[Gusdev-gusdev] Re: LoadTaxon.pm

[Arnaud K. <ax...@sa...>]

I've updated from CVS the files and I'm going to rerun the loading. 
It'll take a while...

Martin Widlake wrote:

>Hi Arnaud,
>
>If the whole file except the last part is processing into the DB OK,
>
that's right

> it
>suggest the end of the file is corrupt.
>  
>
it looks fine though.

>Ora 1041 is an internal error that looks like you have hut an internal
>oracle bug, but in fact is often a result of 3113, losing your
>connection to the DB.
>
>I take it 99.99% of what you are processing is getting into the DB?
>  
>
no because I haven't commited the loading into the database but should 
have been in there otherwise.

>Martin
>  
>
Arnaud

>-----Original Message-----
>From: Arnaud Kerhornou [mailto:ax...@sa...] 
>Sent: 07 March 2003 10:57
>To: gusdev-gusdev
>Cc: db...@sa...
>Subject: Re: LoadTaxon.pm
>
>
>Hi
>
>I've tried to populate the taxonomy files from NCBI into GUS3. it's 
>working fine until it reaches the last node entry, ie the line 173295 in
>
>the nodes.dmp file.
>I now have these 2 errors when populating the nodes file:
>
> > oerr ora 03113
>    03113, 00000, "end-of-file on communication channel"
>    // *Cause:
>    // *Action:
>
> > oerr ora 01041
>    01041, 00000, "internal error. hostdef extension doesn't exist"
>    // *Cause: Pointer to hstdef extension in hstdef is null.
>    // *Action: Report as a bug
>
>Have you come across the same problem ?
>Any idea about the cause of this 'end-of-file on communication channel' 
>error ?
>
>cheers
>Arnaud
>
>./bin/ga GUS::Common::Plugin::LoadTaxon 
>--nodes=/nfs/pathsoft/databases/NCBI/nodes.dmp 
>--names=/nfs/pathsoft/databases/NCBI/names.dmp 
>--gencode=/nfs/pathsoft/databases/NCBI/gencode.dmp --verbose
>
>--------------------------->
>[...]
>
>RetrieveFromDB: select * from SRes.Taxon where  ncbi_tax_id = ?
>  bindValues (89410)
>
>sqlExec:
>    INSERT INTO SRes.Taxon (  row_user_id, user_write, group_write, 
>genetic_code_id, row_project_id, taxon_id, group_r
>ead, row_group_id, other_read, mitochondrial_genetic_code_id, 
>modification_date, user_read, row_alg_invocation_id, oth er_write,
>ncbi_tax_id, rank )
>    VALUES   (  ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, SYSDATE, ?, ?, ?, ?, ? )
>  bindValues (1, 1, 1, 2, 1, 142133, 1, 1, 1, 2, 1, 9, 0, 89410, genus)
>DbiHandle:sqlExec:insert succeeded 1 row(s) processed ncbi_tax_id :
>89410
>
>^CDBD::Oracle::st execute failed: ORA-03113: end-of-file on 
>communication channel (DBD ERROR: OCIStmtExecute) at /nfs/
>team81/axk/projects/gus/gus.deployment/lib/perl/GUS/Common/Plugin/LoadTa
>xon.pm 
>line 242, <NODES> line 173295.
>DBD::Oracle::st fetchrow_array failed: ERROR no statement executing 
>(perhaps you need to call execute first) at /nfs/t
>eam81/axk/projects/gus/gus.deployment/lib/perl/GUS/Common/Plugin/LoadTax
>on.pm 
>line 243, <NODES> line 173295.
>
>RetrieveFromDB: select * from SRes.Taxon where  ncbi_tax_id = ?
>  bindValues (110556)
>
>
>sqlExec:
>    INSERT INTO SRes.Taxon (  row_user_id, user_write, group_write, 
>genetic_code_id, row_project_id, taxon_id, group_r
>ead, row_group_id, other_read, mitochondrial_genetic_code_id, 
>modification_date, user_read, row_alg_invocation_id, oth er_write,
>ncbi_tax_id, rank )
>    VALUES   (  ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, SYSDATE, ?, ?, ?, ?, ? )
>  bindValues (1, 1, 1, 2, 1, 142134, 1, 1, 1, 2, 1, 9, 0, 110556,
>species)  DbiHandle:sqlExec:insert succeeded 1 row(s) processed
>ncbi_tax_id : 110556 DBD::Oracle::db prepare failed: Error while trying
>to retrieve text for 
>error ORA-01041 (DBD ERROR: OCIStmtExecute/Des
>cribe) at 
>/nfs/team81/axk/projects/gus/gus.deployment/lib/perl/GUS/Common/Plugin/L
>oadTaxon.pm 
>line 241, <NODES> line 1
>73295.
>
>
>sqlExec:
>    UPDATE  Core.AlgorithmInvocation
>    SET    
>        end_time = SYSDATE,
>        row_alg_invocation_id = ?,
>        modification_date = SYSDATE
>    WHERE   algorithm_invocation_id = ?
>  bindValues (9, 9)
> DbiHandle:sqlExec:insert succeeded 1 row(s)
>Can't call method "execute" on an undefined value at 
>/nfs/team81/axk/projects/gus/gus.deployment/lib/perl/GUS/Common/P
>lugin/LoadTaxon.pm line 242, <NODES> line 173295.
><------------------------------------
>
>  
>

-- 
Arnaud Kerhornou

The Wellcome Trust Sanger Institute
The Pathogen Sequencing Unit
Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
Work: +44 (0) 1223 494955
Fax:  +44 (0) 1223 494919