<div>Hi Barry,</div><div></div><div>I'm cross-posting my response to Don Gilbert, creator of GMODTools, and the Chado list where others can see it.</div><div></div><div>On Fri, Apr 24, 2009 at 7:50 AM, Barry Dancis <span dir="ltr"><<a href="mailto:bdancis@digiconasp.com">bdancis@digiconasp.com</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;">Hi --<br>
<br>
I am trying to learn the Bulk files processing methods(<a href="http://gmod.org/wiki/GMODTools_TestCase" target="_blank">http://gmod.org/wiki/GMODTools_TestCase</a>) but when I ran the upload on the converted file into my exisitng Chado db<br>
<br>
perl $lbin/gmod_bulk_load_gff3.pl -gfffile gff3/EU852811.gbk.gff -organism fromdata -dbname Chado -debug >& gmod-load.log<br>
<br>
I got the following errors from in my log file:<br>
<br>
Preparing data for inserting into the Chado database<br>
(This may take a while ...)<br>
Organism Bio::Annotation::SimpleValue=HASH(0xa37a7d8) from data<br>
DBD::Pg::st fetchrow_array failed: no statement executing at /usr/local/share/pe<br>
rl/5.10.0/Bio/GMOD/DB/Adapter.pm line 1112, <GEN0> line 7.<br>
Bio::Annotation::SimpleValue=HASH(0xa37a7d8) organism not found in the database<br>
at /usr/local/bin/gmod_bulk_load_gff3.pl line 711, <GEN0> line 7.<br>
Issuing rollback() for database handle being DESTROY'd without explicit disconne<br>
ct() at /usr/local/bin/gmod_bulk_load_gff3.pl line 711.</blockquote><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;"><br>
<br>
The top of the original genbank file is<br>
LOCUS EU852811 70578 bp DNA circular PLN 05-MAR-2009<br>
DEFINITION Saccharomyces pastorianus Weihenstephan 34/70 mitochondrion,<br>
complete genome.<br>
ACCESSION EU852811<br>
<br>
and the organism is not one of the 12 that got loaded in the organism table during the installation of the Chado db.<br>
<br>
Is there a separate source for allowable organisms or should the bulk loader be able to load organisms not in the organism table?</blockquote><div></div><div>You can define any organism by inserting it into the organism table (<a href="http://gmod.org/wiki/Chado_Organism_Module#Table:_organism">http://gmod.org/wiki/Chado_Organism_Module#Table:_organism</a>). What I don't know is how GMODTools maps the DEFINITION line to the organism table. That is, I don't know what part of "Saccharomyces pastorianus Weihenstephan 34/70 mitochondrion, complete genome." GMODTools looks for in the organism table.</div>
<div></div><div>Don, any advice on this?</div><div> </div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;"><br>
Looking at the GBrowse Configuration HOWTO document( </blockquote><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;"><a href="http://gmod.org/wiki/GBrowse_Configuration_HOWTO" target="_blank">http://gmod.org/wiki/GBrowse_Configuration_HOWTO</a>) it describes the use of bp_bulk_load_gff.pl for creating databases from scratch, but when I run<br>
</blockquote><div></div><div>bp_full_load_gff.pl creates a database specifically tuned to power GBrowse. This is an entirely different beast than Chado. For loading Chado, stick with GMODTools. </div><div></div><div>Dave C.</div>
<div></div><div> </div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;"> perl $lbin/bp_bulk_load_gff3.pl -gfffile gff3/EU852811.gbk.gff -organism fromdata -dbname Chado -user postgres -passwd postgres -debug >& gmod-load.log<br>
<br>
I get<br>
<br>
Can't open perl script "/usr/local/bin/bp_bulk_load_gff3.pl": No such file or directory<br>
<br>
and I can't find the file in either the GMODTools tree or the GMOD installation kit.<br>
<br>
What is the diff betw gmod_bulk_load_gff3.pl and bp_bulk_load_gff3.pl? Do they have diff purposes?<br>
<br>
Thanks,<br>
<font color="#888888"><br>
Barry<br>
</font><br>
ps I also posted this on <a href="http://osdir.com/ml/science.biology.gmod.devel/2008-02/msg00000.html" target="_blank">http://osdir.com/ml/science.biology.gmod.devel/2008-02/msg00000.html</a> but I got no reply so I am posting it again here.<br>
<br>
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