[GUSDEV] LoadTaxon tax_id null error

[Weichen W. <we...@se...>]

My GUS 3.5 instance is complete new and I am loading NCBI Taxon data files 
using LoadTaxon.pm plugin. I have this problem about null value of tax_id. 
Do I need load anything else before loading taxon?
The log is as follows:

[wewu@noodle ncbi_taxon]$     ga GUS::Supported::Plugin::LoadTaxon --nodes 
nodes.dmp --names names.dmp --gencode gencode.dmp --merged merged.dmp
Mon Oct 10 16:37:29 2005        ARGS    algoinvo        1
<... skip some lines>
Mon Oct 10 16:37:29 2005        Doing merge and NCBI tax id '12' not in 
database, skipping
<...skip many lines>
Mon Oct 10 16:37:33 2005        Doing merge and NCBI tax id '349635' not in 
database, skipping
Mon Oct 10 16:37:33 2005        Updating and inserting SRes.GeneticCode
Mon Oct 10 16:37:50 2005        Number processed: 1000
<...skip many lines>
Mon Oct 10 16:54:33 2005        Number processed: 278000
Mon Oct 10 16:54:34 2005        Inserting and updating TaxonName

DBD::Pg::st execute failed: ERROR:  null value in column "taxon_id" violates 
not-null constraint
ERROR:
 SQL ERROR!! involving
    INSERT INTO SRes.TaxonName (  unique_name_variant, group_write, 
other_read, group_read, name, taxon_id, user_read, row_user_id, 
modification_date, name_class, other_write, row_alg_invocation_id, 
row_project_id, taxon_name_id, row_group_id, user_write )
    VALUES   (  null, ?, ?, ?, ?, null, ?, ?, now(), ?, ?, ?, ?, ?, ?, ? )
 Values: 1, 1, 1, Tellervini, 1, 1, scientific name, 0, 7, 1, 1, 1, 1 at 
/home/wewu/work/6_gus/gus_home/lib/perl/GUS/ObjRelP/DbiDbHandle.pm line 166

Thanks,
Weichen



----- Original Message ----- 
From: "Steve Fischer" <sfi...@pc...>
To: "Weichen Wu" <we...@se...>
Cc: <gus...@li...>
Sent: Saturday, October 08, 2005 7:29 AM
Subject: Re: [GUSDEV] mapping file


> yes, the mapping file is required.  you can use the genbank2gus.xml file 
> if your embl file uses features and qualifiers that conform to the 
> genbank/embl/ddbj feature table (see 
> http://www.ncbi.nlm.nih.gov/collab/FT/).
> but, you must understand that input often does not conform, or, places 
> data into qualifiers in the wrong way.
>
> in this case, you will need to provide your own mapping file.
>
> here is a snip from the documentation from the plugin (i just improved the 
> doc in latest plugin version):
>
> --------
> Another way to generate a template mapping file is by using the command 
> reportFeatureQualifiers.  This command analyzes a set of input files, and 
> reports the feature/qualifier structure found in them.  It can output the 
> report in simple text form, or in XML that is a template for the mapping 
> file.
> --------
>
> steve
>
> Weichen Wu wrote:
>
>> Hi,
>>
>> To use InsertSequenceFeatures plugin, is the mapping file is required? 
>> There is a genebank2gus.xml. Is there a mapping file for EMBL format 
>> available?
>>
>> Thanks,
>> Weichen
>>
>>
>>
>>
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