unable to find srcfeature Php00a00001.00001 in the database.

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unable to find srcfeature Php00a00001.00001 in the database.

alessa85
Hi,

I am trying to upload a .gff3 file to a GMOD database,
but I got this error. I
had tried some of the posts that are in this blog
but it did not worked. Could
you help? I really appreciate you help.

This is the command line that I used:

gmod_bulk_load_gff3.pl --organism pera --gfffile
 GBgff3.gff --dbname chado
--dbuser postgres --dbhost localhost --analysis

Error message:

Preparing data for inserting into the chado database
(This may take a while ...)
Unable to find srcfeature Php00a00001.00001 in the database.
Perhaps you need to rerun your data load with the
'--recreate_cache' option. at
/usr/local/lib/perl5/site_perl/5.10.1 /Bio/GMOD/DB/Adapter.pm
line 4555
       
Bio::GMOD::DB::Adapter::src_second_chance('Bio::GMOD::
DB::Adapter=HASH(0x670670)',
'Bio::SeqFeature::Annotated=HASH(0x1f06168)') called at
/usr/ local/bin/gmod_bulk_load_gff3.pl line 841

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...

An this is the .gff that i am trying to upload:

Php00a00001.00001       Newbler mRNA    1       4135    .       .       .
ID=Php00a00001.00001;name=Php00a00001.00001
Php00a00001.00001       Blastx_to_Swissprot     protein_match   1411    2576  
.       .       .
ID=Php00a00001.00001:hit:1;name=Php00a00001.00001

Thanks


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Re: unable to find srcfeature Php00a00001.00001 in the database.

Scott Cain
Hi Gina,

One potential problem I can see is that the GFF you posted uses a
"name" tag but the GFF3 spec and the Chado loader require that to be
"Name" in order to get used as the name of the feature.

Scott


On Mon, May 21, 2012 at 11:52 PM, alessa85 <[hidden email]> wrote:

> Hi,
>
> I am trying to upload a .gff3 file to a GMOD database,
> but I got this error. I
> had tried some of the posts that are in this blog
> but it did not worked. Could
> you help? I really appreciate you help.
>
> This is the command line that I used:
>
> gmod_bulk_load_gff3.pl --organism pera --gfffile
>  GBgff3.gff --dbname chado
> --dbuser postgres --dbhost localhost --analysis
>
> Error message:
>
> Preparing data for inserting into the chado database
> (This may take a while ...)
> Unable to find srcfeature Php00a00001.00001 in the database.
> Perhaps you need to rerun your data load with the
> '--recreate_cache' option. at
> /usr/local/lib/perl5/site_perl/5.10.1 /Bio/GMOD/DB/Adapter.pm
> line 4555
>
> Bio::GMOD::DB::Adapter::src_second_chance('Bio::GMOD::
> DB::Adapter=HASH(0x670670)',
> 'Bio::SeqFeature::Annotated=HASH(0x1f06168)') called at
> /usr/ local/bin/gmod_bulk_load_gff3.pl line 841
>
> 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...
>
> An this is the .gff that i am trying to upload:
>
> Php00a00001.00001       Newbler mRNA    1       4135    .       .       .
> ID=Php00a00001.00001;name=Php00a00001.00001
> Php00a00001.00001       Blastx_to_Swissprot     protein_match   1411    2576
> .       .       .
> ID=Php00a00001.00001:hit:1;name=Php00a00001.00001
>
> Thanks
>
>
> ------------------------------------------------------------------------------
> Live Security Virtual Conference
> Exclusive live event will cover all the ways today's security and
> threat landscape has changed and how IT managers can respond. Discussions
> will include endpoint security, mobile security and the latest in malware
> threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/
> _______________________________________________
> Gmod-schema mailing list
> [hidden email]
> https://lists.sourceforge.net/lists/listinfo/gmod-schema



--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research

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Exclusive live event will cover all the ways today's security and
threat landscape has changed and how IT managers can respond. Discussions
will include endpoint security, mobile security and the latest in malware
threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/
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Re: unable to find srcfeature Php00a00001.00001 in the database.

Scott Cain
Hi Gina,

The GFF file you sent me (in which looks like all you did was fix the
Name tags) loads in to one of my Chado instances without errors.
Perhaps your Chado instance is "confused" in some way due to loading
problems (it's not supposed to happen, but nothing is perfect).  Could
you try loading this GFF into another Chado instance (perhaps one you
could create from a dump that you have from before you started having
problems--you have one, right? :-)

Scott


On Tue, May 22, 2012 at 12:51 PM, Gina Garzon <[hidden email]> wrote:

> Hi Scott,
>
> I tried again, but I keep having the same error. Could you look my gff,
> please and see if I have another error. I validate it and it seems to be
> fine.
>
> Thanks a lot,
>
> I really appreciate your help.
>
> Gina
>
> On Tue, May 22, 2012 at 8:36 AM, Scott Cain <[hidden email]> wrote:
>>
>> Hi Gina,
>>
>> One potential problem I can see is that the GFF you posted uses a
>> "name" tag but the GFF3 spec and the Chado loader require that to be
>> "Name" in order to get used as the name of the feature.
>>
>> Scott
>>
>>
>> On Mon, May 21, 2012 at 11:52 PM, alessa85 <[hidden email]> wrote:
>> > Hi,
>> >
>> > I am trying to upload a .gff3 file to a GMOD database,
>> > but I got this error. I
>> > had tried some of the posts that are in this blog
>> > but it did not worked. Could
>> > you help? I really appreciate you help.
>> >
>> > This is the command line that I used:
>> >
>> > gmod_bulk_load_gff3.pl --organism pera --gfffile
>> >  GBgff3.gff --dbname chado
>> > --dbuser postgres --dbhost localhost --analysis
>> >
>> > Error message:
>> >
>> > Preparing data for inserting into the chado database
>> > (This may take a while ...)
>> > Unable to find srcfeature Php00a00001.00001 in the database.
>> > Perhaps you need to rerun your data load with the
>> > '--recreate_cache' option. at
>> > /usr/local/lib/perl5/site_perl/5.10.1 /Bio/GMOD/DB/Adapter.pm
>> > line 4555
>> >
>> > Bio::GMOD::DB::Adapter::src_second_chance('Bio::GMOD::
>> > DB::Adapter=HASH(0x670670)',
>> > 'Bio::SeqFeature::Annotated=HASH(0x1f06168)') called at
>> > /usr/ local/bin/gmod_bulk_load_gff3.pl line 841
>> >
>> > 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...
>> >
>> > An this is the .gff that i am trying to upload:
>> >
>> > Php00a00001.00001       Newbler mRNA    1       4135    .       .
>> > .
>> > ID=Php00a00001.00001;name=Php00a00001.00001
>> > Php00a00001.00001       Blastx_to_Swissprot     protein_match   1411
>> >  2576
>> > .       .       .
>> > ID=Php00a00001.00001:hit:1;name=Php00a00001.00001
>> >
>> > Thanks
>> >
>> >
>> >
>> > ------------------------------------------------------------------------------
>> > Live Security Virtual Conference
>> > Exclusive live event will cover all the ways today's security and
>> > threat landscape has changed and how IT managers can respond.
>> > Discussions
>> > will include endpoint security, mobile security and the latest in
>> > malware
>> > threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/
>> > _______________________________________________
>> > Gmod-schema mailing list
>> > [hidden email]
>> > https://lists.sourceforge.net/lists/listinfo/gmod-schema
>>
>>
>>
>> --
>> ------------------------------------------------------------------------
>> Scott Cain, Ph. D.                                   scott at scottcain
>> dot net
>> GMOD Coordinator (http://gmod.org/)                     216-392-3087
>> Ontario Institute for Cancer Research
>
>
>
>
> --
> Gina A. Garzon M.
>



--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research

------------------------------------------------------------------------------
Live Security Virtual Conference
Exclusive live event will cover all the ways today's security and
threat landscape has changed and how IT managers can respond. Discussions
will include endpoint security, mobile security and the latest in malware
threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/
_______________________________________________
Gmod-schema mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-schema