Loading data ( gff3 with domain info) into Chado

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Loading data ( gff3 with domain info) into Chado

claudia
To whom it may concern,
  I am having problems loading a GFF3 file (with InterProscan domain information) into CHADO. I have posted the errors below. I had a similar problem with loading a gff3 file that did not contain protein domain information, but that was resolved with a script edit. Any help is greatly appreciated.

Thank you in advance, Claudia.


root@crick:/usr/local/genome/trunk/chado# gmod_bulk_load_gff3.pl --remove_lock --recreate_cache --noexon --analysis --organism bean --gfffile '/usr/local/genome/trunk/chado/bean-1.all.fixed.sorted.gff'
(Re)creating the uniquename cache in the database...
Creating table...
Populating table...
Creating indexes...
Adjusting the primary key sequences (if necessary)...Done.
Preparing data for inserting into the chado database
(This may take a while ...)
Unable to find srcfeature contig00004 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 4555
Bio::GMOD::DB::Adapter::src_second_chance('Bio::GMOD::DB::Adapter=HASH(0x3899250)', 'Bio::SeqFeature::Annotated=HASH(0x3be2a20)') called at /usr/local/bin/gmod_bulk_load_gff3.pl line 843
Abnormal termination, trying to clean up...
Attempting to clean up the loader temp table (so that --recreate_cache
won't be needed)...
Trying to remove the run lock (so that --remove_lock won't be needed)...
Exiting...
root@crick:/usr/local/genome/trunk/chado# gmod_bulk_load_gff3.pl --remove_lock --recreate_cache --noexon --analysis --organism bean --gfffile '/usr/local/genome/trunk/chado/bean-3.all.fixed.sorted.gff'
(Re)creating the uniquename cache in the database...
Creating table...
Populating table...
Creating indexes...
Adjusting the primary key sequences (if necessary)...Done.
Preparing data for inserting into the chado database
(This may take a while ...)
Unable to find srcfeature contig00003 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 4555
Bio::GMOD::DB::Adapter::src_second_chance('Bio::GMOD::DB::Adapter=HASH(0x38fa250)', 'Bio::SeqFeature::Annotated=HASH(0x3c43920)') called at /usr/local/bin/gmod_bulk_load_gff3.pl line 843
Abnormal termination, trying to clean up...
Attempting to clean up the loader temp table (so that --recreate_cache
won't be needed)...
Trying to remove the run lock (so that --remove_lock won't be needed)...
Exiting...
root@crick:/usr/local/genome/trunk/chado# perldoc gmod_bulk_load_gff.pl
No documentation found for "gmod_bulk_load_gff.pl".
root@crick:/usr/local/genome/trunk/chado#

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Re: Loading data ( gff3 with domain info) into Chado

Carson Hinton Holt
Re: Loading data ( gff3 with domain info)  into Chado The error ‘Unable to find srcfeature contig00004 in the database’ indicates you have not loaded the sequence of the contig into your database yet.

You need to load it before loading your analysis file.

You should be able to do this with a GFF3 that contains the ‘contig/chromosome’ line at the first and the fasta sequence at the end, or by using the --fastafile option.

--Carson

On 2/17/11 10:27 AM, "claudia" <dinatal@...> wrote:

  To whom it may concern,
   I am having problems loading a GFF3 file (with InterProscan domain information) into CHADO. I have posted the errors below. I had a similar problem with loading a gff3 file that did not contain protein domain information, but that was resolved with a script edit. Any help is greatly appreciated.
 
 Thank you in advance, Claudia.
 


 root@crick:/usr/local/genome/trunk/chado# gmod_bulk_load_gff3.pl --remove_lock --recreate_cache --noexon --analysis --organism bean --gfffile '/usr/local/genome/trunk/chado/bean-1.all.fixed.sorted.gff'
 (Re)creating the uniquename cache in the database...
 Creating table...
 Populating table...
 Creating indexes...
 Adjusting the primary key sequences (if necessary)...Done.
 Preparing data for inserting into the chado database
 (This may take a while ...)
 Unable to find srcfeature contig00004 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 4555
 Bio::GMOD::DB::Adapter::src_second_chance('Bio::GMOD::DB::Adapter=HASH(0x3899250)', 'Bio::SeqFeature::Annotated=HASH(0x3be2a20)') called at /usr/local/bin/gmod_bulk_load_gff3.pl line 843
 Abnormal termination, trying to clean up...
 Attempting to clean up the loader temp table (so that --recreate_cache
 won't be needed)...
 Trying to remove the run lock (so that --remove_lock won't be needed)...
 Exiting...
 root@crick:/usr/local/genome/trunk/chado# gmod_bulk_load_gff3.pl --remove_lock --recreate_cache --noexon --analysis --organism bean --gfffile '/usr/local/genome/trunk/chado/bean-3.all.fixed.sorted.gff'
 (Re)creating the uniquename cache in the database...
 Creating table...
 Populating table...
 Creating indexes...
 Adjusting the primary key sequences (if necessary)...Done.
 Preparing data for inserting into the chado database
 (This may take a while ...)
 Unable to find srcfeature contig00003 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 4555
 Bio::GMOD::DB::Adapter::src_second_chance('Bio::GMOD::DB::Adapter=HASH(0x38fa250)', 'Bio::SeqFeature::Annotated=HASH(0x3c43920)') called at /usr/local/bin/gmod_bulk_load_gff3.pl line 843
 Abnormal termination, trying to clean up...
 Attempting to clean up the loader temp table (so that --recreate_cache
 won't be needed)...
 Trying to remove the run lock (so that --remove_lock won't be needed)...
 Exiting...
 root@crick:/usr/local/genome/trunk/chado# perldoc gmod_bulk_load_gff.pl
 No documentation found for "gmod_bulk_load_gff.pl".
 root@crick:/usr/local/genome/trunk/chado#
 

------------------------------------------------------------------------------
The ultimate all-in-one performance toolkit: Intel(R) Parallel Studio XE:
Pinpoint memory and threading errors before they happen.
Find and fix more than 250 security defects in the development cycle.
Locate bottlenecks in serial and parallel code that limit performance.
http://p.sf.net/sfu/intel-dev2devfeb
_______________________________________________
Gmod-schema mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-schema