tutorial gff upload

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tutorial gff upload

elswob
Hi,

I am following the tutorial and am now trying to load the Citrus_sinensis-orange1.1g015632m.g.gff3 file into my database. I get the following error:

WD tripal_core: chado_execute_prepared: wrong argument type supplied for 'ins_feature_all' statement. Expected    [error]
bool but recieved 'false'
WD tripal_core: tripal_core_chado_insert: Cannot insert record into feature table: Array                          [error]
(
    [organism_id] => 15
    [name] => scaffold00001
    [uniquename] => scaffold00001
    [residues] => 
    [seqlen] => 0
    [md5checksum] => d41d8cd98f00b204e9800998ecf8427e
    [type_id] => 405
    [is_analysis] => false
    [is_obsolete] => false
)

The error file states this:

Parsing line 3 (1.20%).
   Adding feature 'scaffold00001' (supercontig)
ERROR: failed to insert feature 'scaffold00001' (supercontig)
Parsing line 4 (2.00%).
ERROR: the landmark 'scaffold00001' cannot be found for this organism. Please add the landmark and then retry the import ofhis GFF3 file.

Any help would be most appreciated.

Regards,

Ben

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Re: tutorial gff upload

Stephen Ficklin-2
Hi Ben,

An unfortunate side effect of using the development branch of Tripal is that the code changes and sometimes we inadvertently break things.  Because we have not yet released v1.0 of Tripal the tutorial uses the development branch.  I think though that the problem you are encountering is for a bug that has already been fixed.   If you could update your Tripal code (both the module and the theme) then I think the problem should be resolved:

cd /var/www/sites/all/modules/tripal
git pull

cd /var/www/sites/all/themes/tripal_theme
git pull

If not let me know and we can look further at the problem for you.
Stephen

On 10/4/2012 9:58 AM, Ben Elsworth wrote:
Hi,

I am following the tutorial and am now trying to load the Citrus_sinensis-orange1.1g015632m.g.gff3 file into my database. I get the following error:

WD tripal_core: chado_execute_prepared: wrong argument type supplied for 'ins_feature_all' statement. Expected    [error]
bool but recieved 'false'
WD tripal_core: tripal_core_chado_insert: Cannot insert record into feature table: Array                          [error]
(
    [organism_id] => 15
    [name] => scaffold00001
    [uniquename] => scaffold00001
    [residues] => 
    [seqlen] => 0
    [md5checksum] => d41d8cd98f00b204e9800998ecf8427e
    [type_id] => 405
    [is_analysis] => false
    [is_obsolete] => false
)

The error file states this:

Parsing line 3 (1.20%).
   Adding feature 'scaffold00001' (supercontig)
ERROR: failed to insert feature 'scaffold00001' (supercontig)
Parsing line 4 (2.00%).
ERROR: the landmark 'scaffold00001' cannot be found for this organism. Please add the landmark and then retry the import ofhis GFF3 file.

Any help would be most appreciated.

Regards,

Ben


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Re: tutorial gff upload

elswob
Hi Stephen,

Thanks for getting back to me. That fixed it, and I managed to load the three files. However, when I try to sync them I get this:

Tripal Job Launcher
Running as user 'administrator'
-------------------
Calling: tripal_feature_sync_features(0, 15, <p>gene mRNA</p>
, 30)
Looking for features of type: <p>gene mRNA</p> 
array_fill(): Number of elements must be positive database.inc:253                                                                               [warning]
implode(): Invalid arguments passed database.inc:253                                                                                             [warning]
array_keys() expects parameter 1 to be array, null given user.module:528                                                                         [warning]
pg_query(): Query failed: ERROR:  syntax error at or near ")"                                                                                    [warning]
LINE 1: ...r INNER JOIN permission p ON p.rid = r.rid WHERE r.rid IN ()
                                                                      ^ database.pgsql.inc:138
ERROR:  syntax error at or near &quot;)&quot;                                                                                                    [warning]
LINE 1: ...r INNER JOIN permission p ON p.rid = r.rid WHERE r.rid IN ()
                                                                      ^
query: SELECT p.perm FROM role r INNER JOIN permission p ON p.rid = r.rid WHERE r.rid IN () database.pgsql.inc:159
Created new vocabulary Feature Type.                                                                                                             [status]
Created new vocabulary Organism.                                                                                                                 [status]
Created new vocabulary Library.                                                                                                                  [status]
Created new vocabulary Analysis.   

And a search of the sequence features reveals nothing?

Regards,

Ben

On 4 October 2012 16:10, Stephen Ficklin <[hidden email]> wrote:
Hi Ben,

An unfortunate side effect of using the development branch of Tripal is that the code changes and sometimes we inadvertently break things.  Because we have not yet released v1.0 of Tripal the tutorial uses the development branch.  I think though that the problem you are encountering is for a bug that has already been fixed.   If you could update your Tripal code (both the module and the theme) then I think the problem should be resolved:

cd /var/www/sites/all/modules/tripal
git pull

cd /var/www/sites/all/themes/tripal_theme
git pull

If not let me know and we can look further at the problem for you.
Stephen


On 10/4/2012 9:58 AM, Ben Elsworth wrote:
Hi,

I am following the tutorial and am now trying to load the Citrus_sinensis-orange1.1g015632m.g.gff3 file into my database. I get the following error:

WD tripal_core: chado_execute_prepared: wrong argument type supplied for 'ins_feature_all' statement. Expected    [error]
bool but recieved 'false'
WD tripal_core: tripal_core_chado_insert: Cannot insert record into feature table: Array                          [error]
(
    [organism_id] => 15
    [name] => scaffold00001
    [uniquename] => scaffold00001
    [residues] => 
    [seqlen] => 0
    [md5checksum] => d41d8cd98f00b204e9800998ecf8427e
    [type_id] => 405
    [is_analysis] => false
    [is_obsolete] => false
)

The error file states this:

Parsing line 3 (1.20%).
   Adding feature 'scaffold00001' (supercontig)
ERROR: failed to insert feature 'scaffold00001' (supercontig)
Parsing line 4 (2.00%).
ERROR: the landmark 'scaffold00001' cannot be found for this organism. Please add the landmark and then retry the import ofhis GFF3 file.

Any help would be most appreciated.

Regards,

Ben


------------------------------------------------------------------------------
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Deploy New Relic app performance management and know exactly
what is happening inside your Ruby, Python, PHP, Java, and .NET app
Try New Relic at no cost today and get our sweet Data Nerd shirt too!
http://p.sf.net/sfu/newrelic-dev2dev


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Re: tutorial gff upload

Stephen Ficklin-2
Hi Ben,

Do you have the ckeditor installed?  It looks like somehow you are getting <p> tags around your feature types (e.g. <p> gene mRNA </p>).   if you can switch off whatever editor you may have so that it submits the types without the <p> tag I believe that should solve the problem.

Stephen

On 10/4/2012 11:50 AM, Ben Elsworth wrote:
Hi Stephen,

Thanks for getting back to me. That fixed it, and I managed to load the three files. However, when I try to sync them I get this:

Tripal Job Launcher
Running as user 'administrator'
-------------------
Calling: tripal_feature_sync_features(0, 15, <p>gene mRNA</p>
, 30)
Looking for features of type: <p>gene mRNA</p> 
array_fill(): Number of elements must be positive database.inc:253                                                                               [warning]
implode(): Invalid arguments passed database.inc:253                                                                                             [warning]
array_keys() expects parameter 1 to be array, null given user.module:528                                                                         [warning]
pg_query(): Query failed: ERROR:  syntax error at or near ")"                                                                                    [warning]
LINE 1: ...r INNER JOIN permission p ON p.rid = r.rid WHERE r.rid IN ()
                                                                      ^ database.pgsql.inc:138
ERROR:  syntax error at or near &quot;)&quot;                                                                                                    [warning]
LINE 1: ...r INNER JOIN permission p ON p.rid = r.rid WHERE r.rid IN ()
                                                                      ^
query: SELECT p.perm FROM role r INNER JOIN permission p ON p.rid = r.rid WHERE r.rid IN () database.pgsql.inc:159
Created new vocabulary Feature Type.                                                                                                             [status]
Created new vocabulary Organism.                                                                                                                 [status]
Created new vocabulary Library.                                                                                                                  [status]
Created new vocabulary Analysis.   

And a search of the sequence features reveals nothing?

Regards,

Ben

On 4 October 2012 16:10, Stephen Ficklin <[hidden email]> wrote:
Hi Ben,

An unfortunate side effect of using the development branch of Tripal is that the code changes and sometimes we inadvertently break things.  Because we have not yet released v1.0 of Tripal the tutorial uses the development branch.  I think though that the problem you are encountering is for a bug that has already been fixed.   If you could update your Tripal code (both the module and the theme) then I think the problem should be resolved:

cd /var/www/sites/all/modules/tripal
git pull

cd /var/www/sites/all/themes/tripal_theme
git pull

If not let me know and we can look further at the problem for you.
Stephen


On 10/4/2012 9:58 AM, Ben Elsworth wrote:
Hi,

I am following the tutorial and am now trying to load the Citrus_sinensis-orange1.1g015632m.g.gff3 file into my database. I get the following error:

WD tripal_core: chado_execute_prepared: wrong argument type supplied for 'ins_feature_all' statement. Expected    [error]
bool but recieved 'false'
WD tripal_core: tripal_core_chado_insert: Cannot insert record into feature table: Array                          [error]
(
    [organism_id] => 15
    [name] => scaffold00001
    [uniquename] => scaffold00001
    [residues] => 
    [seqlen] => 0
    [md5checksum] => d41d8cd98f00b204e9800998ecf8427e
    [type_id] => 405
    [is_analysis] => false
    [is_obsolete] => false
)

The error file states this:

Parsing line 3 (1.20%).
   Adding feature 'scaffold00001' (supercontig)
ERROR: failed to insert feature 'scaffold00001' (supercontig)
Parsing line 4 (2.00%).
ERROR: the landmark 'scaffold00001' cannot be found for this organism. Please add the landmark and then retry the import ofhis GFF3 file.

Any help would be most appreciated.

Regards,

Ben


------------------------------------------------------------------------------
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Deploy New Relic app performance management and know exactly
what is happening inside your Ruby, Python, PHP, Java, and .NET app
Try New Relic at no cost today and get our sweet Data Nerd shirt too!
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Deploy New Relic app performance management and know exactly
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Re: tutorial gff upload

elswob
Hi Stephen, 

Yes, I was using the default rich text editor, switching to the plain text editor fixed it.

Thanks again,

Ben

On 4 October 2012 16:56, Stephen Ficklin <[hidden email]> wrote:
Hi Ben,

Do you have the ckeditor installed?  It looks like somehow you are getting <p> tags around your feature types (e.g. <p> gene mRNA </p>).   if you can switch off whatever editor you may have so that it submits the types without the <p> tag I believe that should solve the problem.

Stephen


On 10/4/2012 11:50 AM, Ben Elsworth wrote:
Hi Stephen,

Thanks for getting back to me. That fixed it, and I managed to load the three files. However, when I try to sync them I get this:

Tripal Job Launcher
Running as user 'administrator'
-------------------
Calling: tripal_feature_sync_features(0, 15, <p>gene mRNA</p>
, 30)
Looking for features of type: <p>gene mRNA</p> 
array_fill(): Number of elements must be positive database.inc:253                                                                               [warning]
implode(): Invalid arguments passed database.inc:253                                                                                             [warning]
array_keys() expects parameter 1 to be array, null given user.module:528                                                                         [warning]
pg_query(): Query failed: ERROR:  syntax error at or near ")"                                                                                    [warning]
LINE 1: ...r INNER JOIN permission p ON p.rid = r.rid WHERE r.rid IN ()
                                                                      ^ database.pgsql.inc:138
ERROR:  syntax error at or near &quot;)&quot;                                                                                                    [warning]
LINE 1: ...r INNER JOIN permission p ON p.rid = r.rid WHERE r.rid IN ()
                                                                      ^
query: SELECT p.perm FROM role r INNER JOIN permission p ON p.rid = r.rid WHERE r.rid IN () database.pgsql.inc:159
Created new vocabulary Feature Type.                                                                                                             [status]
Created new vocabulary Organism.                                                                                                                 [status]
Created new vocabulary Library.                                                                                                                  [status]
Created new vocabulary Analysis.   

And a search of the sequence features reveals nothing?

Regards,

Ben

On 4 October 2012 16:10, Stephen Ficklin <[hidden email]> wrote:
Hi Ben,

An unfortunate side effect of using the development branch of Tripal is that the code changes and sometimes we inadvertently break things.  Because we have not yet released v1.0 of Tripal the tutorial uses the development branch.  I think though that the problem you are encountering is for a bug that has already been fixed.   If you could update your Tripal code (both the module and the theme) then I think the problem should be resolved:

cd /var/www/sites/all/modules/tripal
git pull

cd /var/www/sites/all/themes/tripal_theme
git pull

If not let me know and we can look further at the problem for you.
Stephen


On 10/4/2012 9:58 AM, Ben Elsworth wrote:
Hi,

I am following the tutorial and am now trying to load the Citrus_sinensis-orange1.1g015632m.g.gff3 file into my database. I get the following error:

WD tripal_core: chado_execute_prepared: wrong argument type supplied for 'ins_feature_all' statement. Expected    [error]
bool but recieved 'false'
WD tripal_core: tripal_core_chado_insert: Cannot insert record into feature table: Array                          [error]
(
    [organism_id] => 15
    [name] => scaffold00001
    [uniquename] => scaffold00001
    [residues] => 
    [seqlen] => 0
    [md5checksum] => d41d8cd98f00b204e9800998ecf8427e
    [type_id] => 405
    [is_analysis] => false
    [is_obsolete] => false
)

The error file states this:

Parsing line 3 (1.20%).
   Adding feature 'scaffold00001' (supercontig)
ERROR: failed to insert feature 'scaffold00001' (supercontig)
Parsing line 4 (2.00%).
ERROR: the landmark 'scaffold00001' cannot be found for this organism. Please add the landmark and then retry the import ofhis GFF3 file.

Any help would be most appreciated.

Regards,

Ben


------------------------------------------------------------------------------
Don't let slow site performance ruin your business. Deploy New Relic APM
Deploy New Relic app performance management and know exactly
what is happening inside your Ruby, Python, PHP, Java, and .NET app
Try New Relic at no cost today and get our sweet Data Nerd shirt too!
http://p.sf.net/sfu/newrelic-dev2dev


_______________________________________________
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[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-tripal





------------------------------------------------------------------------------
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Deploy New Relic app performance management and know exactly
what is happening inside your Ruby, Python, PHP, Java, and .NET app
Try New Relic at no cost today and get our sweet Data Nerd shirt too!
http://p.sf.net/sfu/newrelic-dev2dev
_______________________________________________
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