Problems with gmod_bulk_load_gff3

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Problems with gmod_bulk_load_gff3

anja
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Re: Problems with gmod_bulk_load_gff3

Scott Cain
Hi Anja,

Assuming the Sequence Ontology is loaded properly*, I would suggest
that you check your GFF file for trailing white space on the third
column.  For instance, if your third column is "region " instead of
"region", it will fail.

Scott

*To double check SO, you can try this query:

  SELECT c.* FROM cvterm cvt join cv USING (cv_id) WHERE cvt.name =
'region' AND cv.name = 'sequence'

which should return one line.

On Tue, Jun 15, 2010 at 3:29 PM, Anja Friedrich
<[hidden email]> wrote:

> Hi all,
>
> I'm writing my diploma thesis and use Jbrowse to visualize some data.
> I installed postgresql, chado and jbrowse on my computer. Now I tried as written
> in the tutorial to load gff data into the database.
>
> load/bin/gmod_bulk_load_gff3.pl --organism Lemna_minor --recreate_cache
> --gfffile NC_010109.gff
>
> I got this error message:
>
> (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 ...)
>
> ------------- EXCEPTION: Bio::Root::Exception -------------
> MSG: no cvterm for region
> STACK: Error::throw
> STACK: Bio::Root::Root::throw /usr/local/share/perl/5.10.1/Bio/Root/Root.pm:368
> STACK: Bio::GMOD::DB::Adapter::get_type
> /usr/local/share/perl/5.10.1/Bio/GMOD/DB/Adapter.pm:4579
> STACK: load/bin/gmod_bulk_load_gff3.pl:835
> -----------------------------------------------------------
>
> 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...
>
> When I was searching in google, I have seen that this questions has already been
> answered in this thread. The problem is that the answer doesn't help me at all,
> because I was running the step make ontologies successfully and was loading all
> except the GO.
>
> Any help is appreciated
>
> Kind Regards,
> Anja
>
>
>
>
> ------------------------------------------------------------------------------
> ThinkGeek and WIRED's GeekDad team up for the Ultimate
> GeekDad Father's Day Giveaway. ONE MASSIVE PRIZE to the
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>



--
------------------------------------------------------------------------
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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Re: Problems with gmod_bulk_load_gff3

Scott Cain
Hi Anja,

Please keep the schema list in the loop.

What do you mean "somehow (your) Lemna data disappeared"?  Data
doesn't just disappear out of a database, that is kind of the point of
using a RDMS.  So, the real problem you have is, how did the data
disappear and what else bad happened to the database as a result?

Scott


On Tue, Jun 15, 2010 at 4:00 PM, Anja Friedrich
<[hidden email]> wrote:

> Hi Scott,
>
> the problem is that the data were already loaded yesterday using the same
> command. Today I tried to add some data and somehow my Lemna data
> disappeared out of the database. I thought I can load them again using the
> same command, but I got this error... When they were already loaded should
> my gff file be right, shouldn't it?
>
> Regards, Anja
>
> ________________________________
> Gewinnen Sie eins von drei tollen WM-Hotmail-Fan-Paketen!



--
------------------------------------------------------------------------
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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GeekDad Father's Day Giveaway. ONE MASSIVE PRIZE to the
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Re: Problems with gmod_bulk_load_gff3

anja
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Re: Problems with gmod_bulk_load_gff3

Scott Cain
Hi Anja,

The reason it's telling you that the ontologies are already load is
not, as you might think, that it is looking into the database and
determining that they are already loaded, but because it is looking in
the directory where the OBO files are downloaded to and seeing that a
lock file is there, assumes that the ontology has already been loaded
(that's why it says to remove the touchfile if you want to load them
again).

You should try the SQL command I suggested in my earlier email to see
if there is still a region term in your cvterm table.  Also, you
should double check that /usr/loca/gmod/conf/default.conf points at
the database that you think it should.

Scott


On Tue, Jun 15, 2010 at 4:37 PM, Anja Friedrich
<[hidden email]> wrote:

> Hi Scott,
>
> nothing else happened. I just couldn't find the data anymore, the feature table
> was empty...
> I tried to install the Chado Schema again and to load the ontologies...
>
> Which ontologies would you like to load (Comma delimited)? [0]  1,2,4,6
> fetching files for Relationship Ontology
>  +http://www.obofoundry.org/ro/ro.obo
>  already loaded, remove touchfile to reload.  skipping
> fetching files for Sequence Ontology
>  +http://song.cvs.sourceforge.net/*checkout*/song/ontology/so.obo
>  already loaded, remove touchfile to reload.  skipping
> fetching files for Chado Feature Properties
>  +load/etc/feature_property.obo
>    loading...done!
> fetching files for Plant Ontology
>
> +http://palea.cgrb.oregonstate.edu/viewsvn/Poc/trunk/ontology/OBO_format/po_anatomy.obo?view=co
>  already loaded, remove touchfile to reload.  skipping
>
> Is there anything wrong?
>
> Regards, Anja
>
>
> ------------------------------------------------------------------------------
> ThinkGeek and WIRED's GeekDad team up for the Ultimate
> GeekDad Father's Day Giveaway. ONE MASSIVE PRIZE to the
> lucky parental unit.  See the prize list and enter to win:
> http://p.sf.net/sfu/thinkgeek-promo
> _______________________________________________
> 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

------------------------------------------------------------------------------
ThinkGeek and WIRED's GeekDad team up for the Ultimate
GeekDad Father's Day Giveaway. ONE MASSIVE PRIZE to the
lucky parental unit.  See the prize list and enter to win:
http://p.sf.net/sfu/thinkgeek-promo
_______________________________________________
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Re: Problems with gmod_bulk_load_gff3

anja
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Re: Problems with gmod_bulk_load_gff3

Scott Cain
Hi Anja,

It does make sense, as a path to recovery, but you might want to look
at a way to keep your database backed up in the future  :-)

There are two ways to remove the touch file in two ways:

1. the command `make rm_locks` which just removes the touch/lock files

or

2. issuing the command rm -rf ./tmp (careful about that '.' :-)  which
will cause the loader to download fresh copies of all the ontologies.

Scott


On Tue, Jun 15, 2010 at 4:55 PM, Anja Friedrich
<[hidden email]> wrote:

> Hi Scott,
>
> I tried the SQL command you were suggesting and I didn't get a result, thats
> why I was trying to load the ontologies again.
> The default.conf contains this:
>
> DBUSER=anou
> DBHOST=localhost
> DEFAULT=y
> DBDRIVER=Pg
> DBNAME=chado
> DBPORT=5432
> DBORGANISM=common name
> DBPASS=...
> //I removed
> SQLFILE=/usr/local/gmod/src/chado/modules/complete.sql
>
> I can remove the touchfile and load the ontologies again, if it makes any
> sense
>
> Regards,
> Anja
>
>> Date: Tue, 15 Jun 2010 16:47:06 -0400
>> Subject: Re: [Gmod-schema] Problems with gmod_bulk_load_gff3
>> From: [hidden email]
>> To: [hidden email]
>> CC: [hidden email]
>>
>> Hi Anja,
>>
>> The reason it's telling you that the ontologies are already load is
>> not, as you might think, that it is looking into the database and
>> determining that they are already loaded, but because it is looking in
>> the directory where the OBO files are downloaded to and seeing that a
>> lock file is there, assumes that the ontology has already been loaded
>> (that's why it says to remove the touchfile if you want to load them
>> again).
>>
>> You should try the SQL command I suggested in my earlier email to see
>> if there is still a region term in your cvterm table. Also, you
>> should double check that /usr/loca/gmod/conf/default.conf points at
>> the database that you think it should.
>>
>> Scott
>>
>>
>> On Tue, Jun 15, 2010 at 4:37 PM, Anja Friedrich
>> <[hidden email]> wrote:
>> > Hi Scott,
>> >
>> > nothing else happened. I just couldn't find the data anymore, the
>> > feature table
>> > was empty...
>> > I tried to install the Chado Schema again and to load the ontologies...
>> >
>> > Which ontologies would you like to load (Comma delimited)? [0]  1,2,4,6
>> > fetching files for Relationship Ontology
>> >  +http://www.obofoundry.org/ro/ro.obo
>> >  already loaded, remove touchfile to reload.  skipping
>> > fetching files for Sequence Ontology
>> >  +http://song.cvs.sourceforge.net/*checkout*/song/ontology/so.obo
>> >  already loaded, remove touchfile to reload.  skipping
>> > fetching files for Chado Feature Properties
>> >  +load/etc/feature_property.obo
>> >    loading...done!
>> > fetching files for Plant Ontology
>> >
>> >
>> > +http://palea.cgrb.oregonstate.edu/viewsvn/Poc/trunk/ontology/OBO_format/po_anatomy.obo?view=co
>> >  already loaded, remove touchfile to reload.  skipping
>> >
>> > Is there anything wrong?
>> >
>> > Regards, Anja
>> >
>> >
>> >
>> > ------------------------------------------------------------------------------
>> > ThinkGeek and WIRED's GeekDad team up for the Ultimate
>> > GeekDad Father's Day Giveaway. ONE MASSIVE PRIZE to the
>> > lucky parental unit.  See the prize list and enter to win:
>> > http://p.sf.net/sfu/thinkgeek-promo
>> > _______________________________________________
>> > 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
>
> ________________________________
> Künftig E-Mails ohne Werbung – Nutzen Sie Hotmail auch geschäftlich.



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

------------------------------------------------------------------------------
ThinkGeek and WIRED's GeekDad team up for the Ultimate
GeekDad Father's Day Giveaway. ONE MASSIVE PRIZE to the
lucky parental unit.  See the prize list and enter to win:
http://p.sf.net/sfu/thinkgeek-promo
_______________________________________________
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Re: Problems with gmod_bulk_load_gff3

anja
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