[Gusdev-gusdev] Re: LoadTaxon.pm

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

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/LoadTaxon.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/LoadTaxon.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/LoadTaxon.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.
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