[Gmod-help] Re:Re: [GMOD-devel] help

[wangjun19820303]

hi,
 I did it as you said and I imported data  to database sucessfully. Thank you very much!!!


Wangjun
在2010-04-15 03:35:22，"Dave Clements, GMOD Help Desk" <help at gmod.org> 写道：

You need to first define the reference feature, "408J" in GFF3.  Something like:



408J Sequence whatever408JisInSO 1 howeverLong408JIs . . . Name=408J


This could be the first feature defined in your file, or it could be in a separate file.


Dave C.


2010/4/12 wangjun19820303 <wangjun19820303 at 163.com>
hi All,
    I have a question about gmod_bulk_load_gff3.pl. When I used gmod_bulk_load_gff3.pl load data into chado database.There are errors.So I can't import data into database.I don't know why.
command:(algae has already existed.)
   gmod_bulk_load_gff3.pl --organism 'algae'  --gfffile  taihuanother.gbk.gff
error:
   (Re)creating the uniquename cache in the database... 
Creating table...
Populating table...
Creating indexes...Done.
Preparing data for inserting into the chado database
(This may take a while ...)
Unable to find srcfeature 408J in the database.
Perhaps you need to rerun your data load with the '--recreate_cache' option. at /usr/local/share/perl/5.10.1/Bio/GMOD/DB/Adapter.pm line 4026
    Bio::GMOD::DB::Adapter::src_second_chance('Bio::GMOD::DB::Adapter=HASH(0x34cc5a8)', 'Bio::SeqFeature::Annotated=HASH(0x38cc280)') called at /usr/local/bin/gmod_bulk_load_gff3.pl line 758
Issuing rollback() due to DESTROY without explicit disconnect() of DBD::Pg::db handle dbname=chado;port=5432;host=localhost at /usr/share/perl/5.10/Carp.pm line 45.

when I used '--recreate_cache' option,I got the same error.

I'm looking forward  to your reply. Thank you !!!




------------------------------------------------------------------------------
Download Intel&#174; Parallel Studio Eval
Try the new software tools for yourself. Speed compiling, find bugs
proactively, and fine-tune applications for parallel performance.
See why Intel Parallel Studio got high marks during beta.
http://p.sf.net/sfu/intel-sw-dev
_______________________________________________
Gmod-devel mailing list
Gmod-devel at lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/gmod-devel





-- 
===> PLEASE KEEP RESPONSES ON THE LIST <===
http://gmod.org/wiki/GMOD_Logo_Program
http://gmod.org/wiki/GMOD_News
Was this helpful? http://gmod.org/wiki/Help_Desk_Feedback
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://brie4.cshl.edu/pipermail/gmod-help/attachments/20100415/368eaba2/attachment.html>