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 4:15 PM
Subject: Re: loading scripts not working
To: Scott Cain <[hidden email]>
Cc: "Gbrowse (E-mail)" <[hidden email]>


I have added the '-c' flag and ending in an access denied error (my previous mail has the STACK error and the steps I took to initialize the database)


On Mon, Oct 6, 2014 at 4:12 PM, Scott Cain <[hidden email]> wrote:
Hi Asma,

Let's stick with bp_seqfeature_load.pl, since that is the loader for a Bio:DB::SeqFeature::Store database, which is much better to use with GFF3 data.  The bp_bulk_load_gff.pl script works with Bio:DB::GFF databases, and works better with GFF2 data.

The message about a table not existing is the clue to the problem: the command you provided lacks the "create" flag to create the database tables before loading the data, so you should add "-c" or "--create" to the seqfeature_load command.  Be careful with this flag though, because it will wipe out any data that is already in the database, so you should use it only the first time you are loading data into the database.  If you want to load data after the initial load, be sure to drop the create flag.


On Mon, Oct 6, 2014 at 12:55 PM, Asma Riyaz <[hidden email]> wrote:

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
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:

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?


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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