hi , chado help!

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hi , chado help!

zhenyang guo
hi , i am a chado novice ,and meet with some problems when i load sequences in to chado database. don't know how to fix them ,hoping that i can get help from you.
the sequence i am loading into database  comes from human enterovirus A seq.  the procedure  of transforming gb-file into gff-file is ok,whenever i load the gff file into chado ,it won't  work.
the following is  sections from the terminal:
"
guo@guo-desktop:~$ gmod_bulk_load_gff3.pl  --dbname demo  --dbuser guo1 --dbpass 123456  --gfffile  ./hev-a.gb.gff  --organism EV --recreate_cache
(Re)creating the uniquename cache in the database...
Creating table...
Populating table...
Creating indexes...Done.
Preparing data for inserting into the demo database
(This may take a while ...)


There is a five_prime_UTR feature with no parent (ID:GenBank:five_prime_UTR:GU196833:1:554)  I think that is wrong!


This GFF file has CDS and/or UTR features that do not belong to a
'central dogma' gene (ie, gene/transcript/CDS).  The features of
this type are being stored in the database as is.

There is a CDS feature with no parent (ID:polyprotein)  I think that is wrong!

There is a three_prime_UTR feature with no parent (ID:GenBank:three_prime_UTR:GU196833:7137:7214)  I think that is wrong!

There is a five_prime_UTR feature with no parent (ID:GenBank:five_prime_UTR:GQ994992:1:734)  I think that is wrong!

There is a CDS feature with no parent (ID:polyprotein)  I think that is wrong!

There is a three_prime_UTR feature with no parent (ID:GenBank:three_prime_UTR:GQ994992:7317:7396)  I think that is wrong!

  “

also , the terminal says rerunning the loader with the “ --recreate_cache "option , but it still doesn't work,
i don't know if i describe problem clearly ,hoping  it works.
thanks very much.

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Re: hi , chado help!

Scott Cain
Hi Zhenyang,

>From the warning messages, it seems that the genbank to gff script
produced some pretty strange looking GFF.  It looks to me that it did
load though, because those messages are warnings not errors (that is,
they didn't stop the loader from running).  Is there more information
you can share with us?  You could send the GFF that you used to the
list and we can take a look.

Scott


On Mon, May 24, 2010 at 5:04 AM, zhenyang guo <[hidden email]> wrote:

> hi , i am a chado novice ,and meet with some problems when i load sequences
> in to chado database. don't know how to fix them ,hoping that i can get help
> from you.
> the sequence i am loading into database  comes from human enterovirus A
> seq.  the procedure  of transforming gb-file into gff-file is ok,whenever i
> load the gff file into chado ,it won't  work.
> the following is  sections from the terminal:
> "
> guo@guo-desktop:~$ gmod_bulk_load_gff3.pl  --dbname demo  --dbuser guo1
> --dbpass 123456  --gfffile  ./hev-a.gb.gff  --organism EV --recreate_cache
> (Re)creating the uniquename cache in the database...
> Creating table...
> Populating table...
> Creating indexes...Done.
> Preparing data for inserting into the demo database
> (This may take a while ...)
>
>
> There is a five_prime_UTR feature with no parent
> (ID:GenBank:five_prime_UTR:GU196833:1:554)  I think that is wrong!
>
>
> This GFF file has CDS and/or UTR features that do not belong to a
> 'central dogma' gene (ie, gene/transcript/CDS).  The features of
> this type are being stored in the database as is.
>
> There is a CDS feature with no parent (ID:polyprotein)  I think that is
> wrong!
>
> There is a three_prime_UTR feature with no parent
> (ID:GenBank:three_prime_UTR:GU196833:7137:7214)  I think that is wrong!
>
> There is a five_prime_UTR feature with no parent
> (ID:GenBank:five_prime_UTR:GQ994992:1:734)  I think that is wrong!
>
> There is a CDS feature with no parent (ID:polyprotein)  I think that is
> wrong!
>
> There is a three_prime_UTR feature with no parent
> (ID:GenBank:three_prime_UTR:GQ994992:7317:7396)  I think that is wrong!
>
>   “
>
> also , the terminal says rerunning the loader with the “ --recreate_cache
> "option , but it still doesn't work,
> i don't know if i describe problem clearly ,hoping  it works.
> thanks very much.
>
> ------------------------------------------------------------------------------
>
>
> _______________________________________________
> Gmod-schema mailing list
> [hidden email]
> https://lists.sourceforge.net/lists/listinfo/gmod-schema
>
>



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GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research

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Re: hi , chado help!

nancy
Hi zhenyang and Scott, et al,

This is a thread that posted long ago. But i having a same problem as
zhenyang faced, so i was wondering you had solve the problem. And hope you
all may help.
I intend to load gff3 file into chado database and i get the error message
as following:


##########################################################3
(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_test3 database
(This may take a while ...)

This GFF file has CDS and/or UTR features that do not belong to a
'central dogma' gene (ie, gene/transcript/CDS).  The features of
this type are being stored in the database as is.


This file was not declared as analysis results (with the --analysis flag,
but this file contains attributes that imply that it is:
* Has a match feature type
You can safely ignore this message if you don't need to access scores
associated with these features.



There is a CDS feature with no parent (ID:)  I think that is wrong!


no parent YAL030W_mRNA (YAL030W_mRNA);
you probably need to rerun the loader with the --recreate_cache option

 at /usr/local/share/perl5/Bio/GMOD/DB/Adapter.pm line 4442

Bio::GMOD::DB::Adapter::handle_parent('Bio::GMOD::DB::Adapter=HASH(0xa263b50)',
'Bio::SeqFeature::Annotated=HASH(0x9c883f0)') called at
/usr/local/bin/gmod_bulk_load_gff3.pl line 859

Abnormal termination, trying to clean up...

Attempting to clean up the loader temp table (so that --recreate_cache
won't be needed)...

######################################################


Do you have any idea what is happening?



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Re: hi , chado help!

zhenyang guo
Sorry, nancy. I remember I fixed this problem then, but can't remember how I solved it. It has been a long time since I shifted my work from chado. 
Maybe Scott can answer your question, since he is expert on it.  hope you get your solution soon!

zhenyang


2013/5/23 nancy <[hidden email]>
Hi zhenyang and Scott, et al,

This is a thread that posted long ago. But i having a same problem as
zhenyang faced, so i was wondering you had solve the problem. And hope you
all may help.
I intend to load gff3 file into chado database and i get the error message
as following:


##########################################################3
(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_test3 database
(This may take a while ...)

This GFF file has CDS and/or UTR features that do not belong to a
'central dogma' gene (ie, gene/transcript/CDS).  The features of
this type are being stored in the database as is.


This file was not declared as analysis results (with the --analysis flag,
but this file contains attributes that imply that it is:
* Has a match feature type
You can safely ignore this message if you don't need to access scores
associated with these features.



There is a CDS feature with no parent (ID:)  I think that is wrong!


no parent YAL030W_mRNA (YAL030W_mRNA);
you probably need to rerun the loader with the --recreate_cache option

 at /usr/local/share/perl5/Bio/GMOD/DB/Adapter.pm line 4442

Bio::GMOD::DB::Adapter::handle_parent('Bio::GMOD::DB::Adapter=HASH(0xa263b50)',
'Bio::SeqFeature::Annotated=HASH(0x9c883f0)') called at
/usr/local/bin/gmod_bulk_load_gff3.pl line 859

Abnormal termination, trying to clean up...

Attempting to clean up the loader temp table (so that --recreate_cache
won't be needed)...

######################################################


Do you have any idea what is happening?



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Best Regards,
Zhenyang Guo
Institute of Viral Disease Control and Prevention, China CDC


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Re: hi , chado help!

Gwendoline Andres
Hi,

If you are sure that YAL030W_mRNA (id) is on your gff3 file, then you need to use bin/gmod_gff3_preprocessor.pl to make sure that parents will come before children in your gff3 file.

Gwendoline

Le 23/05/2013 13:59, concer guo a écrit :
Sorry, nancy. I remember I fixed this problem then, but can't remember how I solved it. It has been a long time since I shifted my work from chado. 
Maybe Scott can answer your question, since he is expert on it.  hope you get your solution soon!

zhenyang


2013/5/23 nancy <[hidden email]>
Hi zhenyang and Scott, et al,

This is a thread that posted long ago. But i having a same problem as
zhenyang faced, so i was wondering you had solve the problem. And hope you
all may help.
I intend to load gff3 file into chado database and i get the error message
as following:


##########################################################3
(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_test3 database
(This may take a while ...)

This GFF file has CDS and/or UTR features that do not belong to a
'central dogma' gene (ie, gene/transcript/CDS).  The features of
this type are being stored in the database as is.


This file was not declared as analysis results (with the --analysis flag,
but this file contains attributes that imply that it is:
* Has a match feature type
You can safely ignore this message if you don't need to access scores
associated with these features.



There is a CDS feature with no parent (ID:)  I think that is wrong!


no parent YAL030W_mRNA (YAL030W_mRNA);
you probably need to rerun the loader with the --recreate_cache option

 at /usr/local/share/perl5/Bio/GMOD/DB/Adapter.pm line 4442

Bio::GMOD::DB::Adapter::handle_parent('Bio::GMOD::DB::Adapter=HASH(0xa263b50)',
'Bio::SeqFeature::Annotated=HASH(0x9c883f0)') called at
/usr/local/bin/gmod_bulk_load_gff3.pl line 859

Abnormal termination, trying to clean up...

Attempting to clean up the loader temp table (so that --recreate_cache
won't be needed)...

######################################################


Do you have any idea what is happening?



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29688 ROSCOFF CEDEX
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Tel : (+33) 2 98 29 56 46

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Re: hi , chado help!

nancy
Hi Gwendoline Andres,

Thanks. After the gff3 file has been processed /gmod_gff3_preprocessor.pl/,
it successfully load into chado database even through there are few
sequences failed in loading into database.

And i getting an errror message as below:

#########################################################
couldn't find GO:0034500 's cvterm_id in cvterm table
couldn't find GO:0070683 's cvterm_id in cvterm table
couldn't find GO:0031575 's cvterm_id in cvterm table
couldn't find GO:0031576 's cvterm_id in cvterm table
couldn't find GO:0070683 's cvterm_id in cvterm table
couldn't find GO:0006467 's cvterm_id in cvterm table
...
(#PS: I wondering what this error message about, it keep prompt me this
error msg while i attempt to load data into database, i suspect that the
gene ontology that i downloaded wasn't complete, so i manually download gene
ontology and load the new gene.chado.xml into database, and it still give me
the same error.)

This GFF file has CDS and/or UTR features that do not belong to a
'central dogma' gene (ie, gene/transcript/CDS).  The features of
this type are being stored in the database as is.

There are both CDS and exon features in this file, but
you did not set the --noexon option, which you probably want.
Please see `perldoc gmod_bulk_load_gff3.pl` for more information.
....

No features where found with a unqiuename of chr01
and an organism_id of 13.  Are you sure you have the uniquename
right?  It might have been changed when loaded into the database to ensure
uniqueness.  Skipping this sequence...

No features where found with a unqiuename of chr02
and an organism_id of 13.  Are you sure you have the uniquename
right?  It might have been changed when loaded into the database to ensure
uniqueness.  Skipping this sequence...
.....

Skipping organism table since the load file is empty...
Skipping analysis table since the load file is empty...
Skipping db table since the load file is empty...
Loading data into dbxref table ...
Skipping cv table since the load file is empty...
Loading data into cvterm table ...
Loading data into feature table ...
Loading data into featureloc table ...
Loading data into feature_relationship table ...
Loading data into featureprop table ...
Loading data into feature_cvterm table ...
Loading data into synonym table ...
Loading data into feature_synonym table ...
Loading data into feature_dbxref table ...
Skipping analysisfeature table since the load file is empty...
Adding cvtermprop=MapReferenceType for 'chromosome' ...
Adding cvtermprop=MapReferenceType to chromosome ...
Loading sequences (if any) ...

###################################################

Since the data has successfully has loaded into database even through there
are some minor sequence which cannot be loaded into. So suppose i can have
see some "outcome" in gbrowse right? Sad case it give me error message
again..
<http://generic-model-organism-system-database.450254.n5.nabble.com/file/n5711336/Screenshot.png>
Gosh, im newbie and Gbrowse really drive me crazy.





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Re: hi , chado help!

Scott Cain
Hi Nancy,

I just responded to your GBrowse query on the GBrowse mailing list.  Since you are a self-professed newbie, I have to ask: are you sure you need Chado?  Frequently people only want GBrowse, and if that's the case, Chado is not the database schema you want to use with it.  The most common database schema you'd probably want to use is the one that works with the Bio::DB::SeqFeature::Store modules in BioPerl, which is much faster that Chado when it comes to GBrowse.  The is the database that is used with the GBrowse tutorial that comes with GBrowse.

Scott



On Sun, May 26, 2013 at 10:10 PM, nancy <[hidden email]> wrote:
Hi Gwendoline Andres,

Thanks. After the gff3 file has been processed /gmod_gff3_preprocessor.pl/,
it successfully load into chado database even through there are few
sequences failed in loading into database.

And i getting an errror message as below:

#########################################################
couldn't find GO:0034500 's cvterm_id in cvterm table
couldn't find GO:0070683 's cvterm_id in cvterm table
couldn't find GO:0031575 's cvterm_id in cvterm table
couldn't find GO:0031576 's cvterm_id in cvterm table
couldn't find GO:0070683 's cvterm_id in cvterm table
couldn't find GO:0006467 's cvterm_id in cvterm table
...
(#PS: I wondering what this error message about, it keep prompt me this
error msg while i attempt to load data into database, i suspect that the
gene ontology that i downloaded wasn't complete, so i manually download gene
ontology and load the new gene.chado.xml into database, and it still give me
the same error.)

This GFF file has CDS and/or UTR features that do not belong to a
'central dogma' gene (ie, gene/transcript/CDS).  The features of
this type are being stored in the database as is.

There are both CDS and exon features in this file, but
you did not set the --noexon option, which you probably want.
Please see `perldoc gmod_bulk_load_gff3.pl` for more information.
....

No features where found with a unqiuename of chr01
and an organism_id of 13.  Are you sure you have the uniquename
right?  It might have been changed when loaded into the database to ensure
uniqueness.  Skipping this sequence...

No features where found with a unqiuename of chr02
and an organism_id of 13.  Are you sure you have the uniquename
right?  It might have been changed when loaded into the database to ensure
uniqueness.  Skipping this sequence...
.....

Skipping organism table since the load file is empty...
Skipping analysis table since the load file is empty...
Skipping db table since the load file is empty...
Loading data into dbxref table ...
Skipping cv table since the load file is empty...
Loading data into cvterm table ...
Loading data into feature table ...
Loading data into featureloc table ...
Loading data into feature_relationship table ...
Loading data into featureprop table ...
Loading data into feature_cvterm table ...
Loading data into synonym table ...
Loading data into feature_synonym table ...
Loading data into feature_dbxref table ...
Skipping analysisfeature table since the load file is empty...
Adding cvtermprop=MapReferenceType for 'chromosome' ...
Adding cvtermprop=MapReferenceType to chromosome ...
Loading sequences (if any) ...

###################################################

Since the data has successfully has loaded into database even through there
are some minor sequence which cannot be loaded into. So suppose i can have
see some "outcome" in gbrowse right? Sad case it give me error message
again..
<http://generic-model-organism-system-database.450254.n5.nabble.com/file/n5711336/Screenshot.png>
Gosh, im newbie and Gbrowse really drive me crazy.





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GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research

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Re: hi , chado help!

nancy
Hi Scott.

Ya i'm interested in exploring chado, because i going to deal with large
dataset in the future. I guess chado would be the best option or probably
the proper schema if you plan to expand your database, isn't it?


Regards,
Nancy



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Re: hi , chado help!

Scott Cain
Hi Nancy,

I wouldn't start with it in terms of learning GBrowse; additionally, depending on what you plan on doing with that data set, it still may not be the appropriate tool: are you (or people you support) going to be doing active editing/curating of the data in the database?  Do you need to support access to data that isn't sequence features (like you will use GBrowse for)?  If you're editing, WebApollo (which works with Chado, though doesn't require it) is a nicely evolving sequence feature editor.  If you need to allow access to other data types, Tripal is a good web interface that runs on Chado; and if you're starting from scratch and need Chado, I'd suggest you start with Tripal, since it will install Chado for you and handle many of the low level management issues.

If you aren't doing these things and just need a genome browser (even for a large data set), then don't use Chado and instead use Bio::DB::SeqFeature::Store.  You could also look at JBrowse, which may be suitable as well, depending on what you'll be using the genome browser for.

Scott



On Tue, May 28, 2013 at 12:21 PM, nancy <[hidden email]> wrote:
Hi Scott.

Ya i'm interested in exploring chado, because i going to deal with large
dataset in the future. I guess chado would be the best option or probably
the proper schema if you plan to expand your database, isn't it?


Regards,
Nancy



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Re: hi , chado help!

nancy
Hi Scott,

Thanks for your suggestion. I was amazed with what tripal can do, and i wanted to have something like this (Have to discuss with my work superior anyway). Between i found that tripal is not support vary type of sequence data format, like BAM file & ab1 file (where Gbrowse can display track for this type of data).

So i was wondering did Tripal is in the midst of developing more advanced tools like what GBrowse can do and support more future next gen data. If that so, tripal would be perfect choice for me.

Regards,
Nancy


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Re: hi , chado help!

Stephen Ficklin-2
Hi Nancy,

Most likely Tripal will never have an alignment viewer like GBrowse, as GBrowse provides that functionality already and the two can be integrated.  Tripal and GBrowse can both use the same Chado database and there is an extension module for Tripal that integrates GBrowse and Tripal in the event you don't want to use Chado for both. And you can manually configure each one to link to the either.  For all of the genome database sites I've worked on we have used both Tripal and GBrowse together. 

Aside from alignment viewing, is there other support you would like for BAM and ab1 (or other) files in Tripal?

Thanks,
Stephen

On 6/18/2013 10:29 PM, nancy wrote:
Hi Scott,

Thanks for your suggestion. I was amazed with what tripal can do, and i wanted to have something like this (Have to discuss with my work superior anyway). Between i found that tripal is not support vary type of sequence data format, like BAM file & ab1 file (where Gbrowse can display track for this type of data).

So i was wondering did Tripal is in the midst of developing more advanced tools like what GBrowse can do and support more future next gen data. If that so, tripal would be perfect choice for me.

Regards,
Nancy


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Re: hi , chado help!

nancy
Hi Stephen,

Thanks for the explaination. However i've slight confused about integration of Tripal and GBrowse.
Let's see this scenario, If i have install GBrowse and load all the data into it including all those alignment files as well.. And GBrowse display all this feature well in the page. After that, i install tripal and try to integrate my current gbrowse into it as well. Would it be able to display all these alignment files in tripal?

Best regards,
Choong yin


On 19 June 2013 21:11, Stephen Ficklin-3 [via Generic Model Organism System Database] <[hidden email]> wrote:
Hi Nancy,

Most likely Tripal will never have an alignment viewer like GBrowse, as GBrowse provides that functionality already and the two can be integrated.  Tripal and GBrowse can both use the same Chado database and there is an extension module for Tripal that integrates GBrowse and Tripal in the event you don't want to use Chado for both. And you can manually configure each one to link to the either.  For all of the genome database sites I've worked on we have used both Tripal and GBrowse together. 

Aside from alignment viewing, is there other support you would like for BAM and ab1 (or other) files in Tripal?

Thanks,
Stephen

On 6/18/2013 10:29 PM, nancy wrote:
Hi Scott,

Thanks for your suggestion. I was amazed with what tripal can do, and i wanted to have something like this (Have to discuss with my work superior anyway). Between i found that tripal is not support vary type of sequence data format, like BAM file & ab1 file (where Gbrowse can display track for this type of data).

So i was wondering did Tripal is in the midst of developing more advanced tools like what GBrowse can do and support more future next gen data. If that so, tripal would be perfect choice for me.

Regards,
Nancy


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