[Bioperl-pipeline] Annotation example error
McWilliam, Sean (LI, Uni of Queensland)
Sean.McWilliam@csiro.au
Mon, 21 Oct 2002 16:42:05 +1000
Hi,
Shawn, thanks for the reponse.
I checked out the new CVS for biopipe. This has solved the database problem.
The annotate_pipeline database is now updated.
But when I run PipelineManager.pl (after altering PipeConf.pm to suit) I get
the following output:
///////////////Starting Pipeline//////////////////////
Fetching Analysis From Pipeline annotate_pipeline
7 analysis found.
Running test and setup..
//////////// Analysis Test ////////////
Checking Analysis 1 RepeatMasker ok
Checking Analysis 2 blast ok
Checking Analysis 3 blast ok
Checking Analysis 4 blast ok
Checking Analysis 5 blast ok
Checking Analysis 6 blast ok
Checking Analysis 7 blast ok
///////////////Tests Completed////////////////////////
Starting fresh pipeline run
Fetching Input ids
CREATED Initial jobs!
Fetched 0 incomplete jobs
Fetched 0 completed jobs
Going to snooze for 3 seconds...
Waking up and run again!
Nothing left to run.
///////////////Shutting Down Pipeline//////////////////////
Removing Lock File...
Done
///////////////////////////////////////////////////////////
This looks OK but happens almost instantly, which made we query whether the
ens_test
database had been updated. It appears nothing was added to the ens_test
database.
ens_test does initially contain the 2 test contigs and dna.
So any ideas why the pipeline is not running or the ens_test database not
updated?
Is it possible to get a dump of the annotate_pipeline database for the
example so I can check if it is being updated correctly by Xml2db.pl?
I can run RepeatMasker and blastall from the command line and I have used
bioperl to run Genscan as a test of my setup previously so I assume my path
is OK.
The following is not entirely related but I have a couple of minor
suggestions for altering the code in Xml2db.pl and PipelineManager.pl to fix
some problems I had with them.
In Xml2db.pl change the code in else statement when creating new database
so that command line arguments are used for username and password rather
than
root and null password.
Add -f (force) option so that mysqladmin doesn't wait for confirmation from
user
before dropping database (avoids having to hit enter key again)
else {
system("mysqladmin -u $DBUSER -p$DBPASS -f drop $DBNAME > /dev/null
");
print STDERR "Creating $DBNAME\n ";
system("mysqladmin -u $DBUSER -p$DBPASS create $DBNAME ");
print STDERR "Loading Schema\n";
system("mysql -u $DBUSER -p$DBPASS $DBNAME < $SCHEMA");
}
In PerlManager.pl add line to sub remove_lock.
unlink "$dir/db.db";
otherwise dir is not empty and not deleted (lock not removed).
Cheers and thanks,
Sean
-----Original Message-----
From: shawnh@fugu-sg.org [mailto:shawnh@fugu-sg.org]
Sent: Monday, 21 October 2002 11:43 AM
To: McWilliam, Sean (LI, Uni of Queensland)
Cc: 'bioperl-pipeline@bioperl.org'
Subject: Re: [Bioperl-pipeline] Annotation example error
Hi Sean,
Yup not your fault. We forgot to commit the schema to biosql.So we
have
committed that and you can check that out. We also have the latest schema
stored at
t/data/schema.sql when you check out biopipe.
Also the latest xml file genomic_sequence_annotation.xml
is committed so play around with that.
You will also need to download a tar ball containing the sample data at:
http://www.biopipe.org/bioperl-pipeline-download.html
and checkout the BioToEns conversion utiltity module, information
as the same page.
This pipeline is simple just repeatmask + a bunch of blasts.
We will be adding the genscan and genewise analysis shortly.
do let us know if u face anymore problems.
cheers,
shawn
On Fri, 18 Oct 2002, McWilliam, Sean (LI, Uni of Queensland) wrote:
> Hi,
>
> I have been trying to run the example annotation at
> http://www.biopipe.org/bioperl-pipeline-run.html
>
> I think I have everything set up as detailed but when I run Xml2db.pl as
> follows
>
> perl Xml2Db.pl -dbhost localhost -dbname annotate_pipeline -dbuser *******
> -dbpass ****** -p templates/genomic_sequence_annotation.xml
>
> I get the following error message
>
> Using existing db annotate_pipelineReading Data_setup xml :
> templates/genomic_sequence_annotation.xml
> Doing DBAdaptor and IOHandler setup
> Doing Pipeline Flow Setup
> Doing Analysis..
> Doing Rules
> Doing Job Setup...
> DBD::mysql::st execute failed: Column 'current' cannot be null at
> /usr/local/ensembl/bioperl-pipeline/Bio/Pipeline/SQL/RuleAdaptor.pm line
85,
> <STDIN> line 1.
> DBD::mysql::st execute failed: Column 'current' cannot be null at
> /usr/local/ensembl/bioperl-pipeline/Bio/Pipeline/SQL/RuleAdaptor.pm line
85,
> <STDIN> line 1.
>
> Any helpful advice would be greatly appreciated, couldn't find anything in
> the archives.
>
> Cheers,
> Sean
>
> ============================
> Sean McWilliam
> CSIRO Livestock Industries
> Level 3 Gehrmann Labs
> Research Road
> University of Queensland
> St Lucia, 4072
>
> email: sean.mcwilliam@csiro.au
> phone: 07 3346 2504
> fax: 07 3214 2480
> ============================
> _______________________________________________
> bioperl-pipeline mailing list
> bioperl-pipeline@bioperl.org
> http://bioperl.org/mailman/listinfo/bioperl-pipeline
>
--
********************************
* Shawn Hoon
* http://www.fugu-sg.org/~shawnh
********************************