[GUSDEV] problems loading data

[Amruta J. <am...@st...>]

Hi,

I've successfully installed GUS and am trying to load data into it.
I have downloaded Bordetella bronchiseptica ds-DNA sequence in XML =
format from:
(http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=3DNucleotide&cmd=3Dsear=
ch&term=3Dnc_002927)

I tried using LoadGeneFeatureFromXML (v1.878) plugin, but it prints the =
length of submitted sequence as 0.=20
My guess is that the plugin is not able to parse my xml file.=20
Is TIGR XML format different from the Genbank XML file format?
Is there some other plugin that parses xml to load data?=20

I tried using GBParser on data downloaded from the same site in GenBank =
(.gb) format. That too failed with the error:=20
 ------------------ entry number 1 -----------------
You have exceeded the maximum number of allowable objects in memory:
 ------------------ entry number 2 -----------------
Can't call method "getAccession" on an undefined value=20

The complete command and errors are pasted below for reference.


thanks,
Amruta









LoadGeneFeatureFromXML: (Problem-Submitting sequence of length 0)
[amrutaj@asiago gus]$ ga GUS::Common::Plugin::LoadGeneFeaturesFromXML =
--XmlFile=3D"~/genbank_files/nc_002927.xml" \
> --Taxon=3D"Bordetella bronchiseptica RB50" --Project=3D"Bordetella =
bronchiseptica RB50" --SeqTypeID=3D3 \
> --Algorithm=3DGUS::Common::Plugin::LoadGeneFeaturesFromXML =
--extDbRelId=3D5004 -commit
Tue Apr 19 10:03:14 2005        Finding Algorithm
Tue Apr 19 10:03:14 2005        Finding Project
Tue Apr 19 10:03:14 2005        Finding ExternalDatabaseReleaseId
Tue Apr 19 10:03:14 2005        Finding ExternalDatabaseId
Tue Apr 19 10:03:14 2005        Finding Sequence Type Id
Tue Apr 19 10:03:14 2005        Loading XML =
file/home/amrutaj/genbank_files/nc_002927.xml
Loading XML file: /home/amrutaj/genbank_files/nc_002927.xml
Tue Apr 19 10:04:51 2005        Finding TaxonID
Submitting sequence of length 0
Tue Apr 19 10:05:19 2005        RESULT  1
[amrutaj@asiago gus]$=20


GBParser:
 ga GUS::Common::Plugin::GBParser \
--file=3D~/genbank_files/nc_002927.gb --debug \
--gbRel=3D146 --db_rel_id=3D22 --commit=20

 ------------------ entry number 1 -----------------
You have exceeded the maximum number of allowable objects in memory:
  You must use the method 'undefPointerCache()' in each loop
    to clear the cache and allow garbage collection!!
 If you need > 50000 objects at one time,
   then increase the default number with the method =
'setMaximumNumberOfObjects(<number>)' at =
/opt/gus/gus_home/lib/perl/GUS/ObjRelP/DbiDatabase.pm line 512
        =
GUS::ObjRelP::DbiDatabase::addToPointerCache('GUS::ObjRelP::DbiDatabase=3D=
HASH(0x8c371f8)','GUS::Model::DoTS::DbRefNASequence=3DHASH(0x12509d6c)') =
called at /opt/gus/gus_home/lib/perl/GUS/Model/GusRow.pm line 28
        GUS::Model::GusRow::new('GUS::Model::DoTS::DbRefNASequence') =
called at /opt/gus/gus_home/lib/perl/GUS/Common/Plugin/GBParser.pm line =
779
        =
GUS::Common::Plugin::GBParser::buildDbXRef('CBIL::Bio::GenBank::Qualifier=
=3DHASH(0xbfd4144)','GUS::Model::DoTS::ExternalNASequence=3DHASH(0xdee73b=
8)') called at /opt/gus/gus_home/lib/perl/GUS/Common/Plugin/GBParser.pm =
line 503
        =
GUS::Common::Plugin::GBParser::buildFeatures('GUS::Common::Plugin::GBPars=
er=3DHASH(0x85a0b90)','CBIL::Bio::GenBank::Entry=3DHASH(0xa374394)','GUS:=
:Model::DoTS::ExternalNASequence=3DHASH(0xdee73b8)') called at =
/opt/gus/gus_home/lib/perl/GUS/Common/Plugin/GBParser.pm line 251
        =
GUS::Common::Plugin::GBParser::processEntry('GUS::Common::Plugin::GBParse=
r=3DHASH(0x85a0b90)','CBIL::Bio::GenBank::ArrayStream=3DHASH(0xa374328)')=
 called at /opt/gus/gus_home/lib/perl/GUS/Common/Plugin/GBParser.pm line =
185
        eval {...} called at =
/opt/gus/gus_home/lib/perl/GUS/Common/Plugin/GBParser.pm line 184
        =
GUS::Common::Plugin::GBParser::run('GUS::Common::Plugin::GBParser=3DHASH(=
0x85a0b90)','HASH(0x8e4c168)') called at =
/opt/gus/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line 453
        eval {...} called at =
/opt/gus/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line 450
        =
GUS::PluginMgr::GusApplication::doMajorMode_RunOrReport('GUS::PluginMgr::=
GusApplication=3DHASH(0x804c8c4)','GUS::Common::Plugin::GBParser',1) =
called at /opt/gus/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm =
line 383
        =
GUS::PluginMgr::GusApplication::doMajorMode_Run('GUS::PluginMgr::GusAppli=
cation=3DHASH(0x804c8c4)','GUS::Common::Plugin::GBParser') called at =
/opt/gus/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line 289
        =
GUS::PluginMgr::GusApplication::doMajorMode('GUS::PluginMgr::GusApplicati=
on=3DHASH(0x804c8c4)','GUS::Common::Plugin::GBParser') called at =
/opt/gus/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line 198
        =
GUS::PluginMgr::GusApplication::parseAndRun('GUS::PluginMgr::GusApplicati=
on=3DHASH(0x804c8c4)','ARRAY(0x805ff68)') called at =
/opt/gus/gus_home/bin/ga line 11

 ------------------ entry number 2 -----------------
Can't call method "getAccession" on an undefined value at =
/opt/gus/gus_home/lib/perl/GUS/Common/Plugin/GBParser.pm line 218, =
<GEN0> line 230365.

-------------------------------------------------------------------------=
----------------------------------------------------------------