perlbrew/perls/perl-5.20.1/lib/site_perl/5.20.1/Bio/GMOD/DB/Adapter.pm line 1728.

(Maybe you should just omit the defined()?)

defined(@array) is deprecated at /home/bjreadin/perl5/perlbrew/perls/perl-5.20.1/lib/site_perl/5.20.1/Bio/GMOD/DB/Adapter.pm line 1760.

(Maybe you should just omit the defined()?)

defined(@array) is deprecated at /home/bjreadin/perl5/perlbrew/perls/perl-5.20.1/lib/site_perl/5.20.1/Bio/GMOD/DB/Adapter.pm line 1977.

(Maybe you should just omit the defined()?)

defined(@array) is deprecated at /home/bjreadin/perl5/perlbrew/perls/perl-5.20.1/lib/site_perl/5.20.1/Bio/GMOD/DB/Adapter.pm line 2007.

(Maybe you should just omit the defined()?)

defined(@array) is deprecated at /home/bjreadin/perl5/perlbrew/perls/perl-5.20.1/lib/site_perl/5.20.1/Bio/GMOD/DB/Adapter.pm line 2037.

(Maybe you should just omit the defined()?)

defined(@array) is deprecated at /home/bjreadin/perl5/perlbrew/perls/perl-5.20.1/lib/site_perl/5.20.1/Bio/GMOD/DB/Adapter.pm line 2067.

(Maybe you should just omit the defined()?)

defined(@array) is deprecated at /home/bjreadin/perl5/perlbrew/perls/perl-5.20.1/lib/site_perl/5.20.1/Bio/GMOD/DB/Adapter.pm line 2099.

(Maybe you should just omit the defined()?)

defined(@array) is deprecated at /home/bjreadin/perl5/perlbrew/perls/perl-5.20.1/lib/site_perl/5.20.1/Bio/GMOD/DB/Adapter.pm line 2284.

(Maybe you should just omit the defined()?)

defined(@array) is deprecated at /home/bjreadin/perl5/perlbrew/perls/perl-5.20.1/lib/site_perl/5.20.1/Bio/GMOD/DB/Adapter.pm line 2313.

(Maybe you should just omit the defined()?)

defined(@array) is deprecated at /home/bjreadin/perl5/perlbrew/perls/perl-5.20.1/lib/site_perl/5.20.1/Bio/GMOD/DB/Adapter.pm line 2345.

(Maybe you should just omit the defined()?)

defined(@array) is deprecated at /home/bjreadin/perl5/perlbrew/perls/perl-5.20.1/lib/site_perl/5.20.1/Bio/GMOD/DB/Adapter.pm line 2376.

(Maybe you should just omit the defined()?)

defined(@array) is deprecated at /home/bjreadin/perl5/perlbrew/perls/perl-5.20.1/lib/site_perl/5.20.1/Bio/GMOD/DB/Adapter.pm line 2409.

(Maybe you should just omit the defined()?)

defined(@array) is deprecated at /home/bjreadin/perl5/perlbrew/perls/perl-5.20.1/lib/site_perl/5.20.1/Bio/GMOD/DB/Adapter.pm line 2443.

(Maybe you should just omit the defined()?)

defined(@array) is deprecated at /home/bjreadin/perl5/perlbrew/perls/perl-5.20.1/lib/site_perl/5.20.1/Bio/GMOD/DB/Adapter.pm line 2474.

(Maybe you should just omit the defined()?)

defined(@array) is deprecated at /home/bjreadin/perl5/perlbrew/perls/perl-5.20.1/lib/site_perl/5.20.1/Bio/GMOD/DB/Adapter.pm line 2504.

(Maybe you should just omit the defined()?)

defined(@array) is deprecated at /home/bjreadin/perl5/perlbrew/perls/perl-5.20.1/lib/site_perl/5.20.1/Bio/GMOD/DB/Adapter.pm line 4872.

(Maybe you should just omit the defined()?)



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.



(Re)creating the uniquename cache in the database... 

Creating table...

Populating table...

Creating indexes...

Adjusting the primary key sequences (if necessary)...Done.

Creating gff_meta table...

Preparing data for inserting into the sbass_ncsu database

(This may take a while ...)

Skipping organism table since the load file is empty...

Loading data into analysis table ...

Skipping db table since the load file is empty...

Loading data into dbxref table ...

Skipping cv table since the load file is empty...

Skipping cvterm table since the load file is empty...

Loading data into feature table ...

Loading data into featureloc table ...

Loading data into feature_relationship table ...

Loading data into featureprop table ...

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 ...

Loading data into analysisfeature table ...

Adding cvtermprop=MapReferenceType for 'contig' ...

Adding cvtermprop=MapReferenceType to contig ...

Loading sequences (if any) ...


Done.


On Tue, Dec 9, 2014 at 1:08 PM, Shane McCoy <[hidden email]> wrote:
Ha! yeah, i missed that. It has deleted it. 
I'll go ahead and try loading gff again and get back to you. 
Thanks again!
Shane M.

On Tue, Dec 9, 2014 at 1:03 PM, Scott Cain <[hidden email]> wrote:
Hi Shane,

I just left the semicolon off the end of the delete query; try this:

DELETE FROM cvterm WHERE cvterm_id=95;

Scott


On Tue, Dec 9, 2014 at 12:39 PM, Shane McCoy <[hidden email]> wrote:
I tried deleting it using the script, and received error when checking but second attempt shows results w/ external still there. 

sbass_ncsu=> DELETE FROM cvterm WHERE cvterm_id=95

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

ERROR:  syntax error at or near "Select"

LINE 2: Select cvterm.*,cv.name from cvterm join cv using (cv_id) wh...

        ^

sbass_ncsu=> 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 |    15 | part_of |            |       121 |           0 |                   1 | external

(2 rows)


Thanks,

Shane


On Tue, Dec 9, 2014 at 12:33 PM, Scott Cain <[hidden email]> wrote:
I don't know where that would have come from either, and the database adaptor should ignore it but maybe it isn't.  If you try to delete it (ie, DELETE FROM cvterm WHERE cvterm_id=95) does it delete or fail because it is being used as a foreign key somewhere?  If you do delete it, does that fix the problem?


On Tue, Dec 9, 2014 at 12:16 PM, Shane McCoy <[hidden email]> wrote:
Hi Scott, thanks for getting back!

heres the query: 

 cvterm_id | cv_id |  name   | definition | dbxref_id | is_obsolete | is_relationshiptype |     name     

-----------+-------+---------+------------+-----------+-------------+---------------------+--------------

        37 |     7 | part_of |            |        39 |           0 |                   1 | relationship

        95 |    15 | part_of |            |       121 |           0 |                   1 | external

(2 rows)


not sure where the external is coming from?? i don't see that on other posts of peoples results. 

thanks!

shane


On Tue, Dec 9, 2014 at 12:04 PM, Scott Cain <[hidden email]> wrote:
Hi Shane,

In addition, I'm worried about the missing 'part_of'; where there any issues, warnings or errors when you loaded your ontologies?  What happens if you execute this query:

SELECT cvterm.*,cv.name FROM cvterm JOIN cv ON (cvterm.cv_id=cv.cv_id) WHERE cvterm.name = 'part_of';

Scott


On Tue, Dec 9, 2014 at 10:30 AM, Andrew Farmer <[hidden email]> wrote:
Hi Shane-
from this error:
On 12/8/14 7:30 PM, Shane McCoy wrote:
striped organism not found in the database at /home/bjreadin/perl5/perlbrew/perls/perl-5.20.1/bin/gmod_bulk_load_gff3.pl line 749, <GEN0> line 2.
I'd guess you simply need to use quotes around the parameter supplied to --organism (ie --organism "striped bass")
so that the shell will recognize it as a single value to be passed in rather than two separate cmdline tokens.

hope that helps

Andrew


-- 
...all concepts in which an entire process is semiotically concentrated
elude definition; only that which has no history is definable.

Friedrich Nietzsche

------------------------------------------------------------------------------
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from Actuate! Instantly Supercharge Your Business Reports and Dashboards
with Interactivity, Sharing, Native Excel Exports, App Integration & more
Get technology previously reserved for billion-dollar corporations, FREE
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_______________________________________________
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--
------------------------------------------------------------------------
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/)                     <a href="tel:216-392-3087" value="+12163923087" target="_blank">216-392-3087
Ontario Institute for Cancer Research



------------------------------------------------------------------------------
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from Actuate! Instantly Supercharge Your Business Reports and Dashboards
with Interactivity, Sharing, Native Excel Exports, App Integration & more
Get technology previously reserved for billion-dollar corporations, FREE
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Re: GFF Bulk Uploader error(s)

Karl O. Pinc
On 12/09/2014 12:13:16 PM, Shane McCoy wrote:
> Well, that was quicker than expected - the part_of warning still
> appears
> and now i have many 'skipping  load file is empty' errors. I'll start
> looking into that but wanted to let you know the part of error is
> still
> appearing.

I seem to remember that at one point Scott looked at the code
and said that the part_of error always appears and should be
ignored.   (As far as our load, there was some other problem,
which I've forgotten.)


Karl <[hidden email]>
Free Software:  "You don't pay back, you pay forward."
                 -- Robert A. Heinlein

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Re: GFF Bulk Uploader error(s)

Scott Cain
Oh, right!  I'm glad somebody is paying attention.  I completely forgot about that; I just wish I could scrape together the time to put out a new release (money for that may be coming soon! fingers crossed).


On Tue, Dec 9, 2014 at 1:23 PM, Karl O. Pinc <[hidden email]> wrote:
On 12/09/2014 12:13:16 PM, Shane McCoy wrote:
> Well, that was quicker than expected - the part_of warning still
> appears
> and now i have many 'skipping  load file is empty' errors. I'll start
> looking into that but wanted to let you know the part of error is
> still
> appearing.

I seem to remember that at one point Scott looked at the code
and said that the part_of error always appears and should be
ignored.   (As far as our load, there was some other problem,
which I've forgotten.)


Karl <[hidden email]>
Free Software:  "You don't pay back, you pay forward."
                 -- Robert A. Heinlein



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

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Re: GFF Bulk Uploader error(s)

Shane McCoy
Ok, so i can just ignore the warning for now. Thanks! 
What about the following errors? Is this an issue w/ my GFF files? 
thanks!
Shane

Skipping organism table since the load file is empty...

Loading data into analysis table ...

Skipping db table since the load file is empty...

Loading data into dbxref table ...

Skipping cv table since the load file is empty...

Skipping cvterm table since the load file is empty...

Loading data into feature table ...

Loading data into featureloc table ...

Loading data into feature_relationship table ...

Loading data into featureprop table ...

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 ...

Loading data into analysisfeature table ...

Adding cvtermprop=MapReferenceType for 'contig' ...

Adding cvtermprop=MapReferenceType to contig ...

Loading sequences (if any) ...




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Re: GFF Bulk Uploader error(s)

Scott Cain
Hi Shane,

None of those messages is a problem; it's skipping organism, feature_cvterm, etc presumably because your GFF file doesn't have any data of that sort to load.


On Tue, Dec 9, 2014 at 3:59 PM, Shane McCoy <[hidden email]> wrote:
Ok, so i can just ignore the warning for now. Thanks! 
What about the following errors? Is this an issue w/ my GFF files? 
thanks!
Shane

Skipping organism table since the load file is empty...

Loading data into analysis table ...

Skipping db table since the load file is empty...

Loading data into dbxref table ...

Skipping cv table since the load file is empty...

Skipping cvterm table since the load file is empty...

Loading data into feature table ...

Loading data into featureloc table ...

Loading data into feature_relationship table ...

Loading data into featureprop table ...

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 ...

Loading data into analysisfeature table ...

Adding cvtermprop=MapReferenceType for 'contig' ...

Adding cvtermprop=MapReferenceType to contig ...

Loading sequences (if any) ...






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

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Re: GFF Bulk Uploader error(s)

Scott Cain
Hi Shane,

If you loaded a 1GB GFF file in 5 seconds, then you were right the first time and it didn't work (unless it loaded before and this time it was just verifying that it's already seen that file).  Can you check that you have the amount of data in your feature table that you would expect?  You can do
SELECT count(*) FROM feature; and you should get a number that is close to the number of GFF lines in your GFF file (it probably won't be exactly the same though).

Scott


On Tue, Dec 9, 2014 at 7:17 PM, Shane McCoy <[hidden email]> wrote:
Hmm. ok. I was expecting a much longer loading time (the full gff files are nearly 1gb) and the process lasted less than 5secs. That(along w/ the errors) led me to believe to whole thing had failed.
I really wasn't expecting that it had worked. ha! Thank you for all your responses.
Very much appreciated,
cheers!
Shane M.

On Tue, Dec 9, 2014 at 6:26 PM, Scott Cain <[hidden email]> wrote:
Hi Shane,

None of those messages is a problem; it's skipping organism, feature_cvterm, etc presumably because your GFF file doesn't have any data of that sort to load.


On Tue, Dec 9, 2014 at 3:59 PM, Shane McCoy <[hidden email]> wrote:
Ok, so i can just ignore the warning for now. Thanks! 
What about the following errors? Is this an issue w/ my GFF files? 
thanks!
Shane

Skipping organism table since the load file is empty...

Loading data into analysis table ...

Skipping db table since the load file is empty...

Loading data into dbxref table ...

Skipping cv table since the load file is empty...

Skipping cvterm table since the load file is empty...

Loading data into feature table ...

Loading data into featureloc table ...

Loading data into feature_relationship table ...

Loading data into featureprop table ...

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 ...

Loading data into analysisfeature table ...

Adding cvtermprop=MapReferenceType for 'contig' ...

Adding cvtermprop=MapReferenceType to contig ...

Loading sequences (if any) ...






--
------------------------------------------------------------------------
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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Re: GFF Bulk Uploader error(s)

Karl O. Pinc
On 12/10/2014 08:52:55 AM, Scott Cain wrote:
> Hi Shane,
>
> If you loaded a 1GB GFF file in 5 seconds, then you were right the
> first
> time and it didn't work (unless it loaded before and this time it was
> just
> verifying that it's already seen that file).

I seem to recall that if you interrupt the load then it thinks
that you've already seen the file.  Then there's something you
need to delete in order to try again.



Karl <[hidden email]>
Free Software:  "You don't pay back, you pay forward."
                 -- Robert A. Heinlein

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Re: GFF Bulk Uploader error(s)

Scott Cain
Hi Karl,

True, though it should either do that automatically or complain loudly that it hasn't been done.


On Wed, Dec 10, 2014 at 10:18 AM, Karl O. Pinc <[hidden email]> wrote:
On 12/10/2014 08:52:55 AM, Scott Cain wrote:
> Hi Shane,
>
> If you loaded a 1GB GFF file in 5 seconds, then you were right the
> first
> time and it didn't work (unless it loaded before and this time it was
> just
> verifying that it's already seen that file).

I seem to recall that if you interrupt the load then it thinks
that you've already seen the file.  Then there's something you
need to delete in order to try again.



Karl <[hidden email]>
Free Software:  "You don't pay back, you pay forward."
                 -- Robert A. Heinlein



--
------------------------------------------------------------------------
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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Get technology previously reserved for billion-dollar corporations, FREE
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Re: GFF Bulk Uploader error(s)

Shane McCoy
In reply to this post by Scott Cain
Hey! Thanks for getting back to me. The quick loading happened on the first try. I actually started back @ perl Makefile.pl and reloaded the ontologies after the first failure just to be sure all was clear.
Here is the output;
sbass_ncsu=> SELECT count(*) FROM feature;
 count
-------
   106
(1 row)

The GFF files have over 150,000 rows.

Here are the notes i have from installing if this helps too;

in /home/bjreadin/trunk/chado
perl Makefile.pl
make
make install
make load_schema
make prepdb
make ontologies *note below
When prompted; 1,2,3,4
Available ontologies:
[1] Relationship Ontology *required
[2] Sequence Ontology *required
[3] Gene Ontology
[4] Chado Feature Properties *highly recommended
[5] Cell Ontology
[6] Plant Ontology

* this step is prone to excessive failure. you can shortcut past this w/ precompiled sql file of 1-6 ontologies. See Chado folder on desktop.

In this case, 'make ontologies' worked on the 12th try.
For every failure in 'make ontologies' in /trunk/chado
run:
rm -rf tmp
make clean

You will restart at perl Makefile.pl

Success?
save your database!!

pg_dump sbass_ncsu > sbass_ncsu.sql

to bring back;
$ psql db_name < db_dump.sql

Check for extra 'part_of' term in data base.
psql <database name>
sbass_ncsu=> Select cvterm.*,cv.name from cvterm join cv using (cv_id) where cvterm.name = 'part_of';

If needed to delete extra line: (cvterm_id=? depending)
sbass_ncsu=> DELETE FROM cvterm WHERE cvterm_id=95;
DELETE 1

gmod_bulk_load_gff3.pl --noexon --analysis --organism stripedbass --gfffile SBDraft_Pt1.all.gff SBDraft_Pt2.all.gff SBDraft_Pt3.all.gff SBDraft_Pt4.all.gff SBDraft_Pt5.all.gff

Add this if you have to redo --recreate_cache

On Wed, Dec 10, 2014 at 9:52 AM, Scott Cain <[hidden email]> wrote:
Hi Shane,

If you loaded a 1GB GFF file in 5 seconds, then you were right the first time and it didn't work (unless it loaded before and this time it was just verifying that it's already seen that file).  Can you check that you have the amount of data in your feature table that you would expect?  You can do
SELECT count(*) FROM feature; and you should get a number that is close to the number of GFF lines in your GFF file (it probably won't be exactly the same though).

Scott


On Tue, Dec 9, 2014 at 7:17 PM, Shane McCoy <[hidden email]> wrote:
Hmm. ok. I was expecting a much longer loading time (the full gff files are nearly 1gb) and the process lasted less than 5secs. That(along w/ the errors) led me to believe to whole thing had failed.
I really wasn't expecting that it had worked. ha! Thank you for all your responses.
Very much appreciated,
cheers!
Shane M.

On Tue, Dec 9, 2014 at 6:26 PM, Scott Cain <[hidden email]> wrote:
Hi Shane,

None of those messages is a problem; it's skipping organism, feature_cvterm, etc presumably because your GFF file doesn't have any data of that sort to load.


On Tue, Dec 9, 2014 at 3:59 PM, Shane McCoy <[hidden email]> wrote:
Ok, so i can just ignore the warning for now. Thanks! 
What about the following errors? Is this an issue w/ my GFF files? 
thanks!
Shane

Skipping organism table since the load file is empty...

Loading data into analysis table ...

Skipping db table since the load file is empty...

Loading data into dbxref table ...

Skipping cv table since the load file is empty...

Skipping cvterm table since the load file is empty...

Loading data into feature table ...

Loading data into featureloc table ...

Loading data into feature_relationship table ...

Loading data into featureprop table ...

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 ...

Loading data into analysisfeature table ...

Adding cvtermprop=MapReferenceType for 'contig' ...

Adding cvtermprop=MapReferenceType to contig ...

Loading sequences (if any) ...






--
------------------------------------------------------------------------
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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with Interactivity, Sharing, Native Excel Exports, App Integration & more
Get technology previously reserved for billion-dollar corporations, FREE
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Re: GFF Bulk Uploader error(s)

Scott Cain
Hi Shane,

The -gfffile parameter doesn't take multiple file names as arguments--you have to load those one at a time.  I suspect it's loading the first file and ignoring the rest.



On Wed, Dec 10, 2014 at 10:43 AM, Shane McCoy <[hidden email]> wrote:
Hey! Thanks for getting back to me. The quick loading happened on the first try. I actually started back @ perl Makefile.pl and reloaded the ontologies after the first failure just to be sure all was clear.
Here is the output;
sbass_ncsu=> SELECT count(*) FROM feature;
 count
-------
   106
(1 row)

The GFF files have over 150,000 rows.

Here are the notes i have from installing if this helps too;

in /home/bjreadin/trunk/chado
perl Makefile.pl
make
make install
make load_schema
make prepdb
make ontologies *note below
When prompted; 1,2,3,4
Available ontologies:
[1] Relationship Ontology *required
[2] Sequence Ontology *required
[3] Gene Ontology
[4] Chado Feature Properties *highly recommended
[5] Cell Ontology
[6] Plant Ontology

* this step is prone to excessive failure. you can shortcut past this w/ precompiled sql file of 1-6 ontologies. See Chado folder on desktop.

In this case, 'make ontologies' worked on the 12th try.
For every failure in 'make ontologies' in /trunk/chado
run:
rm -rf tmp
make clean

You will restart at perl Makefile.pl

Success?
save your database!!

pg_dump sbass_ncsu > sbass_ncsu.sql

to bring back;
$ psql db_name < db_dump.sql

Check for extra 'part_of' term in data base.
psql <database name>
sbass_ncsu=> Select cvterm.*,cv.name from cvterm join cv using (cv_id) where cvterm.name = 'part_of';

If needed to delete extra line: (cvterm_id=? depending)
sbass_ncsu=> DELETE FROM cvterm WHERE cvterm_id=95;
DELETE 1

gmod_bulk_load_gff3.pl --noexon --analysis --organism stripedbass --gfffile SBDraft_Pt1.all.gff SBDraft_Pt2.all.gff SBDraft_Pt3.all.gff SBDraft_Pt4.all.gff SBDraft_Pt5.all.gff

Add this if you have to redo --recreate_cache

On Wed, Dec 10, 2014 at 9:52 AM, Scott Cain <[hidden email]> wrote:
Hi Shane,

If you loaded a 1GB GFF file in 5 seconds, then you were right the first time and it didn't work (unless it loaded before and this time it was just verifying that it's already seen that file).  Can you check that you have the amount of data in your feature table that you would expect?  You can do
SELECT count(*) FROM feature; and you should get a number that is close to the number of GFF lines in your GFF file (it probably won't be exactly the same though).

Scott


On Tue, Dec 9, 2014 at 7:17 PM, Shane McCoy <[hidden email]> wrote:
Hmm. ok. I was expecting a much longer loading time (the full gff files are nearly 1gb) and the process lasted less than 5secs. That(along w/ the errors) led me to believe to whole thing had failed.
I really wasn't expecting that it had worked. ha! Thank you for all your responses.
Very much appreciated,
cheers!
Shane M.

On Tue, Dec 9, 2014 at 6:26 PM, Scott Cain <[hidden email]> wrote:
Hi Shane,

None of those messages is a problem; it's skipping organism, feature_cvterm, etc presumably because your GFF file doesn't have any data of that sort to load.


On Tue, Dec 9, 2014 at 3:59 PM, Shane McCoy <[hidden email]> wrote:
Ok, so i can just ignore the warning for now. Thanks! 
What about the following errors? Is this an issue w/ my GFF files? 
thanks!
Shane

Skipping organism table since the load file is empty...

Loading data into analysis table ...

Skipping db table since the load file is empty...

Loading data into dbxref table ...

Skipping cv table since the load file is empty...

Skipping cvterm table since the load file is empty...

Loading data into feature table ...

Loading data into featureloc table ...

Loading data into feature_relationship table ...

Loading data into featureprop table ...

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 ...

Loading data into analysisfeature table ...

Adding cvtermprop=MapReferenceType for 'contig' ...

Adding cvtermprop=MapReferenceType to contig ...

Loading sequences (if any) ...






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

------------------------------------------------------------------------------
Download BIRT iHub F-Type - The Free Enterprise-Grade BIRT Server
from Actuate! Instantly Supercharge Your Business Reports and Dashboards
with Interactivity, Sharing, Native Excel Exports, App Integration & more
Get technology previously reserved for billion-dollar corporations, FREE
http://pubads.g.doubleclick.net/gampad/clk?id=164703151&iu=/4140/ostg.clktrk
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Re: GFF Bulk Uploader error(s)

Shane McCoy
ahh. ok. I'll restart and do one at a time.
thank you!
Shane M.

On Wed, Dec 10, 2014 at 10:51 AM, Scott Cain <[hidden email]> wrote:
Hi Shane,

The -gfffile parameter doesn't take multiple file names as arguments--you have to load those one at a time.  I suspect it's loading the first file and ignoring the rest.



On Wed, Dec 10, 2014 at 10:43 AM, Shane McCoy <[hidden email]> wrote:
Hey! Thanks for getting back to me. The quick loading happened on the first try. I actually started back @ perl Makefile.pl and reloaded the ontologies after the first failure just to be sure all was clear.
Here is the output;
sbass_ncsu=> SELECT count(*) FROM feature;
 count
-------
   106
(1 row)

The GFF files have over 150,000 rows.

Here are the notes i have from installing if this helps too;

in /home/bjreadin/trunk/chado
perl Makefile.pl
make
make install
make load_schema
make prepdb
make ontologies *note below
When prompted; 1,2,3,4
Available ontologies:
[1] Relationship Ontology *required
[2] Sequence Ontology *required
[3] Gene Ontology
[4] Chado Feature Properties *highly recommended
[5] Cell Ontology
[6] Plant Ontology

* this step is prone to excessive failure. you can shortcut past this w/ precompiled sql file of 1-6 ontologies. See Chado folder on desktop.

In this case, 'make ontologies' worked on the 12th try.
For every failure in 'make ontologies' in /trunk/chado
run:
rm -rf tmp
make clean

You will restart at perl Makefile.pl

Success?
save your database!!

pg_dump sbass_ncsu > sbass_ncsu.sql

to bring back;
$ psql db_name < db_dump.sql

Check for extra 'part_of' term in data base.
psql <database name>
sbass_ncsu=> Select cvterm.*,cv.name from cvterm join cv using (cv_id) where cvterm.name = 'part_of';

If needed to delete extra line: (cvterm_id=? depending)
sbass_ncsu=> DELETE FROM cvterm WHERE cvterm_id=95;
DELETE 1

gmod_bulk_load_gff3.pl --noexon --analysis --organism stripedbass --gfffile SBDraft_Pt1.all.gff SBDraft_Pt2.all.gff SBDraft_Pt3.all.gff SBDraft_Pt4.all.gff SBDraft_Pt5.all.gff

Add this if you have to redo --recreate_cache

On Wed, Dec 10, 2014 at 9:52 AM, Scott Cain <[hidden email]> wrote:
Hi Shane,

If you loaded a 1GB GFF file in 5 seconds, then you were right the first time and it didn't work (unless it loaded before and this time it was just verifying that it's already seen that file).  Can you check that you have the amount of data in your feature table that you would expect?  You can do
SELECT count(*) FROM feature; and you should get a number that is close to the number of GFF lines in your GFF file (it probably won't be exactly the same though).

Scott


On Tue, Dec 9, 2014 at 7:17 PM, Shane McCoy <[hidden email]> wrote:
Hmm. ok. I was expecting a much longer loading time (the full gff files are nearly 1gb) and the process lasted less than 5secs. That(along w/ the errors) led me to believe to whole thing had failed.
I really wasn't expecting that it had worked. ha! Thank you for all your responses.
Very much appreciated,
cheers!
Shane M.

On Tue, Dec 9, 2014 at 6:26 PM, Scott Cain <[hidden email]> wrote:
Hi Shane,

None of those messages is a problem; it's skipping organism, feature_cvterm, etc presumably because your GFF file doesn't have any data of that sort to load.


On Tue, Dec 9, 2014 at 3:59 PM, Shane McCoy <[hidden email]> wrote:
Ok, so i can just ignore the warning for now. Thanks! 
What about the following errors? Is this an issue w/ my GFF files? 
thanks!
Shane

Skipping organism table since the load file is empty...

Loading data into analysis table ...

Skipping db table since the load file is empty...

Loading data into dbxref table ...

Skipping cv table since the load file is empty...

Skipping cvterm table since the load file is empty...

Loading data into feature table ...

Loading data into featureloc table ...

Loading data into feature_relationship table ...

Loading data into featureprop table ...

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 ...

Loading data into analysisfeature table ...

Adding cvtermprop=MapReferenceType for 'contig' ...

Adding cvtermprop=MapReferenceType to contig ...

Loading sequences (if any) ...






--
------------------------------------------------------------------------
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/)                     <a href="tel:216-392-3087" value="+12163923087" target="_blank">216-392-3087
Ontario Institute for Cancer Research


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