errors while loading NCBI taxonomy

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errors while loading NCBI taxonomy

longbow leo
Hi,

I have updated from Chado svn but encountered new errors while loading NCBI taxonomy into Chado database.

When I tried to load the entire NCBI taxonomy entries, the error message was:

the root_id is 

walking the tree for ...
Setting left index= 2 for parent

Setting right index= 3 for id

Updating the phylonode and phylonode_organism tables

Rolling back!
DBIx::Class::Storage::DBI::__ANON__(): DBI Exception: DBD::Pg::db do failed: ERROR: null value in column "left_idx" violates not-null constraint at load_ncbi_taxonomy.pl line 499

Resetting database sequences...
DBI::db=HASH(0x2902690)->disconnect invalidates 1 active statement handle (either destroy statement handles or call finish on them before disconnecting) at /usr/local/share/perl/5.10.1/DBIx/Class/Storage/DBI.pm line 2576.

Then I tried to load the eucaryota subset taxonomy, a new error encountered:

Rolling back! 
DBIx::Class::ResultSet::single(): [SQL::Abstract::__ANON__] Fatal: unexpected operator 'ilike' with undef operand at load_ncbi_taxonomy.pl line 397

Resetting database sequences...
DBI::db=HASH(0x3cf0940)->disconnect invalidates 1 active statement handle (either destroy statement handles or call finish on them before disconnecting) at /usr/local/share/perl/5.10.1/DBIx/Class/Storage/DBI.pm line 2576.

But the loading archaea completed without any errors.

Are these errors occurred because of the entire and encaryota dataset too large? There are 5027 archaea taxonomy entries whereas 396977 for eukaryota.


Thanks!


Haihzou Liu



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Re: errors while loading NCBI taxonomy

Naama Menda
hi,
could you send me a link to the file you are trying to load, and the options you are running with this script?
The error message indicates the script is not setting the organism_id for the root node.

thanks
-Naama



Naama Menda
Boyce Thompson Institute for Plant Research
Tower Rd
Ithaca NY 14853
USA

(607) 254 3569
Sol Genomics Network
http://solgenomics.net/
[hidden email]


On Tue, Jul 13, 2010 at 6:06 AM, longbow leo <[hidden email]> wrote:
Hi,

I have updated from Chado svn but encountered new errors while loading NCBI taxonomy into Chado database.

When I tried to load the entire NCBI taxonomy entries, the error message was:

the root_id is 

walking the tree for ...
Setting left index= 2 for parent

Setting right index= 3 for id

Updating the phylonode and phylonode_organism tables

Rolling back!
DBIx::Class::Storage::DBI::__ANON__(): DBI Exception: DBD::Pg::db do failed: ERROR: null value in column "left_idx" violates not-null constraint at load_ncbi_taxonomy.pl line 499

Resetting database sequences...
DBI::db=HASH(0x2902690)->disconnect invalidates 1 active statement handle (either destroy statement handles or call finish on them before disconnecting) at /usr/local/share/perl/5.10.1/DBIx/Class/Storage/DBI.pm line 2576.

Then I tried to load the eucaryota subset taxonomy, a new error encountered:

Rolling back! 
DBIx::Class::ResultSet::single(): [SQL::Abstract::__ANON__] Fatal: unexpected operator 'ilike' with undef operand at load_ncbi_taxonomy.pl line 397

Resetting database sequences...
DBI::db=HASH(0x3cf0940)->disconnect invalidates 1 active statement handle (either destroy statement handles or call finish on them before disconnecting) at /usr/local/share/perl/5.10.1/DBIx/Class/Storage/DBI.pm line 2576.

But the loading archaea completed without any errors.

Are these errors occurred because of the entire and encaryota dataset too large? There are 5027 archaea taxonomy entries whereas 396977 for eukaryota.


Thanks!


Haihzou Liu



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