Fwd: loading scripts not working

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Fwd: loading scripts not working

Asma Riyaz

---------- Forwarded message ----------
From: Asma Riyaz <[hidden email]>
Date: Mon, Oct 6, 2014 at 12:55 PM
Subject: loading scripts not working
To: [hidden email], [hidden email]


Hi,

I am trying to load gff3 files for Tribolium using bp_seqfeature_load.pl which fails with this error:

Transaction aborted because DBD::mysql::st execute failed: Table 'tribolium.locationlist' doesn't exist at /usr/share/perl5/Bio/DB/SeqFeature/Store/DBI/mysql.pm line 1571, <GEN0> line 22208.

-------------------- EXCEPTION --------------------
MSG:  should have a primary_id
STACK Bio::DB::SeqFeature::Store::DBI::mysql::_add_SeqFeature /usr/share/perl5/Bio/DB/SeqFeature/Store/DBI/mysql.pm:603
STACK Bio::DB::SeqFeature::Store::add_SeqFeature /usr/share/perl5/Bio/DB/SeqFeature/Store.pm:1525
STACK Bio::DB::SeqFeature::Store::GFF3Loader::build_object_tree_in_tables /usr/share/perl5/Bio/DB/SeqFeature/Store/GFF3Loader.pm:726
STACK Bio::DB::SeqFeature::Store::GFF3Loader::build_object_tree /usr/share/perl5/Bio/DB/SeqFeature/Store/GFF3Loader.pm:699
STACK Bio::DB::SeqFeature::Store::GFF3Loader::finish_load /usr/share/perl5/Bio/DB/SeqFeature/Store/GFF3Loader.pm:343
STACK Bio::DB::SeqFeature::Store::Loader::load_fh /usr/share/perl5/Bio/DB/SeqFeature/Store/Loader.pm:354
STACK Bio::DB::SeqFeature::Store::Loader::load /usr/share/perl5/Bio/DB/SeqFeature/Store/Loader.pm:243
STACK toplevel bp_seqfeature_load.pl:258


Here is the command I use:
perl bp_seqfeature_load.pl -d tribolium -a DBI::mysql --user <user> --password <password> <list of gff3 files>


I have also tried using bp_bulk_load_gff.pl to load data:

"my" variable $AUTH masks earlier declaration in same scope at bp_bulk_load_gff.pl line 656.
"my" variable $db masks earlier declaration in same scope at bp_bulk_load_gff.pl line 666.
This operation will delete all existing data in database dbi:mysql:test.  Continue? Y

159000 features parsed in  0.08s...
You are loading a Bio::DB::GFF database with GFF3 formatted data.
While this will likely work fine, the Bio::DB::GFF schema does not
always faithfully capture the complexity represented in GFF3 files.
Unless you have a specific reason for using Bio::DB::GFF, we suggest
that you use a Bio::DB::SeqFeature::Store database and its corresponding
loader, bp_seqfeature_load.pl.
Total parse time 13.70sin  0.09s...
Loading feature data and analyzing tables.  You may see RDBMS messages here...
ERROR 1045 (28000) at line 1: Access denied for user 'tomoyasulab'@'localhost' (using password: YES)
Total load time  0.00s
done...
Analyzing/optimizing tables. You will see database messages...
Optimization time time  0.00s
FAILURE: Please see standard error for details


Here is command I used:
perl bp_bulk_load_gff.pl -d tribolium --user <user> --password <password> <list of gff3 files>.

In mysql I issued the following commands:

CREATE DATABASE tribolium;
grant select on tribolium.* to nobody@localhost;
grant all privileges on tribolium.* to <user>@localhost;

What am I missing and how can I make this work?

Thanks,
Asma










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Re: loading scripts not working

vkrishna
Hi Asma,

Looking at your `bp_seqfeature_load.pl` command, it seems to be missing the `-c` (--create) flag. This is required for the very first time you load a GFF3 file into a database that has not yet been initialized (the schema has not be created).
For all subsequent loads, you can skip the `-c` parameter, if your plan is to perform incremental loads.


Hope this helps!

Best,
Vivek

On Oct 6, 2014, at 1:14 PM, Asma Riyaz <[hidden email]> wrote:


---------- Forwarded message ----------
From: Asma Riyaz <[hidden email]>
Date: Mon, Oct 6, 2014 at 12:55 PM
Subject: loading scripts not working
To: [hidden email], [hidden email]


Hi,

I am trying to load gff3 files for Tribolium using bp_seqfeature_load.pl which fails with this error:

Transaction aborted because DBD::mysql::st execute failed: Table 'tribolium.locationlist' doesn't exist at /usr/share/perl5/Bio/DB/SeqFeature/Store/DBI/mysql.pm line 1571, <GEN0> line 22208.

-------------------- EXCEPTION --------------------
MSG:  should have a primary_id
STACK Bio::DB::SeqFeature::Store::DBI::mysql::_add_SeqFeature /usr/share/perl5/Bio/DB/SeqFeature/Store/DBI/mysql.pm:603
STACK Bio::DB::SeqFeature::Store::add_SeqFeature /usr/share/perl5/Bio/DB/SeqFeature/Store.pm:1525
STACK Bio::DB::SeqFeature::Store::GFF3Loader::build_object_tree_in_tables /usr/share/perl5/Bio/DB/SeqFeature/Store/GFF3Loader.pm:726
STACK Bio::DB::SeqFeature::Store::GFF3Loader::build_object_tree /usr/share/perl5/Bio/DB/SeqFeature/Store/GFF3Loader.pm:699
STACK Bio::DB::SeqFeature::Store::GFF3Loader::finish_load /usr/share/perl5/Bio/DB/SeqFeature/Store/GFF3Loader.pm:343
STACK Bio::DB::SeqFeature::Store::Loader::load_fh /usr/share/perl5/Bio/DB/SeqFeature/Store/Loader.pm:354
STACK Bio::DB::SeqFeature::Store::Loader::load /usr/share/perl5/Bio/DB/SeqFeature/Store/Loader.pm:243
STACK toplevel bp_seqfeature_load.pl:258


Here is the command I use:
perl bp_seqfeature_load.pl -d tribolium -a DBI::mysql --user <user> --password <password> <list of gff3 files>


I have also tried using bp_bulk_load_gff.pl to load data:

"my" variable $AUTH masks earlier declaration in same scope at bp_bulk_load_gff.pl line 656.
"my" variable $db masks earlier declaration in same scope at bp_bulk_load_gff.pl line 666.
This operation will delete all existing data in database dbi:mysql:test.  Continue? Y

159000 features parsed in  0.08s...
You are loading a Bio::DB::GFF database with GFF3 formatted data.
While this will likely work fine, the Bio::DB::GFF schema does not
always faithfully capture the complexity represented in GFF3 files.
Unless you have a specific reason for using Bio::DB::GFF, we suggest
that you use a Bio::DB::SeqFeature::Store database and its corresponding
loader, bp_seqfeature_load.pl.
Total parse time 13.70sin  0.09s...
Loading feature data and analyzing tables.  You may see RDBMS messages here...
ERROR 1045 (28000) at line 1: Access denied for user 'tomoyasulab'@'localhost' (using password: YES)
Total load time  0.00s
done...
Analyzing/optimizing tables. You will see database messages...
Optimization time time  0.00s
FAILURE: Please see standard error for details


Here is command I used:
perl bp_bulk_load_gff.pl -d tribolium --user <user> --password <password> <list of gff3 files>.

In mysql I issued the following commands:

CREATE DATABASE tribolium;
grant select on tribolium.* to nobody@localhost;
grant all privileges on tribolium.* to <user>@localhost;

What am I missing and how can I make this work?

Thanks,
Asma









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Re: loading scripts not working

Asma Riyaz
I tried -c too while running this file:

perl bp_seqfeature_load.pl -d dbi:mysql:userdata_tribolium -u www-data -p <password> -c [list of gff3 files]

This time it is an access denied error:

-------------------- EXCEPTION --------------------
MSG: Access denied for user 'www-data'@'localhost' (using password: YES)
STACK Bio::DB::SeqFeature::Store::DBI::mysql::init /usr/share/perl5/Bio/DB/SeqFeature/Store/DBI/mysql.pm:217
STACK Bio::DB::SeqFeature::Store::new /usr/share/perl5/Bio/DB/SeqFeature/Store.pm:388

Here is how I created an empty database and granted privileges:
CREATE DATABASE userdata_tribolium;
CREATE USER 'www-data'@'localhost' IDENTIFIED BY <password>;
use userdata_tribolium;
GRANT ALL PRIVILEGES ON `userdata_tribolium.*` TO 'www-data'@'localhost';

Any suggestions?

Thanks
Asma



On Mon, Oct 6, 2014 at 3:54 PM, Krishnakumar, Vivek <[hidden email]> wrote:
Hi Asma,

Looking at your `bp_seqfeature_load.pl` command, it seems to be missing the `-c` (--create) flag. This is required for the very first time you load a GFF3 file into a database that has not yet been initialized (the schema has not be created).
For all subsequent loads, you can skip the `-c` parameter, if your plan is to perform incremental loads.


Hope this helps!

Best,
Vivek

On Oct 6, 2014, at 1:14 PM, Asma Riyaz <[hidden email]> wrote:


---------- Forwarded message ----------
From: Asma Riyaz <[hidden email]>
Date: Mon, Oct 6, 2014 at 12:55 PM
Subject: loading scripts not working
To: [hidden email], [hidden email]


Hi,

I am trying to load gff3 files for Tribolium using bp_seqfeature_load.pl which fails with this error:

Transaction aborted because DBD::mysql::st execute failed: Table 'tribolium.locationlist' doesn't exist at /usr/share/perl5/Bio/DB/SeqFeature/Store/DBI/mysql.pm line 1571, <GEN0> line 22208.

-------------------- EXCEPTION --------------------
MSG:  should have a primary_id
STACK Bio::DB::SeqFeature::Store::DBI::mysql::_add_SeqFeature /usr/share/perl5/Bio/DB/SeqFeature/Store/DBI/mysql.pm:603
STACK Bio::DB::SeqFeature::Store::add_SeqFeature /usr/share/perl5/Bio/DB/SeqFeature/Store.pm:1525
STACK Bio::DB::SeqFeature::Store::GFF3Loader::build_object_tree_in_tables /usr/share/perl5/Bio/DB/SeqFeature/Store/GFF3Loader.pm:726
STACK Bio::DB::SeqFeature::Store::GFF3Loader::build_object_tree /usr/share/perl5/Bio/DB/SeqFeature/Store/GFF3Loader.pm:699
STACK Bio::DB::SeqFeature::Store::GFF3Loader::finish_load /usr/share/perl5/Bio/DB/SeqFeature/Store/GFF3Loader.pm:343
STACK Bio::DB::SeqFeature::Store::Loader::load_fh /usr/share/perl5/Bio/DB/SeqFeature/Store/Loader.pm:354
STACK Bio::DB::SeqFeature::Store::Loader::load /usr/share/perl5/Bio/DB/SeqFeature/Store/Loader.pm:243
STACK toplevel bp_seqfeature_load.pl:258


Here is the command I use:
perl bp_seqfeature_load.pl -d tribolium -a DBI::mysql --user <user> --password <password> <list of gff3 files>


I have also tried using bp_bulk_load_gff.pl to load data:

"my" variable $AUTH masks earlier declaration in same scope at bp_bulk_load_gff.pl line 656.
"my" variable $db masks earlier declaration in same scope at bp_bulk_load_gff.pl line 666.
This operation will delete all existing data in database dbi:mysql:test.  Continue? Y

159000 features parsed in  0.08s...
You are loading a Bio::DB::GFF database with GFF3 formatted data.
While this will likely work fine, the Bio::DB::GFF schema does not
always faithfully capture the complexity represented in GFF3 files.
Unless you have a specific reason for using Bio::DB::GFF, we suggest
that you use a Bio::DB::SeqFeature::Store database and its corresponding
loader, bp_seqfeature_load.pl.
Total parse time 13.70sin  0.09s...
Loading feature data and analyzing tables.  You may see RDBMS messages here...
ERROR 1045 (28000) at line 1: Access denied for user 'tomoyasulab'@'localhost' (using password: YES)
Total load time  0.00s
done...
Analyzing/optimizing tables. You will see database messages...
Optimization time time  0.00s
FAILURE: Please see standard error for details


Here is command I used:
perl bp_bulk_load_gff.pl -d tribolium --user <user> --password <password> <list of gff3 files>.

In mysql I issued the following commands:

CREATE DATABASE tribolium;
grant select on tribolium.* to nobody@localhost;
grant all privileges on tribolium.* to <user>@localhost;

What am I missing and how can I make this work?

Thanks,
Asma









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Re: loading scripts not working

Scott Cain
Hi Asma,

I just sent you an email telling you to add the -c flag, but it didn't make it to the list since the email address was spelled wrong, but I guess no harm, since you already did that anyway.

My recollection of the permission scheme in MySQL is that you have to grant permission to bulk load files has to be given explicitly (that is, it isn't part of "ALL", which is admittedly somewhat confusing).  I think the syntax is something like GRANT FILE TO ...user...  File permission is global, so you don't grant it for a specific database.

Scott


On Mon, Oct 6, 2014 at 4:05 PM, Asma Riyaz <[hidden email]> wrote:
I tried -c too while running this file:

perl bp_seqfeature_load.pl -d dbi:mysql:userdata_tribolium -u www-data -p <password> -c [list of gff3 files]

This time it is an access denied error:

-------------------- EXCEPTION --------------------
MSG: Access denied for user 'www-data'@'localhost' (using password: YES)
STACK Bio::DB::SeqFeature::Store::DBI::mysql::init /usr/share/perl5/Bio/DB/SeqFeature/Store/DBI/mysql.pm:217
STACK Bio::DB::SeqFeature::Store::new /usr/share/perl5/Bio/DB/SeqFeature/Store.pm:388

Here is how I created an empty database and granted privileges:
CREATE DATABASE userdata_tribolium;
CREATE USER 'www-data'@'localhost' IDENTIFIED BY <password>;
use userdata_tribolium;
GRANT ALL PRIVILEGES ON `userdata_tribolium.*` TO 'www-data'@'localhost';

Any suggestions?

Thanks
Asma



On Mon, Oct 6, 2014 at 3:54 PM, Krishnakumar, Vivek <[hidden email]> wrote:
Hi Asma,

Looking at your `bp_seqfeature_load.pl` command, it seems to be missing the `-c` (--create) flag. This is required for the very first time you load a GFF3 file into a database that has not yet been initialized (the schema has not be created).
For all subsequent loads, you can skip the `-c` parameter, if your plan is to perform incremental loads.


Hope this helps!

Best,
Vivek

On Oct 6, 2014, at 1:14 PM, Asma Riyaz <[hidden email]> wrote:


---------- Forwarded message ----------
From: Asma Riyaz <[hidden email]>
Date: Mon, Oct 6, 2014 at 12:55 PM
Subject: loading scripts not working
To: [hidden email], [hidden email]


Hi,

I am trying to load gff3 files for Tribolium using bp_seqfeature_load.pl which fails with this error:

Transaction aborted because DBD::mysql::st execute failed: Table 'tribolium.locationlist' doesn't exist at /usr/share/perl5/Bio/DB/SeqFeature/Store/DBI/mysql.pm line 1571, <GEN0> line 22208.

-------------------- EXCEPTION --------------------
MSG:  should have a primary_id
STACK Bio::DB::SeqFeature::Store::DBI::mysql::_add_SeqFeature /usr/share/perl5/Bio/DB/SeqFeature/Store/DBI/mysql.pm:603
STACK Bio::DB::SeqFeature::Store::add_SeqFeature /usr/share/perl5/Bio/DB/SeqFeature/Store.pm:1525
STACK Bio::DB::SeqFeature::Store::GFF3Loader::build_object_tree_in_tables /usr/share/perl5/Bio/DB/SeqFeature/Store/GFF3Loader.pm:726
STACK Bio::DB::SeqFeature::Store::GFF3Loader::build_object_tree /usr/share/perl5/Bio/DB/SeqFeature/Store/GFF3Loader.pm:699
STACK Bio::DB::SeqFeature::Store::GFF3Loader::finish_load /usr/share/perl5/Bio/DB/SeqFeature/Store/GFF3Loader.pm:343
STACK Bio::DB::SeqFeature::Store::Loader::load_fh /usr/share/perl5/Bio/DB/SeqFeature/Store/Loader.pm:354
STACK Bio::DB::SeqFeature::Store::Loader::load /usr/share/perl5/Bio/DB/SeqFeature/Store/Loader.pm:243
STACK toplevel bp_seqfeature_load.pl:258


Here is the command I use:
perl bp_seqfeature_load.pl -d tribolium -a DBI::mysql --user <user> --password <password> <list of gff3 files>


I have also tried using bp_bulk_load_gff.pl to load data:

"my" variable $AUTH masks earlier declaration in same scope at bp_bulk_load_gff.pl line 656.
"my" variable $db masks earlier declaration in same scope at bp_bulk_load_gff.pl line 666.
This operation will delete all existing data in database dbi:mysql:test.  Continue? Y

159000 features parsed in  0.08s...
You are loading a Bio::DB::GFF database with GFF3 formatted data.
While this will likely work fine, the Bio::DB::GFF schema does not
always faithfully capture the complexity represented in GFF3 files.
Unless you have a specific reason for using Bio::DB::GFF, we suggest
that you use a Bio::DB::SeqFeature::Store database and its corresponding
loader, bp_seqfeature_load.pl.
Total parse time 13.70sin  0.09s...
Loading feature data and analyzing tables.  You may see RDBMS messages here...
ERROR 1045 (28000) at line 1: Access denied for user 'tomoyasulab'@'localhost' (using password: YES)
Total load time  0.00s
done...
Analyzing/optimizing tables. You will see database messages...
Optimization time time  0.00s
FAILURE: Please see standard error for details


Here is command I used:
perl bp_bulk_load_gff.pl -d tribolium --user <user> --password <password> <list of gff3 files>.

In mysql I issued the following commands:

CREATE DATABASE tribolium;
grant select on tribolium.* to nobody@localhost;
grant all privileges on tribolium.* to <user>@localhost;

What am I missing and how can I make this work?

Thanks,
Asma









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