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From: Jonathan S. <js...@pc...> - 2004-05-20 05:25:31
|
Fidel: Here are the relevant files. They belong at this path: Projects/CBIL/Bio/lib/perl/GenBank Let me know they work. Jonathan |
|
From: Madhura S. <sma...@st...> - 2004-05-20 02:07:36
|
Hi All
I am trying to load EMBL files into GUS, but having some problems,
when I try to execute the command :
ga GUS::Common::Plugin::GenericParser2Gus --filetype=3Dembl =
-filepath=3Db.pertussis.embl -sequencetype=3Dds-DNA
without commit, I get the following error:
*********************************************************
***COMMIT TURNED OFF***
Dumping log: $VAR1 =3D '/tmp//GenericParser2Gusdev.pid28608.log';
embl file to parse, b.bronchiseptica.embl...
ID line fine!!!
source feature found, FT source 1..5339179!!
processing bioperl sequence, BB...
sequence not in GUS yet
can't find SequenceType, ds-DNA
number of features =3D 5009
organism, taxon id: Bordetella bronchiseptica,
DBD::Oracle::st execute failed: ORA-01400: cannot insert NULL into =
("DOTS"."NASE
QUENCEIMP"."SEQUENCE_TYPE_ID") (DBD ERROR: OCIStmtExecute) at =
/afs/ir/users/s/m/
smadhura/RA/GUS/lib/perl/GUS/ObjRelP/DbiDbHandle.pm line 145.
(after this along sequence is printed)
ATCGTACGGATTACAGGGCTTACGATGTTTCACGTGAAACGCCGAACGAGGTGCCACTATAATGGCCTCGGAA=
CGCTCTT
TCATCTCTCCCCATC, 1, 1, 1, 5339179, 850606, 0, chr. 1, 853819, 1, 86, =
1825282, 0
at /afs/ir/users/s/m/smadhura/RA/GUS/lib/perl/GUS/ObjRelP/DbiDbHandle.pm =
line 18
5
=20
*************************************************************************=
**
Can someone tell me why this error is occuring?
Thanks!
Madhura
|
|
From: Sucheta T. <su...@vb...> - 2004-05-19 20:46:41
|
Hello, One more question. Does anyone stores the outputs from each gene calling program e.g; genmark, glimmer, genscan, fgenesh etc.. If yes, which is the right table for this? Sucheta > Take a look at InsertNewExternalSequences, it is quite flexible and may do > what you want. > > Debbie > > > > > On Tue, 18 May 2004, Sucheta Tripathy wrote: > >> Hi Debbie, >> >> We have protein data after using the gene calls. These are present in >> raw >> fasta format. To these sequences we did the signalP analysis and other >> annotation. I saw the table format and we can easily parse them onto the >> column names, but I was wondering before that I need to put them onto >> aasequenceImp table. So I thought if I can put my raw protein sequences >> to >> the table with some plugin. >> >> Thanks >> >> Sucheta >> > Hi Sucheta, >> > >> > >> > What is the data that you want to load? It is hard to answer the >> question >> > generally. >> > >> > As you probably know already we load data from the protein nr database >> > files from NCBI and protein motif data from prodom and cdd. Those are >> > loaded with LoadNRDB.pm (written specifically for NCBI nrdb protein >> data) >> > and InsertNewExternalSequences. >> > >> > We also load signal peptide and transmembrane results from the >> analysis >> > of our assemblies. Those plugins are not in cvs repository at Sanger >> and >> > may not be appropriate for your use. >> > >> > Debbie >> > On Tue, 18 May 2004, Sucheta Tripathy >> > wrote: >> > >> >> >> >> Hello All, >> >> >> >> Has anyone tried uploading amino acid related data to GUS(mainly to >> >> aasequenceImp and related tables). Is there a plugin for that? I >> have >> >> lots of amino acid related data like the signalP output and other >> >> annotations. >> >> >> >> Any suggestions? >> >> >> >> Thanks >> >> >> >> Sucheta >> >> >> >> >> >> >> >> >> > >> >> >> > > > > ------------------------------------------------------- > This SF.Net email is sponsored by: SourceForge.net Broadband > Sign-up now for SourceForge Broadband and get the fastest > 6.0/768 connection for only $19.95/mo for the first 3 months! > http://ads.osdn.com/?ad_id=2562&alloc_id=6184&op=click > _______________________________________________ > Gusdev-gusdev mailing list > Gus...@li... > https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev > -- Sucheta Tripathy Virginia Bioinformatics Institute Phase-I Washington street. Virginia Tech. Blacksburg,VA 24061-0447 phone:(540)231-8138 Fax: (540) 231-2606 |
|
From: Madhura S. <sma...@st...> - 2004-05-19 19:01:12
|
Hi Debbie I used the modified LoadTaxon.pm file and looks like it worked! The output is as follows: (putting just the end of output) ------------ processed ncbi_tax_id : 143293 processed ncbi_tax_id : 192120 processed ncbi_tax_id : 192121 processed ncbi_tax_id : 248763 processed ncbi_tax_id : 102264 processed ncbi_tax_id : 40049 processed ncbi_tax_id : 192122 278364 taxon names processed 0 TaxonName entries deleted Wed May 19 11:18:36 2004 RESULT 1 Is this correct output? I currently ran it without commit, let me run it with commit now.. Thanks! Madhura ----- Original Message ----- From: "Deborah F. Pinney" <pi...@pc...> To: "Madhura Sharangpani" <sma...@st...> Sent: Wednesday, May 19, 2004 9:14 AM Subject: Re: [Gusdev-gusdev] Problem using LoadTaxon plugin > Hi Madhura, > > I apologize for the problem. I have added, what I hope is the appropriate > fix and checked it in. I wonder if you could test it again? I tested to > the extent that I know it runs but I don't know if I have fixed the > original problem, running all the way through without commit on. > > I appreciate your collaboration. > > Debbie > > > > On Tue, 18 May 2004, Madhura Sharangpani wrote: > > > Hi Debbie > > > > I got the updated version but I still get the exact same error, except it is > > for getDbHandle instead of getDBHandle this time > > > > Madhura > > > > ----- Original Message ----- > > From: "Deborah F. Pinney" <pi...@pc...> > > To: "Madhura Sharangpani" <sma...@st...> > > Cc: <gus...@li...> > > Sent: Tuesday, May 18, 2004 1:51 PM > > Subject: Re: [Gusdev-gusdev] Problem using LoadTaxon plugin > > > > > > > Hi, > > > > > > > > > I fixed the error that led to this error. getDBHandle should be > > > getDbHandle. I'm checking it in right now. Sorry, perhaps you could check > > > it again? > > > > > > > > > > > > Debbie > > > > > > > > > On Tue, 18 May 2004, Madhura > > > Sharangpani wrote: > > > > > > > Hi Debbie > > > > > > > > I cvs updated LoadTaxon.pm, then did a build and a ga +update for > > > > LoadTaxon.pm plugin, but after that while trying to run the plugin again > > > > without commit, I get the following error, did I miss some step? > > > > > > > > elaine43:~/RA/taxdump> ga > > > > > > GUS::Common::Plugin::LoadTaxon --nodes=nodes.dmp --names=names.dmp --gencode > > > > =gencode.dmp > > > > Reading properties from > > > > /afs/ir/users/s/m/smadhura/RA/GUS/config/GUS-PluginMgr.prop > > > > Reading properties from > > /afs/ir/users/s/m/smadhura/RA/GUS/.gus.properties > > > > > > > > ***COMMIT TURNED OFF*** > > > > processed ncbi_tax_id : 1 > > > > Can't locate object method "getDBHandle" via package > > > > "GUS::Common::Plugin::LoadTaxon" (perhaps you forgot to load > > > > "GUS::Common::Plugin::LoadTaxon"?) at > > > > > > /afs/ir/users/s/m/smadhura/RA/GUS/lib/perl/GUS/Common/Plugin/LoadTaxon.pm > > > > line 239, <NODES> line 217936 > > > > > > > > Madhura > > > > > > > > > > > > > > > > ----- Original Message ----- > > > > From: "Deborah F. Pinney" <pi...@pc...> > > > > To: "Madhura Sharangpani" <sma...@st...> > > > > Cc: <gus...@li...> > > > > Sent: Tuesday, May 18, 2004 12:15 PM > > > > Subject: Re: [Gusdev-gusdev] Problem using LoadTaxon plugin > > > > > > > > > > > > > > > > > > > > > > > I think I have fixed the bug in LoadTaxon.pm. I've checked it into > > cvs. > > > > > Could you give a test with commit off and let us know if it is OK? > > > > > > > > > > > > > > > Debbie > > > > > > > > > > > > > > > > > > > > > ------------------------------------------------------- > > > > This SF.Net email is sponsored by: SourceForge.net Broadband > > > > Sign-up now for SourceForge Broadband and get the fastest > > > > 6.0/768 connection for only $19.95/mo for the first 3 months! > > > > http://ads.osdn.com/?ad_id=2562&alloc_id=6184&op=click > > > > _______________________________________________ > > > > Gusdev-gusdev mailing list > > > > Gus...@li... > > > > https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev > > > > > > > > > > > > > > > ------------------------------------------------------- > > This SF.Net email is sponsored by: SourceForge.net Broadband > > Sign-up now for SourceForge Broadband and get the fastest > > 6.0/768 connection for only $19.95/mo for the first 3 months! > > http://ads.osdn.com/?ad_id=2562&alloc_id=6184&op=click > > _______________________________________________ > > Gusdev-gusdev mailing list > > Gus...@li... > > https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev > > > |
|
From: Steve F. <st...@pc...> - 2004-05-19 11:57:26
|
i will make a new .tar today. in the meantime, jonathan, if its is one file, can you email it? steve Fidel Salas wrote: >Jonathan, > >Hi! > >We do not have access to CBIL's source tree except through compressed >tar files. The most recent file available is from 5/6/2004 and >therefore it does not contain your edits. > >Fidel > > >Jonathan Schug <js...@pc...> writes: > > > Hi Fidel! > > > > I believe I have fixed this error. I have committed files in > > CBIL/Bio/lib/perl/GenBank that contain the changes. > > > > Please let me know if it is working now. > > > > Thanks, > > > > Jonathan > > > > On May 18, 2004, at 9:32 AM, Angel Pizarro wrote: > > >>>Fidel Salas wrote: >>> >>> >>> >>>>There is a bug in the parser that only becomes expressed if the DNA >>>>sequence goes over 99999999 nucleotides. An error gets output like >>>>this: >>>>ERR LINE=2575409 unparsed line 100000021 cggggcgggg >>>>agactaggag aaagctgcca gaggctgctg gcaagagata tccactggtt >>>> >>>> >>>> >>>> >>>Fidel, I suspect that this error is coming from the support gbff >>>parser CBIL::GenBank modules. J. Schug is the author and I'll ask >>>him if he knows what causes this. >>> >>>Angel >>> >>> >>> >>>>The error happens because the parser assumes that there will be spaces >>>>before the number indicating the nucleotide number. That is the case >>>>until the number of nucleotides goes over the threshold value >>>>indicated above. >>>> >>>>Fidel >>>> >>>> >>>> >>>>------------------------------------------------------- >>>>This SF.Net email is sponsored by: SourceForge.net Broadband >>>>Sign-up now for SourceForge Broadband and get the fastest >>>>6.0/768 connection for only $19.95/mo for the first 3 months! >>>>http://ads.osdn.com/?ad_id=2562&alloc_id=6184&op=click >>>>_______________________________________________ >>>>Gusdev-gusdev mailing list >>>>Gus...@li... >>>>https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev >>>> >>>> >>>> >>>> > > Jonathan Schug - js...@pc... > > > >------------------------------------------------------- >This SF.Net email is sponsored by: SourceForge.net Broadband >Sign-up now for SourceForge Broadband and get the fastest >6.0/768 connection for only $19.95/mo for the first 3 months! >http://ads.osdn.com/?ad_id=2562&alloc_id=6184&op=click >_______________________________________________ >Gusdev-gusdev mailing list >Gus...@li... >https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev > > |
|
From: Deborah F. P. <pi...@pc...> - 2004-05-19 11:48:39
|
I'm looking into this. I'll get back to you this morning with a fix.
Debbie
On
Tue, 18 May 2004, Madhura Sharangpani wrote:
> Hi Debbie
>
> I got the updated version but I still get the exact same error, except it is
> for getDbHandle instead of getDBHandle this time
>
> Madhura
>
> ----- Original Message -----
> From: "Deborah F. Pinney" <pi...@pc...>
> To: "Madhura Sharangpani" <sma...@st...>
> Cc: <gus...@li...>
> Sent: Tuesday, May 18, 2004 1:51 PM
> Subject: Re: [Gusdev-gusdev] Problem using LoadTaxon plugin
>
>
> > Hi,
> >
> >
> > I fixed the error that led to this error. getDBHandle should be
> > getDbHandle. I'm checking it in right now. Sorry, perhaps you could check
> > it again?
> >
> >
> >
> > Debbie
> >
> >
> > On Tue, 18 May 2004, Madhura
> > Sharangpani wrote:
> >
> > > Hi Debbie
> > >
> > > I cvs updated LoadTaxon.pm, then did a build and a ga +update for
> > > LoadTaxon.pm plugin, but after that while trying to run the plugin again
> > > without commit, I get the following error, did I miss some step?
> > >
> > > elaine43:~/RA/taxdump> ga
> > >
> GUS::Common::Plugin::LoadTaxon --nodes=nodes.dmp --names=names.dmp --gencode
> > > =gencode.dmp
> > > Reading properties from
> > > /afs/ir/users/s/m/smadhura/RA/GUS/config/GUS-PluginMgr.prop
> > > Reading properties from
> /afs/ir/users/s/m/smadhura/RA/GUS/.gus.properties
> > >
> > > ***COMMIT TURNED OFF***
> > > processed ncbi_tax_id : 1
> > > Can't locate object method "getDBHandle" via package
> > > "GUS::Common::Plugin::LoadTaxon" (perhaps you forgot to load
> > > "GUS::Common::Plugin::LoadTaxon"?) at
> > >
> /afs/ir/users/s/m/smadhura/RA/GUS/lib/perl/GUS/Common/Plugin/LoadTaxon.pm
> > > line 239, <NODES> line 217936
> > >
> > > Madhura
> > >
> > >
> > >
> > > ----- Original Message -----
> > > From: "Deborah F. Pinney" <pi...@pc...>
> > > To: "Madhura Sharangpani" <sma...@st...>
> > > Cc: <gus...@li...>
> > > Sent: Tuesday, May 18, 2004 12:15 PM
> > > Subject: Re: [Gusdev-gusdev] Problem using LoadTaxon plugin
> > >
> > >
> > > >
> > > >
> > > > I think I have fixed the bug in LoadTaxon.pm. I've checked it into
> cvs.
> > > > Could you give a test with commit off and let us know if it is OK?
> > > >
> > > >
> > > > Debbie
> > > >
> > >
> > >
> > >
> > > -------------------------------------------------------
> > > This SF.Net email is sponsored by: SourceForge.net Broadband
> > > Sign-up now for SourceForge Broadband and get the fastest
> > > 6.0/768 connection for only $19.95/mo for the first 3 months!
> > > http://ads.osdn.com/?ad_id=2562&alloc_id=6184&op=click
> > > _______________________________________________
> > > Gusdev-gusdev mailing list
> > > Gus...@li...
> > > https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
> > >
> >
>
|
|
From: Deborah F. P. <pi...@pc...> - 2004-05-19 11:16:09
|
Take a look at InsertNewExternalSequences, it is quite flexible and may do
what you want.
Debbie
On Tue, 18 May 2004, Sucheta Tripathy wrote:
> Hi Debbie,
>
> We have protein data after using the gene calls. These are present in raw
> fasta format. To these sequences we did the signalP analysis and other
> annotation. I saw the table format and we can easily parse them onto the
> column names, but I was wondering before that I need to put them onto
> aasequenceImp table. So I thought if I can put my raw protein sequences to
> the table with some plugin.
>
> Thanks
>
> Sucheta
> > Hi Sucheta,
> >
> >
> > What is the data that you want to load? It is hard to answer the question
> > generally.
> >
> > As you probably know already we load data from the protein nr database
> > files from NCBI and protein motif data from prodom and cdd. Those are
> > loaded with LoadNRDB.pm (written specifically for NCBI nrdb protein data)
> > and InsertNewExternalSequences.
> >
> > We also load signal peptide and transmembrane results from the analysis
> > of our assemblies. Those plugins are not in cvs repository at Sanger and
> > may not be appropriate for your use.
> >
> > Debbie
> > On Tue, 18 May 2004, Sucheta Tripathy
> > wrote:
> >
> >>
> >> Hello All,
> >>
> >> Has anyone tried uploading amino acid related data to GUS(mainly to
> >> aasequenceImp and related tables). Is there a plugin for that? I have
> >> lots of amino acid related data like the signalP output and other
> >> annotations.
> >>
> >> Any suggestions?
> >>
> >> Thanks
> >>
> >> Sucheta
> >>
> >>
> >>
> >>
> >
>
>
>
|
|
From: Fidel S. <fi...@vb...> - 2004-05-19 05:36:38
|
Jonathan,
Hi!
We do not have access to CBIL's source tree except through compressed
tar files. The most recent file available is from 5/6/2004 and
therefore it does not contain your edits.
Fidel
Jonathan Schug <js...@pc...> writes:
> Hi Fidel!
>
> I believe I have fixed this error. I have committed files in
> CBIL/Bio/lib/perl/GenBank that contain the changes.
>
> Please let me know if it is working now.
>
> Thanks,
>
> Jonathan
>
> On May 18, 2004, at 9:32 AM, Angel Pizarro wrote:
>
>> Fidel Salas wrote:
>>
>>> There is a bug in the parser that only becomes expressed if the DNA
>>> sequence goes over 99999999 nucleotides. An error gets output like
>>> this:
>>> ERR LINE=2575409 unparsed line 100000021 cggggcgggg
>>> agactaggag aaagctgcca gaggctgctg gcaagagata tccactggtt
>>>
>>>
>> Fidel, I suspect that this error is coming from the support gbff
>> parser CBIL::GenBank modules. J. Schug is the author and I'll ask
>> him if he knows what causes this.
>>
>> Angel
>>
>>> The error happens because the parser assumes that there will be spaces
>>> before the number indicating the nucleotide number. That is the case
>>> until the number of nucleotides goes over the threshold value
>>> indicated above.
>>>
>>> Fidel
>>>
>>>
>>>
>>> -------------------------------------------------------
>>> This SF.Net email is sponsored by: SourceForge.net Broadband
>>> Sign-up now for SourceForge Broadband and get the fastest
>>> 6.0/768 connection for only $19.95/mo for the first 3 months!
>>> http://ads.osdn.com/?ad_id=2562&alloc_id=6184&op=click
>>> _______________________________________________
>>> Gusdev-gusdev mailing list
>>> Gus...@li...
>>> https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
>>>
>>>
> Jonathan Schug - js...@pc...
|
|
From: <tw...@cs...> - 2004-05-19 03:55:18
|
I am experiencing a problem with Oracle 9i, on Redhat 8,
using Perl v5.8.4 built for i686-linux, I get this problem
with the GUS object layer:
DBI subclasses 'GUS::ObjRelP::DbiDbHandle::db' and ::st are not setup,
RootClass ignored at /farm/gus/gushome/lib/perl/GUS/ObjRelP/DbiDatabase.pm line 152
I have installed the Perl modules/packages DBI and DBD::Oracle
without a problem, it seems. DBD::Oracle in the Perl install recognizes
GUS. A snippet from the output during installation:
Oraperl emulation interface version 1.44
DBD::Oracle 1.15 using OCI8 by Tim Bunce
DBI 1.42 by Tim Bunce
Data sources:
dbi:Oracle:EXTPROC_CONNECTION_DATA.ITTC.KU.EDU
dbi:Oracle:GUS.ITTC.KU.EDU
dbi:Oracle:INST1_HTTP.ITTC.KU.EDU
dbi:Oracle:gus
Does anyone have any idea what could be the matter?
Is there an order dependence on the Perl database interface
and the GUS install?
DBD::ODBC won't install; it complains about not having a device
driver. Is DBD::ODBC necessary?
Even though this is a jolly time, any advice to help me move
on would be so greatly appreciated.
Terry
|
|
From: MICHAEL L. <lu...@cs...> - 2004-05-19 02:26:41
|
I think I can take the second question: > 2) --db_rel_id : As the documentation describes, this is external database id. Do I create this id on my own? Do I need to keep this entry in any other table? Does this id has one to one correspondence with the project I am working on (and the one I described in my .gus.properties file?) Yes, you need to create this ID on your own. Almost every piece of biological data that you put into GUS has an external_database_release_id. This helps keep track of versions, and could help you to be able to compose some really complex queries if you knew something really complex to look for(I don't necessarily). There is a table called SRes.externaldatabaserelease which needs an entry in it. Check out all the tables at the cool tool www.gusdb.org/cgi-bin/schemaBrowser If you look at SRes.externaldatabaserelease you will notice that it has a foreign primary key(not sure necessarily of the appropriate jargon on this, but I mean something that cannot be null, and should have a representation in another table) of external_database_id. So first you must make an entry into the table SRes.externaldatabase, also available for viewing at the above stated location. The recursion bottoms out here. Put in the information for where you get the data--Sanger, TIGR, etc. and then put a release in the release table. This is helpful if you get new data, then you can just make a new entry into SRes.externaldatabaserelease and state your queries so that they only fetch the data with the appropriate release number. > > > Any help will be really appreciated > > > thanks > --Jinal > > > > > > ------------------------------------------------------- > This SF.Net email is sponsored by: SourceForge.net Broadband > Sign-up now for SourceForge Broadband and get the fastest > 6.0/768 connection for only $19.95/mo for the first 3 months! > http://ads.osdn.com/?ad_id=2562&alloc_id=6184&op=click > _______________________________________________ > Gusdev-gusdev mailing list > Gus...@li... > https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev > |
|
From: jinal j. <jh...@us...> - 2004-05-18 23:04:03
|
Hi, I have some questions regarding the GBParser module 1) First required field is --gbRel. As I understand this is genbank's db realease id. Now where do I get this number from? ( genbanks website????) Does anybody has idea about what is the release right now on web? 2) --db_rel_id : As the documentation describes, this is external database id. Do I create this id on my own? Do I need to keep this entry in any other table? Does this id has one to one correspondence with the project I am working on (and the one I described in my .gus.properties file?) 3) --algoinvo=s: What is this? (I looked at the docs but they talk about some invocation id. Is this to change the algorithm to be invoked?) Any help will be really appreciated thanks --Jinal |
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From: Madhura S. <sma...@st...> - 2004-05-18 21:53:25
|
Hi Debbie I got the updated version but I still get the exact same error, except it is for getDbHandle instead of getDBHandle this time Madhura ----- Original Message ----- From: "Deborah F. Pinney" <pi...@pc...> To: "Madhura Sharangpani" <sma...@st...> Cc: <gus...@li...> Sent: Tuesday, May 18, 2004 1:51 PM Subject: Re: [Gusdev-gusdev] Problem using LoadTaxon plugin > Hi, > > > I fixed the error that led to this error. getDBHandle should be > getDbHandle. I'm checking it in right now. Sorry, perhaps you could check > it again? > > > > Debbie > > > On Tue, 18 May 2004, Madhura > Sharangpani wrote: > > > Hi Debbie > > > > I cvs updated LoadTaxon.pm, then did a build and a ga +update for > > LoadTaxon.pm plugin, but after that while trying to run the plugin again > > without commit, I get the following error, did I miss some step? > > > > elaine43:~/RA/taxdump> ga > > GUS::Common::Plugin::LoadTaxon --nodes=nodes.dmp --names=names.dmp --gencode > > =gencode.dmp > > Reading properties from > > /afs/ir/users/s/m/smadhura/RA/GUS/config/GUS-PluginMgr.prop > > Reading properties from /afs/ir/users/s/m/smadhura/RA/GUS/.gus.properties > > > > ***COMMIT TURNED OFF*** > > processed ncbi_tax_id : 1 > > Can't locate object method "getDBHandle" via package > > "GUS::Common::Plugin::LoadTaxon" (perhaps you forgot to load > > "GUS::Common::Plugin::LoadTaxon"?) at > > /afs/ir/users/s/m/smadhura/RA/GUS/lib/perl/GUS/Common/Plugin/LoadTaxon.pm > > line 239, <NODES> line 217936 > > > > Madhura > > > > > > > > ----- Original Message ----- > > From: "Deborah F. Pinney" <pi...@pc...> > > To: "Madhura Sharangpani" <sma...@st...> > > Cc: <gus...@li...> > > Sent: Tuesday, May 18, 2004 12:15 PM > > Subject: Re: [Gusdev-gusdev] Problem using LoadTaxon plugin > > > > > > > > > > > > > I think I have fixed the bug in LoadTaxon.pm. I've checked it into cvs. > > > Could you give a test with commit off and let us know if it is OK? > > > > > > > > > Debbie > > > > > > > > > > > ------------------------------------------------------- > > This SF.Net email is sponsored by: SourceForge.net Broadband > > Sign-up now for SourceForge Broadband and get the fastest > > 6.0/768 connection for only $19.95/mo for the first 3 months! > > http://ads.osdn.com/?ad_id=2562&alloc_id=6184&op=click > > _______________________________________________ > > Gusdev-gusdev mailing list > > Gus...@li... > > https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev > > > |
|
From: jinal j. <jh...@us...> - 2004-05-18 21:11:37
|
Steve, Yes I realized that but it seems like most of the things till ga registration and ga Create are working fine (except the two I pointed out in my previous mails) thanks --Jinal ----- Original Message ----- From: Steve Fischer <sfi...@pc...> Date: Tuesday, May 18, 2004 2:03 pm Subject: Re: [Gusdev-gusdev] Error in Building > we have just checked in the code to support platform independence (ie, > oracle & postgres), so there may be a couple of more glitches. > > Dave Barkan wrote: > > >Hey Jinal, > > > >Yes, you are correct. I fixed the problem and put it into CVS. > > > >Dave > > > > > >On Tue, 18 May 2004, jinal jhaveri wrote: > > > > > > > >>Dave, > >>It seems like there is bug in Oracle.pm module > >> > >>The line 144 should be my $seqname=$table."_SQ."; > >> > >>Note that the end is missing "." in the original file > >> > >>thanks > >>--Jinal > >> > >> > >> > > > > > > > >------------------------------------------------------- > >This SF.Net email is sponsored by: SourceForge.net Broadband > >Sign-up now for SourceForge Broadband and get the fastest > >6.0/768 connection for only $19.95/mo for the first 3 months! > >http://ads.osdn.com/?ad_id=2562&alloc_id=6184&op=click > >_______________________________________________ > >Gusdev-gusdev mailing list > >Gus...@li... > >https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev > > > > > > |
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From: Steve F. <sfi...@pc...> - 2004-05-18 21:03:28
|
we have just checked in the code to support platform independence (ie, oracle & postgres), so there may be a couple of more glitches. Dave Barkan wrote: >Hey Jinal, > >Yes, you are correct. I fixed the problem and put it into CVS. > >Dave > > >On Tue, 18 May 2004, jinal jhaveri wrote: > > > >>Dave, >>It seems like there is bug in Oracle.pm module >> >>The line 144 should be my $seqname=$table."_SQ."; >> >>Note that the end is missing "." in the original file >> >>thanks >>--Jinal >> >> >> > > > >------------------------------------------------------- >This SF.Net email is sponsored by: SourceForge.net Broadband >Sign-up now for SourceForge Broadband and get the fastest >6.0/768 connection for only $19.95/mo for the first 3 months! >http://ads.osdn.com/?ad_id=2562&alloc_id=6184&op=click >_______________________________________________ >Gusdev-gusdev mailing list >Gus...@li... >https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev > > |
|
From: Deborah F. P. <pi...@pc...> - 2004-05-18 20:51:30
|
Hi,
I fixed the error that led to this error. getDBHandle should be
getDbHandle. I'm checking it in right now. Sorry, perhaps you could check
it again?
Debbie
On Tue, 18 May 2004, Madhura
Sharangpani wrote:
> Hi Debbie
>
> I cvs updated LoadTaxon.pm, then did a build and a ga +update for
> LoadTaxon.pm plugin, but after that while trying to run the plugin again
> without commit, I get the following error, did I miss some step?
>
> elaine43:~/RA/taxdump> ga
> GUS::Common::Plugin::LoadTaxon --nodes=nodes.dmp --names=names.dmp --gencode
> =gencode.dmp
> Reading properties from
> /afs/ir/users/s/m/smadhura/RA/GUS/config/GUS-PluginMgr.prop
> Reading properties from /afs/ir/users/s/m/smadhura/RA/GUS/.gus.properties
>
> ***COMMIT TURNED OFF***
> processed ncbi_tax_id : 1
> Can't locate object method "getDBHandle" via package
> "GUS::Common::Plugin::LoadTaxon" (perhaps you forgot to load
> "GUS::Common::Plugin::LoadTaxon"?) at
> /afs/ir/users/s/m/smadhura/RA/GUS/lib/perl/GUS/Common/Plugin/LoadTaxon.pm
> line 239, <NODES> line 217936
>
> Madhura
>
>
>
> ----- Original Message -----
> From: "Deborah F. Pinney" <pi...@pc...>
> To: "Madhura Sharangpani" <sma...@st...>
> Cc: <gus...@li...>
> Sent: Tuesday, May 18, 2004 12:15 PM
> Subject: Re: [Gusdev-gusdev] Problem using LoadTaxon plugin
>
>
> >
> >
> > I think I have fixed the bug in LoadTaxon.pm. I've checked it into cvs.
> > Could you give a test with commit off and let us know if it is OK?
> >
> >
> > Debbie
> >
>
>
>
> -------------------------------------------------------
> This SF.Net email is sponsored by: SourceForge.net Broadband
> Sign-up now for SourceForge Broadband and get the fastest
> 6.0/768 connection for only $19.95/mo for the first 3 months!
> http://ads.osdn.com/?ad_id=2562&alloc_id=6184&op=click
> _______________________________________________
> Gusdev-gusdev mailing list
> Gus...@li...
> https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
>
|
|
From: Madhura S. <sma...@st...> - 2004-05-18 20:44:23
|
Hi Debbie I cvs updated LoadTaxon.pm, then did a build and a ga +update for LoadTaxon.pm plugin, but after that while trying to run the plugin again without commit, I get the following error, did I miss some step? elaine43:~/RA/taxdump> ga GUS::Common::Plugin::LoadTaxon --nodes=nodes.dmp --names=names.dmp --gencode =gencode.dmp Reading properties from /afs/ir/users/s/m/smadhura/RA/GUS/config/GUS-PluginMgr.prop Reading properties from /afs/ir/users/s/m/smadhura/RA/GUS/.gus.properties ***COMMIT TURNED OFF*** processed ncbi_tax_id : 1 Can't locate object method "getDBHandle" via package "GUS::Common::Plugin::LoadTaxon" (perhaps you forgot to load "GUS::Common::Plugin::LoadTaxon"?) at /afs/ir/users/s/m/smadhura/RA/GUS/lib/perl/GUS/Common/Plugin/LoadTaxon.pm line 239, <NODES> line 217936 Madhura ----- Original Message ----- From: "Deborah F. Pinney" <pi...@pc...> To: "Madhura Sharangpani" <sma...@st...> Cc: <gus...@li...> Sent: Tuesday, May 18, 2004 12:15 PM Subject: Re: [Gusdev-gusdev] Problem using LoadTaxon plugin > > > I think I have fixed the bug in LoadTaxon.pm. I've checked it into cvs. > Could you give a test with commit off and let us know if it is OK? > > > Debbie > |
|
From: Sucheta T. <su...@vb...> - 2004-05-18 20:40:32
|
Hi Debbie, We have protein data after using the gene calls. These are present in raw fasta format. To these sequences we did the signalP analysis and other annotation. I saw the table format and we can easily parse them onto the column names, but I was wondering before that I need to put them onto aasequenceImp table. So I thought if I can put my raw protein sequences to the table with some plugin. Thanks Sucheta > Hi Sucheta, > > > What is the data that you want to load? It is hard to answer the question > generally. > > As you probably know already we load data from the protein nr database > files from NCBI and protein motif data from prodom and cdd. Those are > loaded with LoadNRDB.pm (written specifically for NCBI nrdb protein data) > and InsertNewExternalSequences. > > We also load signal peptide and transmembrane results from the analysis > of our assemblies. Those plugins are not in cvs repository at Sanger and > may not be appropriate for your use. > > Debbie > On Tue, 18 May 2004, Sucheta Tripathy > wrote: > >> >> Hello All, >> >> Has anyone tried uploading amino acid related data to GUS(mainly to >> aasequenceImp and related tables). Is there a plugin for that? I have >> lots of amino acid related data like the signalP output and other >> annotations. >> >> Any suggestions? >> >> Thanks >> >> Sucheta >> >> >> >> > -- Sucheta Tripathy Virginia Bioinformatics Institute Phase-I Washington street. Virginia Tech. Blacksburg,VA 24061-0447 phone:(540)231-8138 Fax: (540) 231-2606 |
|
From: Deborah F. P. <pi...@pc...> - 2004-05-18 20:30:26
|
Hi Sucheta,
What is the data that you want to load? It is hard to answer the question
generally.
As you probably know already we load data from the protein nr database
files from NCBI and protein motif data from prodom and cdd. Those are
loaded with LoadNRDB.pm (written specifically for NCBI nrdb protein data)
and InsertNewExternalSequences.
We also load signal peptide and transmembrane results from the analysis
of our assemblies. Those plugins are not in cvs repository at Sanger and
may not be appropriate for your use.
Debbie
On Tue, 18 May 2004, Sucheta Tripathy
wrote:
>
> Hello All,
>
> Has anyone tried uploading amino acid related data to GUS(mainly to
> aasequenceImp and related tables). Is there a plugin for that? I have
> lots of amino acid related data like the signalP output and other
> annotations.
>
> Any suggestions?
>
> Thanks
>
> Sucheta
>
>
>
>
|
|
From: Dave B. <db...@pc...> - 2004-05-18 20:20:15
|
Hey Jinal, Yes, you are correct. I fixed the problem and put it into CVS. Dave On Tue, 18 May 2004, jinal jhaveri wrote: > Dave, > It seems like there is bug in Oracle.pm module > > The line 144 should be my $seqname=$table."_SQ."; > > Note that the end is missing "." in the original file > > thanks > --Jinal > |
|
From: Jonathan S. <js...@pc...> - 2004-05-18 20:12:41
|
Hi Fidel! I believe I have fixed this error. I have committed files in CBIL/Bio/lib/perl/GenBank that contain the changes. Please let me know if it is working now. Thanks, Jonathan On May 18, 2004, at 9:32 AM, Angel Pizarro wrote: > Fidel Salas wrote: > >> There is a bug in the parser that only becomes expressed if the DNA >> sequence goes over 99999999 nucleotides. An error gets output like >> this: >> ERR LINE=2575409 unparsed line 100000021 cggggcgggg >> agactaggag aaagctgcca gaggctgctg gcaagagata tccactggtt >> >> > Fidel, I suspect that this error is coming from the support gbff > parser CBIL::GenBank modules. J. Schug is the author and I'll ask him > if he knows what causes this. > > Angel > >> The error happens because the parser assumes that there will be spaces >> before the number indicating the nucleotide number. That is the case >> until the number of nucleotides goes over the threshold value >> indicated above. >> >> Fidel >> >> >> >> ------------------------------------------------------- >> This SF.Net email is sponsored by: SourceForge.net Broadband >> Sign-up now for SourceForge Broadband and get the fastest >> 6.0/768 connection for only $19.95/mo for the first 3 months! >> http://ads.osdn.com/?ad_id=2562&alloc_id=6184&op=click >> _______________________________________________ >> Gusdev-gusdev mailing list >> Gus...@li... >> https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev >> >> Jonathan Schug - js...@pc... |
|
From: jinal j. <jh...@us...> - 2004-05-18 20:00:33
|
Dave, It seems like there is bug in Oracle.pm module The line 144 should be my $seqname=$table."_SQ."; Note that the end is missing "." in the original file thanks --Jinal |
|
From: Dave B. <db...@pc...> - 2004-05-18 19:33:06
|
Try now; there was a small bug where that variable was being used out of
scope in an error message. (do a cvs update first on DbiTable).
Dave
On Tue, 18 May 2004, jinal jhaveri wrote:
> Hi,
>
> I finally managed to solve the error. The problem was that I was not re-using the original build file which involves object creation. But now I have another problem as follows
> [exec] Global symbol "$query" requires explicit package name at /home/gus/gushome/lib/perl/GUS/ObjRelP/DbiTable.pm line 554.
> [exec] Compilation failed in require at /home/gus/gushome/lib/perl/GUS/ObjRelP/DbiDatabase.pm line 21.
> [exec] BEGIN failed--compilation aborted at /home/gus/gushome/lib/perl/GUS/ObjRelP/DbiDatabase.pm line 21.
> [exec] Compilation failed in require at /home/gus/gushome/bin/generateGusObjects line 5.
> [exec] BEGIN failed--compilation aborted at /home/gus/gushome/bin/generateGusObjects line 5.
>
> BUILD FAILED
> /home/gus/projects/install/build.xml:25: Following error occured while executing this line
> /home/gus/projects/GUS/build.xml:194: exec returned: -1
>
>
> ----- Original Message -----
> From: Dave Barkan <db...@pc...>
> Date: Tuesday, May 18, 2004 10:09 am
> Subject: Re: [Gusdev-gusdev] Error in Building
>
> > Hey Jinal,
> >
> > These are all 'hand edited' GUS objects; we add additional functionality
> > to them other than that provided by the default java object generator.
> >
> > They should be in CVS right now; their location is
> > {Project_Home}/GUS/Model/src/java/org/gusdb/model/hand_edited. Do you
> > have this directory checked out of CVS?
> >
> > In the hand_edited directory, there are subdirectories corresponding to
> > the GUS schemas. Each hand edited object is within its appropriate
> > schema subdiretory (For example, Taxon.java.man is in SRes and
> > BLATAlignment.java.man is in DoTS.) Make sure you have everything checked
> > out; if you can see the hand edited objects and the build is still
> > failing, let me know.
> >
> > Dave
> >
> >
> > On Tue, 18 May 2004, jinal jhaveri wrote:
> >
> > > Hi,
> > >
> > > I am getting following error while building GUS. It seems like
> > BLATAlignment_Row, and ... files are missing in the current CVS download.
> > Can anyone has an insight into why this could have happened?
> > >
> > > Created dir: /home/gus/gushome/doc/GUS/Model
> > > [mkdir] Created dir: /home/gus/projects/GUS/Model/classes
> > > [javac] Compiling 3 source files to /home/gus/projects/GUS/Model/classes
> > > [javac]
> > /home/gus/projects/GUS/Model/src/java/org/gusdb/model/DoTS/BLATAlignment.java:26: cannot resolve symbol
> > > [javac] symbol : class BLATAlignment_Row
> > > [javac] location: class org.gusdb.model.DoTS.BLATAlignment
> > > [javac] public class BLATAlignment extends BLATAlignment_Row {
> > > [javac] ^
> > > [javac]
> > /home/gus/projects/GUS/Model/src/java/org/gusdb/model/DoTS/NASequence.java:26: cannot resolve symbol
> > > [javac] symbol : class NASequence_Row
> > > [javac] location: class org.gusdb.model.DoTS.NASequence
> > > [javac] public class NASequence extends NASequence_Row {
> > > [javac] ^
> > > [javac]
> > /home/gus/projects/GUS/Model/src/java/org/gusdb/model/SRes/Taxon.java:16: cannot resolve symbol
> > > [javac] symbol : class Taxon_Row
> > > [javac] location: class org.gusdb.model.SRes.Taxon
> > > [javac] public class Taxon extends Taxon_Row {
> > > [javac] ^
> > > [javac]
> > /home/gus/projects/GUS/Model/src/java/org/gusdb/model/DoTS/BLATAlignment.java:34: cannot resolve symbol
> > > [javac] symbol : method getQstarts ()
> > > [javac] location: class org.gusdb.model.DoTS.BLATAlignment
> > > [javac] String starts = getQstarts();
> > > [javac] ^
> > > [javac]
> > /home/gus/projects/GUS/Model/src/java/org/gusdb/model/DoTS/BLATAlignment.java:39: cannot resolve symbol
> > > [javac] symbol : method getBlocksizes ()
> > > [javac] location: class org.gusdb.model.DoTS.BLATAlignment
> > > [javac] String lengths = getBlocksizes();
> > > [javac] ^
> > > [javac]
> > /home/gus/projects/GUS/Model/src/java/org/gusdb/model/DoTS/BLATAlignment.java:44: cannot resolve symbol
> > > [javac] symbol : method getTstarts ()
> > > [javac] location: class org.gusdb.model.DoTS.BLATAlignment
> > > [javac] String tStarts = getTstarts();
> > > [javac] ^
> > > [javac]
> > /home/gus/projects/GUS/Model/src/java/org/gusdb/model/DoTS/NASequence.java:42: cannot resolve symbol
> > > [javac] symbol : method getSequenceLobLength ()
> > > [javac] location: class org.gusdb.model.DoTS.NASequence
> > > [javac] return this.getSequenceAsSymbolList(1,
> > this.getSequenceLobLength().longValue());> [javac]
> > ^
> > > [javac]
> > /home/gus/projects/GUS/Model/src/java/org/gusdb/model/DoTS/NASequence.java:53: cannot resolve symbol
> > > [javac] symbol : method getSequence (long,long)
> > > [javac] location: class org.gusdb.model.DoTS.NASequence
> > > [javac] char seqData[] = this.getSequence(start, end);
> > > [javac] ^
> > > [javac]
> > /home/gus/projects/GUS/Model/src/java/org/gusdb/model/SRes/Taxon.java:34: cannot resolve symbol
> > > [javac] symbol : method getTaxonNameList (boolean)
> > > [javac] location: class org.gusdb.model.SRes.Taxon
> > > [javac] Vector allTaxonNames = getTaxonNameList(false);
> > > [javac] ^
> > > [javac]
> > /home/gus/projects/GUS/Model/src/java/org/gusdb/model/SRes/Taxon.java:57: cannot resolve symbol
> > > [javac] symbol : method getTaxonNameList (boolean)
> > > [javac] location: class org.gusdb.model.SRes.Taxon
> > > [javac] kids = this.getTaxonNameList(true);
> > > [javac] ^
> > > [javac]
> > /home/gus/projects/GUS/Model/src/java/org/gusdb/model/SRes/Taxon.java:66: cannot resolve symbol
> > > [javac] symbol : class TaxonName
> > > [javac] location: class org.gusdb.model.SRes.Taxon
> > > [javac] TaxonName tn = (TaxonName)(kids.elementAt(i));
> > > [javac] ^
> > > [javac]
> > /home/gus/projects/GUS/Model/src/java/org/gusdb/model/SRes/Taxon.java:66: cannot resolve symbol
> > > [javac] symbol : class TaxonName
> > > [javac] location: class org.gusdb.model.SRes.Taxon
> > > [javac] TaxonName tn = (TaxonName)(kids.elementAt(i));
> > > [javac] ^
> > > [javac] 12 errors
> > >
> > >
> > > thanks
> > > --Jinal
> > >
> > >
> > >
> > >
> > > -------------------------------------------------------
> > > This SF.Net email is sponsored by: SourceForge.net Broadband
> > > Sign-up now for SourceForge Broadband and get the fastest
> > > 6.0/768 connection for only $19.95/mo for the first 3 months!
> > > http://ads.osdn.com/?ad_id=2562&alloc_id=6184&op=click
> > > _______________________________________________
> > > Gusdev-gusdev mailing list
> > > Gus...@li...
> > > https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
> > >
> >
> >
>
>
>
> -------------------------------------------------------
> This SF.Net email is sponsored by: SourceForge.net Broadband
> Sign-up now for SourceForge Broadband and get the fastest
> 6.0/768 connection for only $19.95/mo for the first 3 months!
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> https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev
>
|
|
From: Deborah F. P. <pi...@pc...> - 2004-05-18 19:15:50
|
I think I have fixed the bug in LoadTaxon.pm. I've checked it into cvs.
Could you give a test with commit off and let us know if it is OK?
Debbie
|
|
From: Madhura S. <sma...@st...> - 2004-05-18 19:01:32
|
The space was inserted when I copied it, the error is: "SRES"."TAXONNAME"."TAXON_ID") Let me try loading with commit on Thanks! Madhura ----- Original Message ----- From: "Deborah F. Pinney" <pi...@pc...> To: "Madhura Sharangpani" <sma...@st...> Cc: <gus...@li...> Sent: Tuesday, May 18, 2004 11:46 AM Subject: Re: [Gusdev-gusdev] Problem using LoadTaxon plugin > Sorry, I forgot to ask if your Oracle error was as printed > below, "SRES"."TAXO NNAME"."TAXON_ID")On Tue, 18 May 2004 or a space was > inserted when you copied it. > > > > > > Deborah F. Pinney wrote: > > > There is a bug in LoadNRDB.pm that has not been fixed yet. If you run the > > plugin without commit, the transaction closes after loading entries into > > sres.taxon and a new one is opened to load sres.taxonname. That means that > > all the inserts into taxon have been rolled back. Can you load with commit > > on? The bug will be fixed soon. > > > > Debbie > > > > > > On Tue, 18 May 2004, > > Madhura Sharangpani wrote: > > > > > Hi All > > > > > > I am trying to use the LoadTaxon plugin to load NCBI taxonomy files, I downloaded the taxdump files from ncbi.nih.gov, I also created bootstrap rows using xml file input and that worked fine, but when I was running the LoadTaxon plugin to load the NCBI taxonomy files using command: > > > > > > ga GUS::Common::Plugin::LoadTaxon --nodes=nodes.dmp > > > --names=names.dmp --gencode=gencode.dmp > > > > > > I got following error: > > > > > > Initially it went on for a while printing the tax_ids processed, > > > > > > processed ncbi_tax_id : 40049 > > > processed ncbi_tax_id : 192122 > > > ------- > > > so on > > > > > > and then it stopped with following error > > > > > > DBD::Oracle::st execute failed: ORA-01400: cannot insert NULL into ("SRES"."TAXO NNAME"."TAXON_ID") (DBD ERROR: OCIStmtExecute) at /afs/ir/users/s/m/smadhura/RA/GUS/lib/perl/GUS/ObjRelP/DbiDbHandle.pm line 145, > > > <NODES> line 217936. SQL ERROR!! involving INSERT INTO Res.TaxonName ( row_user_id, other_read,unique_name_variant,user_write, group_write, name_class, row_project_id, name, taxon_id,modification_date, ser_read, row_alg_invocation_id, group_read, other_write, row_group_id, taxon_name_id ) VALUES ( ?, ?, '', ?, ?, ?, ?, ?, '', SYSDATE, ?, ?, ?, ?, ?, ? ) > > > Values: 1, 1, 1, 1, scientific name, 1, Influenza C virus (C/Miyagi/9/96), 1, 91, 1, 0, 1, 1 > > > at/afs/ir/users/s/m/smadhura/RA/GUS/lib/perl/GUS/ObjRelP/DbiDbHan dle.pm line 185 > > > > > > Could someone explain what am I doing wrong? > > > > > > Thanks! > > > > > > > > > Madhura > > > > > > > > > > > > > > ------------------------------------------------------- > > This SF.Net email is sponsored by: SourceForge.net Broadband > > Sign-up now for SourceForge Broadband and get the fastest > > 6.0/768 connection for only $19.95/mo for the first 3 months! > > http://ads.osdn.com/?ad_id=2562&alloc_id=6184&op=click > > _______________________________________________ > > Gusdev-gusdev mailing list > > Gus...@li... > > https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev > > > > > > ------------------------------------------------------- > This SF.Net email is sponsored by: SourceForge.net Broadband > Sign-up now for SourceForge Broadband and get the fastest > 6.0/768 connection for only $19.95/mo for the first 3 months! > http://ads.osdn.com/?ad_id=2562&alloc_id=6184&op=click > _______________________________________________ > Gusdev-gusdev mailing list > Gus...@li... > https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev |
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From: Deborah F. P. <pi...@pc...> - 2004-05-18 18:46:36
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Sorry, I forgot to ask if your Oracle error was as printed below, "SRES"."TAXO NNAME"."TAXON_ID")On Tue, 18 May 2004 or a space was inserted when you copied it. Deborah F. Pinney wrote: > There is a bug in LoadNRDB.pm that has not been fixed yet. If you run the > plugin without commit, the transaction closes after loading entries into > sres.taxon and a new one is opened to load sres.taxonname. That means that > all the inserts into taxon have been rolled back. Can you load with commit > on? The bug will be fixed soon. > > Debbie > > > On Tue, 18 May 2004, > Madhura Sharangpani wrote: > > > Hi All > > > > I am trying to use the LoadTaxon plugin to load NCBI taxonomy files, I downloaded the taxdump files from ncbi.nih.gov, I also created bootstrap rows using xml file input and that worked fine, but when I was running the LoadTaxon plugin to load the NCBI taxonomy files using command: > > > > ga GUS::Common::Plugin::LoadTaxon --nodes=nodes.dmp > > --names=names.dmp --gencode=gencode.dmp > > > > I got following error: > > > > Initially it went on for a while printing the tax_ids processed, > > > > processed ncbi_tax_id : 40049 > > processed ncbi_tax_id : 192122 > > ------- > > so on > > > > and then it stopped with following error > > > > DBD::Oracle::st execute failed: ORA-01400: cannot insert NULL into ("SRES"."TAXO NNAME"."TAXON_ID") (DBD ERROR: OCIStmtExecute) at /afs/ir/users/s/m/smadhura/RA/GUS/lib/perl/GUS/ObjRelP/DbiDbHandle.pm line 145, > > <NODES> line 217936. SQL ERROR!! involving INSERT INTO Res.TaxonName ( row_user_id, other_read,unique_name_variant,user_write, group_write, name_class, row_project_id, name, taxon_id,modification_date, ser_read, row_alg_invocation_id, group_read, other_write, row_group_id, taxon_name_id ) VALUES ( ?, ?, '', ?, ?, ?, ?, ?, '', SYSDATE, ?, ?, ?, ?, ?, ? ) > > Values: 1, 1, 1, 1, scientific name, 1, Influenza C virus (C/Miyagi/9/96), 1, 91, 1, 0, 1, 1 > > at/afs/ir/users/s/m/smadhura/RA/GUS/lib/perl/GUS/ObjRelP/DbiDbHan dle.pm line 185 > > > > Could someone explain what am I doing wrong? > > > > Thanks! > > > > > > Madhura > > > > > > > > ------------------------------------------------------- > This SF.Net email is sponsored by: SourceForge.net Broadband > Sign-up now for SourceForge Broadband and get the fastest > 6.0/768 connection for only $19.95/mo for the first 3 months! > http://ads.osdn.com/?ad_id=2562&alloc_id=6184&op=click > _______________________________________________ > Gusdev-gusdev mailing list > Gus...@li... > https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev > |
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