question about gmod_bulk_load_gff3.pl
|
View:
New views
12 Messages
—
Rating Filter:
Alert me
|
 |
question about gmod_bulk_load_gff3.pl
by Li Jin
::
Rate this Message:
Dear gmod developer,
I am using gmod_bulk_load_gff3.pl to load gff file into Chado DB. But I get the follwoing error message. Could you please help to figure it out? Preparing data for inserting into the Chado database (This may take a while ...) Can't locate object method "database" via package "Bio::Annotation::SimpleValue" at /usr/local/lib/perl5/site_perl/5.8.3/Bio/GMOD/DB/Adapter.pm line 3061, <GEN0> line 1. Issuing rollback() for database handle being DESTROY'd without explicit disconnect(). Thanks, Li ---------------------------------------------- Li Jin Computer and Information Sciences Department University of Delaware Newark, DE 19716 ------------------------------------------------------------------------- This SF.net email is sponsored by: Microsoft Defy all challenges. Microsoft(R) Visual Studio 2008. http://clk.atdmt.com/MRT/go/vse0120000070mrt/direct/01/ _______________________________________________ Gmod-devel mailing list Gmod-devel@... https://lists.sourceforge.net/lists/listinfo/gmod-devel |
|
|
Re: question about gmod_bulk_load_gff3.pl
by Scott Cain-3
::
Rate this Message:
Hi Li,
My first guess is that your bioperl isn't up to date. Did you get it from svn or did you download a release? The most recent release is not new enough; you need to get bioperl-live from svn: http://www.bioperl.org/wiki/Using_Subversion#Instructions_for_downloading_any_BioPerl_repository_using_anonymous_SVN Scott On Sat, 2008-01-26 at 23:49 -0500, Li Jin wrote: > Dear gmod developer, > > I am using gmod_bulk_load_gff3.pl to load gff file into Chado DB. But I > get the follwoing error message. Could you please help to figure it out? > > Preparing data for inserting into the Chado database > (This may take a while ...) > Can't locate object method "database" via package > "Bio::Annotation::SimpleValue" at > /usr/local/lib/perl5/site_perl/5.8.3/Bio/GMOD/DB/Adapter.pm line > 3061, <GEN0> line 1. > Issuing rollback() for database handle being DESTROY'd without > explicit disconnect(). > > Thanks, > > Li > > > > ---------------------------------------------- > Li Jin > Computer and Information Sciences Department > University of Delaware > Newark, DE 19716 > > > ------------------------------------------------------------------------- > This SF.net email is sponsored by: Microsoft > Defy all challenges. Microsoft(R) Visual Studio 2008. > http://clk.atdmt.com/MRT/go/vse0120000070mrt/direct/01/ > _______________________________________________ > Gmod-devel mailing list > Gmod-devel@... > https://lists.sourceforge.net/lists/listinfo/gmod-devel ------------------------------------------------------------------------ Scott Cain, Ph. D. cain@... GMOD Coordinator (http://www.gmod.org/) 216-392-3087 Cold Spring Harbor Laboratory ------------------------------------------------------------------------- This SF.net email is sponsored by: Microsoft Defy all challenges. Microsoft(R) Visual Studio 2008. http://clk.atdmt.com/MRT/go/vse0120000070mrt/direct/01/ _______________________________________________ Gmod-devel mailing list Gmod-devel@... https://lists.sourceforge.net/lists/listinfo/gmod-devel |
|
|
Re: question about gmod_bulk_load_gff3.pl
by Li Jin
::
Rate this Message:
Dear Scott,
Thank you so much for your support. Following your suggestion, I checked out bioperl-live from svn and reinstall it. But it still does not work. The same error message pumps out. Could you please give me any suggestion? Thanks, Li On Mon, 28 Jan 2008, Scott Cain wrote: > Hi Li, > > My first guess is that your bioperl isn't up to date. Did you get it > from svn or did you download a release? The most recent release is not > new enough; you need to get bioperl-live from svn: > > http://www.bioperl.org/wiki/Using_Subversion#Instructions_for_downloading_any_BioPerl_repository_using_anonymous_SVN > > Scott > > On Sat, 2008-01-26 at 23:49 -0500, Li Jin wrote: >> Dear gmod developer, >> >> I am using gmod_bulk_load_gff3.pl to load gff file into Chado DB. But I >> get the follwoing error message. Could you please help to figure it out? >> >> Preparing data for inserting into the Chado database >> (This may take a while ...) >> Can't locate object method "database" via package >> "Bio::Annotation::SimpleValue" at >> /usr/local/lib/perl5/site_perl/5.8.3/Bio/GMOD/DB/Adapter.pm line >> 3061, <GEN0> line 1. >> Issuing rollback() for database handle being DESTROY'd without >> explicit disconnect(). >> >> Thanks, >> >> Li >> >> >> >> ---------------------------------------------- >> Li Jin >> Computer and Information Sciences Department >> University of Delaware >> Newark, DE 19716 >> >> >> ------------------------------------------------------------------------- >> This SF.net email is sponsored by: Microsoft >> Defy all challenges. Microsoft(R) Visual Studio 2008. >> http://clk.atdmt.com/MRT/go/vse0120000070mrt/direct/01/ >> _______________________________________________ >> Gmod-devel mailing list >> Gmod-devel@... >> https://lists.sourceforge.net/lists/listinfo/gmod-devel > -- > ------------------------------------------------------------------------ > Scott Cain, Ph. D. cain@... > GMOD Coordinator (http://www.gmod.org/) 216-392-3087 > Cold Spring Harbor Laboratory > > ------------------------------------------------------------------------- This SF.net email is sponsored by: Microsoft Defy all challenges. Microsoft(R) Visual Studio 2008. http://clk.atdmt.com/MRT/go/vse0120000070mrt/direct/01/ _______________________________________________ Gmod-devel mailing list Gmod-devel@... https://lists.sourceforge.net/lists/listinfo/gmod-devel |
|
|
Re: question about gmod_bulk_load_gff3.pl
by Li Jin
::
Rate this Message:
Hi, Scott,
I reinstalled my OS system from Redhat to CentOS. When I tried to load gff3 file to chado, I got the following error. It looks similar as the problem http://www.mail-archive.com/gmod-gbrowse@.../msg00080.html. But I am not sure. If this problem can be solved by adding data to chado analysisfeatures, what data should I load? Thanks, Li gmod_bulk_load_gff3.pl --organism yeast --gfffile saccharomyces_cerevisiae.sorted.gff (Re)creating the uniquename cache in the database... Creating table... Populating table... Creating indexes...Done. Preparing data for inserting into the Chado database (This may take a while ...) Operation "ne": no method found, left argument in overloaded package Bio::Annotation::SimpleValue, right argument has no overloaded magic at /usr/local/bin/gmod_bulk_load_gff3.pl line 811, <GEN0> line 1. ---------------------------------------------- Li Jin Computer and Information Sciences Department University of Delaware Newark, DE 19716 On Mon, 28 Jan 2008, Scott Cain wrote: > Hi Li, > > My first guess is that your bioperl isn't up to date. Did you get it > from svn or did you download a release? The most recent release is not > new enough; you need to get bioperl-live from svn: > > http://www.bioperl.org/wiki/Using_Subversion#Instructions_for_downloading_any_BioPerl_repository_using_anonymous_SVN > > Scott > > On Sat, 2008-01-26 at 23:49 -0500, Li Jin wrote: >> Dear gmod developer, >> >> I am using gmod_bulk_load_gff3.pl to load gff file into Chado DB. But I >> get the follwoing error message. Could you please help to figure it out? >> >> Preparing data for inserting into the Chado database >> (This may take a while ...) >> Can't locate object method "database" via package >> "Bio::Annotation::SimpleValue" at >> /usr/local/lib/perl5/site_perl/5.8.3/Bio/GMOD/DB/Adapter.pm line >> 3061, <GEN0> line 1. >> Issuing rollback() for database handle being DESTROY'd without >> explicit disconnect(). >> >> Thanks, >> >> Li >> >> >> >> ---------------------------------------------- >> Li Jin >> Computer and Information Sciences Department >> University of Delaware >> Newark, DE 19716 >> >> >> ------------------------------------------------------------------------- >> This SF.net email is sponsored by: Microsoft >> Defy all challenges. Microsoft(R) Visual Studio 2008. >> http://clk.atdmt.com/MRT/go/vse0120000070mrt/direct/01/ >> _______________________________________________ >> Gmod-devel mailing list >> Gmod-devel@... >> https://lists.sourceforge.net/lists/listinfo/gmod-devel > -- > ------------------------------------------------------------------------ > Scott Cain, Ph. D. cain@... > GMOD Coordinator (http://www.gmod.org/) 216-392-3087 > Cold Spring Harbor Laboratory > > ------------------------------------------------------------------------- Check out the new SourceForge.net Marketplace. It's the best place to buy or sell services for just about anything Open Source. http://ad.doubleclick.net/clk;164216239;13503038;w?http://sf.net/marketplace _______________________________________________ Gmod-devel mailing list Gmod-devel@... https://lists.sourceforge.net/lists/listinfo/gmod-devel |
|
|
Re: question about gmod_bulk_load_gff3.pl
by Scott Cain-3
::
Rate this Message:
Hi Li,
I still think you need to get bioperl-live from svn; take a look at this page for directions: http://www.bioperl.org/wiki/Using_Subversion#Instructions_for_downloading_any_BioPerl_repository_using_anonymous_SVN You will probably want to get gmod 1.0 when it gets released tomorrow (!) Scott On Sat, Mar 29, 2008 at 5:12 PM, Li Jin <jin@...> wrote: > Hi, Scott, > I reinstalled my OS system from Redhat to CentOS. > When I tried to load gff3 file to chado, I got the following error. It > looks similar as the problem > http://www.mail-archive.com/gmod-gbrowse@.../msg00080.html. > But I am not sure. > If this problem can be solved by adding data to chado analysisfeatures, > what data should I load? > Thanks, > > Li > > gmod_bulk_load_gff3.pl --organism yeast --gfffile > saccharomyces_cerevisiae.sorted.gff > (Re)creating the uniquename cache in the database... > Creating table... > Populating table... > Creating indexes...Done. > > Preparing data for inserting into the Chado database > (This may take a while ...) > Operation "ne": no method found, > left argument in overloaded package Bio::Annotation::SimpleValue, > right argument has no overloaded magic at > /usr/local/bin/gmod_bulk_load_gff3.pl line 811, <GEN0> line 1. > > > > > ---------------------------------------------- > Li Jin > Computer and Information Sciences Department > University of Delaware > Newark, DE 19716 > > > > On Mon, 28 Jan 2008, Scott Cain wrote: > > > > > Hi Li, > > > > My first guess is that your bioperl isn't up to date. Did you get it > > from svn or did you download a release? The most recent release is not > > new enough; you need to get bioperl-live from svn: > > > > http://www.bioperl.org/wiki/Using_Subversion#Instructions_for_downloading_any_BioPerl_repository_using_anonymous_SVN > > > > Scott > > > > On Sat, 2008-01-26 at 23:49 -0500, Li Jin wrote: > >> Dear gmod developer, > >> > >> I am using gmod_bulk_load_gff3.pl to load gff file into Chado DB. But I > >> get the follwoing error message. Could you please help to figure it out? > >> > >> Preparing data for inserting into the Chado database > >> (This may take a while ...) > >> Can't locate object method "database" via package > >> "Bio::Annotation::SimpleValue" at > >> /usr/local/lib/perl5/site_perl/5.8.3/Bio/GMOD/DB/Adapter.pm line > >> 3061, <GEN0> line 1. > >> Issuing rollback() for database handle being DESTROY'd without > >> explicit disconnect(). > >> > >> Thanks, > >> > >> Li > >> > >> > >> > >> ---------------------------------------------- > >> Li Jin > >> Computer and Information Sciences Department > >> University of Delaware > >> Newark, DE 19716 > >> > >> > >> ------------------------------------------------------------------------- > >> This SF.net email is sponsored by: Microsoft > >> Defy all challenges. Microsoft(R) Visual Studio 2008. > >> http://clk.atdmt.com/MRT/go/vse0120000070mrt/direct/01/ > >> _______________________________________________ > >> Gmod-devel mailing list > >> Gmod-devel@... > >> https://lists.sourceforge.net/lists/listinfo/gmod-devel > > -- > > ------------------------------------------------------------------------ > > Scott Cain, Ph. D. cain@... > > GMOD Coordinator (http://www.gmod.org/) 216-392-3087 > > Cold Spring Harbor Laboratory > > > > > ------------------------------------------------------------------------- Check out the new SourceForge.net Marketplace. It's the best place to buy or sell services for just about anything Open Source. http://ad.doubleclick.net/clk;164216239;13503038;w?http://sf.net/marketplace _______________________________________________ Gmod-devel mailing list Gmod-devel@... https://lists.sourceforge.net/lists/listinfo/gmod-devel |
|
|
Re: question about gmod_bulk_load_gff3.pl
by Li Jin
::
Rate this Message:
Hi, Scott,
You are correct. The problem I ever met disappered. But I have another problem relating Gene Ontology. I have loaded gene ontology for one day, but the process is still working, not done. The machine seems writing a lot to hard disk. Is it because the memory is too small? My personal PC only has 128M memory. I am wondering how big memory is required at least? Thank you so much! Li On Sun, 30 Mar 2008, Scott Cain wrote: > Hi Li, > > I still think you need to get bioperl-live from svn; take a look at > this page for directions: > > http://www.bioperl.org/wiki/Using_Subversion#Instructions_for_downloading_any_BioPerl_repository_using_anonymous_SVN > > You will probably want to get gmod 1.0 when it gets released tomorrow (!) > > Scott > > > On Sat, Mar 29, 2008 at 5:12 PM, Li Jin <jin@...> wrote: >> Hi, Scott, >> I reinstalled my OS system from Redhat to CentOS. >> When I tried to load gff3 file to chado, I got the following error. It >> looks similar as the problem >> http://www.mail-archive.com/gmod-gbrowse@.../msg00080.html. >> But I am not sure. >> If this problem can be solved by adding data to chado analysisfeatures, >> what data should I load? >> Thanks, >> >> Li >> >> gmod_bulk_load_gff3.pl --organism yeast --gfffile >> saccharomyces_cerevisiae.sorted.gff >> (Re)creating the uniquename cache in the database... >> Creating table... >> Populating table... >> Creating indexes...Done. >> >> Preparing data for inserting into the Chado database >> (This may take a while ...) >> Operation "ne": no method found, >> left argument in overloaded package Bio::Annotation::SimpleValue, >> right argument has no overloaded magic at >> /usr/local/bin/gmod_bulk_load_gff3.pl line 811, <GEN0> line 1. >> >> >> >> >> ---------------------------------------------- >> Li Jin >> Computer and Information Sciences Department >> University of Delaware >> Newark, DE 19716 >> >> >> >> On Mon, 28 Jan 2008, Scott Cain wrote: >> >> >> >>> Hi Li, >> > >> > My first guess is that your bioperl isn't up to date. Did you get it >> > from svn or did you download a release? The most recent release is not >> > new enough; you need to get bioperl-live from svn: >> > >> > http://www.bioperl.org/wiki/Using_Subversion#Instructions_for_downloading_any_BioPerl_repository_using_anonymous_SVN >> > >> > Scott >> > >> > On Sat, 2008-01-26 at 23:49 -0500, Li Jin wrote: >> >> Dear gmod developer, >> >> >> >> I am using gmod_bulk_load_gff3.pl to load gff file into Chado DB. But I >> >> get the follwoing error message. Could you please help to figure it out? >> >> >> >> Preparing data for inserting into the Chado database >> >> (This may take a while ...) >> >> Can't locate object method "database" via package >> >> "Bio::Annotation::SimpleValue" at >> >> /usr/local/lib/perl5/site_perl/5.8.3/Bio/GMOD/DB/Adapter.pm line >> >> 3061, <GEN0> line 1. >> >> Issuing rollback() for database handle being DESTROY'd without >> >> explicit disconnect(). >> >> >> >> Thanks, >> >> >> >> Li >> >> >> >> >> >> >> >> ---------------------------------------------- >> >> Li Jin >> >> Computer and Information Sciences Department >> >> University of Delaware >> >> Newark, DE 19716 >> >> >> >> >> >> ------------------------------------------------------------------------- >> >> This SF.net email is sponsored by: Microsoft >> >> Defy all challenges. Microsoft(R) Visual Studio 2008. >> >> http://clk.atdmt.com/MRT/go/vse0120000070mrt/direct/01/ >> >> _______________________________________________ >> >> Gmod-devel mailing list >> >> Gmod-devel@... >> >> https://lists.sourceforge.net/lists/listinfo/gmod-devel >> > -- >> > ------------------------------------------------------------------------ >> > Scott Cain, Ph. D. cain@... >> > GMOD Coordinator (http://www.gmod.org/) 216-392-3087 >> > Cold Spring Harbor Laboratory >> > >> > >> > ------------------------------------------------------------------------- Check out the new SourceForge.net Marketplace. It's the best place to buy or sell services for just about anything Open Source. http://ad.doubleclick.net/clk;164216239;13503038;w?http://sf.net/marketplace _______________________________________________ Gmod-devel mailing list Gmod-devel@... https://lists.sourceforge.net/lists/listinfo/gmod-devel |
|
|
Re: question about gmod_bulk_load_gff3.pl
by Scott Cain-3
::
Rate this Message:
Hi Li,
128M is not much. I would guess that you are swapping a lot. Did you look at `top` to see what processes are running? There are two steps performed to load ontologies after the file is downloaded. First it is converted to oboxml using go2fmt.pl from go-perl. The resulting oboxml file will go in tmp/go/go.oboxml (assuming you accepted the default directory when you ran perl Makefile.PL). If you look at the end of that file with `tail tmp/go/go.oboxml`, you should see </chado> on the last line. The other step is to load the oboxml into chado using stag-storenode.pl. That can run quite a while. One way to see if it is still running is to go into the database with psql and execute the query select count(*) from cvterm; and then wait a little while and execute it again to see if the count is increasing. I am a little concerned that your OS will run out of memory and the database server will be killed by the OS to keep the OS from crashing, but until that happens, there isn't much reason to make it stop. Scott On Mon, 2008-03-31 at 22:47 -0400, Li Jin wrote: > Hi, Scott, > > You are correct. The problem I ever met disappered. > But I have another problem relating Gene Ontology. I have loaded gene > ontology for one day, but the process is still working, not done. The > machine seems writing a lot to hard disk. Is it because the memory is too > small? My personal PC only has 128M memory. I am wondering how big memory > is required at least? > > Thank you so much! > > Li > > On Sun, 30 Mar 2008, Scott Cain wrote: > > > Hi Li, > > > > I still think you need to get bioperl-live from svn; take a look at > > this page for directions: > > > > http://www.bioperl.org/wiki/Using_Subversion#Instructions_for_downloading_any_BioPerl_repository_using_anonymous_SVN > > > > You will probably want to get gmod 1.0 when it gets released tomorrow (!) > > > > Scott > > > > > > On Sat, Mar 29, 2008 at 5:12 PM, Li Jin <jin@...> wrote: > >> Hi, Scott, > >> I reinstalled my OS system from Redhat to CentOS. > >> When I tried to load gff3 file to chado, I got the following error. It > >> looks similar as the problem > >> http://www.mail-archive.com/gmod-gbrowse@.../msg00080.html. > >> But I am not sure. > >> If this problem can be solved by adding data to chado analysisfeatures, > >> what data should I load? > >> Thanks, > >> > >> Li > >> > >> gmod_bulk_load_gff3.pl --organism yeast --gfffile > >> saccharomyces_cerevisiae.sorted.gff > >> (Re)creating the uniquename cache in the database... > >> Creating table... > >> Populating table... > >> Creating indexes...Done. > >> > >> Preparing data for inserting into the Chado database > >> (This may take a while ...) > >> Operation "ne": no method found, > >> left argument in overloaded package Bio::Annotation::SimpleValue, > >> right argument has no overloaded magic at > >> /usr/local/bin/gmod_bulk_load_gff3.pl line 811, <GEN0> line 1. > >> > >> > >> > >> > >> ---------------------------------------------- > >> Li Jin > >> Computer and Information Sciences Department > >> University of Delaware > >> Newark, DE 19716 > >> > >> > >> > >> On Mon, 28 Jan 2008, Scott Cain wrote: > >> > >> > >> > >>> Hi Li, > >> > > >> > My first guess is that your bioperl isn't up to date. Did you get it > >> > from svn or did you download a release? The most recent release is not > >> > new enough; you need to get bioperl-live from svn: > >> > > >> > http://www.bioperl.org/wiki/Using_Subversion#Instructions_for_downloading_any_BioPerl_repository_using_anonymous_SVN > >> > > >> > Scott > >> > > >> > On Sat, 2008-01-26 at 23:49 -0500, Li Jin wrote: > >> >> Dear gmod developer, > >> >> > >> >> I am using gmod_bulk_load_gff3.pl to load gff file into Chado DB. But I > >> >> get the follwoing error message. Could you please help to figure it out? > >> >> > >> >> Preparing data for inserting into the Chado database > >> >> (This may take a while ...) > >> >> Can't locate object method "database" via package > >> >> "Bio::Annotation::SimpleValue" at > >> >> /usr/local/lib/perl5/site_perl/5.8.3/Bio/GMOD/DB/Adapter.pm line > >> >> 3061, <GEN0> line 1. > >> >> Issuing rollback() for database handle being DESTROY'd without > >> >> explicit disconnect(). > >> >> > >> >> Thanks, > >> >> > >> >> Li > >> >> > >> >> > >> >> > >> >> ---------------------------------------------- > >> >> Li Jin > >> >> Computer and Information Sciences Department > >> >> University of Delaware > >> >> Newark, DE 19716 > >> >> > >> >> > >> >> ------------------------------------------------------------------------- > >> >> This SF.net email is sponsored by: Microsoft > >> >> Defy all challenges. Microsoft(R) Visual Studio 2008. > >> >> http://clk.atdmt.com/MRT/go/vse0120000070mrt/direct/01/ > >> >> _______________________________________________ > >> >> Gmod-devel mailing list > >> >> Gmod-devel@... > >> >> https://lists.sourceforge.net/lists/listinfo/gmod-devel > >> > -- > >> > ------------------------------------------------------------------------ > >> > Scott Cain, Ph. D. cain@... > >> > GMOD Coordinator (http://www.gmod.org/) 216-392-3087 > >> > Cold Spring Harbor Laboratory > >> > > >> > > >> > > ------------------------------------------------------------------------ Scott Cain, Ph. D. cain.cshl@... GMOD Coordinator (http://www.gmod.org/) 216-392-3087 Cold Spring Harbor Laboratory ------------------------------------------------------------------------- Check out the new SourceForge.net Marketplace. It's the best place to buy or sell services for just about anything Open Source. http://ad.doubleclick.net/clk;164216239;13503038;w?http://sf.net/marketplace _______________________________________________ Gmod-devel mailing list Gmod-devel@... https://lists.sourceforge.net/lists/listinfo/gmod-devel |
|
|
Re: question about gmod_bulk_load_gff3.pl
by Li Jin
::
Rate this Message:
Hi, Scott,
Thank you! I believe the second step is still running on my pc. Now our group is going to install GMOD on a new machine of 16G memory. I believe GMOD will like our new machine. Our administrator asked if GMOD requires CentOS4 because the default version of postgres with centos4 is 7.4. I would like to make sure with you about Centos4 and postgres8.1. Thanks, Li On Tue, 1 Apr 2008, Scott Cain wrote: > Hi Li, > > 128M is not much. I would guess that you are swapping a lot. Did you > look at `top` to see what processes are running? There are two steps > performed to load ontologies after the file is downloaded. First it is > converted to oboxml using go2fmt.pl from go-perl. The resulting oboxml > file will go in tmp/go/go.oboxml (assuming you accepted the default > directory when you ran perl Makefile.PL). If you look at the end of > that file with `tail tmp/go/go.oboxml`, you should see </chado> on the > last line. > > The other step is to load the oboxml into chado using stag-storenode.pl. > That can run quite a while. One way to see if it is still running is to > go into the database with psql and execute the query > > select count(*) from cvterm; > > and then wait a little while and execute it again to see if the count is > increasing. > > I am a little concerned that your OS will run out of memory and the > database server will be killed by the OS to keep the OS from crashing, > but until that happens, there isn't much reason to make it stop. > > Scott > > On Mon, 2008-03-31 at 22:47 -0400, Li Jin wrote: >> Hi, Scott, >> >> You are correct. The problem I ever met disappered. >> But I have another problem relating Gene Ontology. I have loaded gene >> ontology for one day, but the process is still working, not done. The >> machine seems writing a lot to hard disk. Is it because the memory is too >> small? My personal PC only has 128M memory. I am wondering how big memory >> is required at least? >> >> Thank you so much! >> >> Li >> >> On Sun, 30 Mar 2008, Scott Cain wrote: >> >>> Hi Li, >>> >>> I still think you need to get bioperl-live from svn; take a look at >>> this page for directions: >>> >>> http://www.bioperl.org/wiki/Using_Subversion#Instructions_for_downloading_any_BioPerl_repository_using_anonymous_SVN >>> >>> You will probably want to get gmod 1.0 when it gets released tomorrow (!) >>> >>> Scott >>> >>> >>> On Sat, Mar 29, 2008 at 5:12 PM, Li Jin <jin@...> wrote: >>>> Hi, Scott, >>>> I reinstalled my OS system from Redhat to CentOS. >>>> When I tried to load gff3 file to chado, I got the following error. It >>>> looks similar as the problem >>>> http://www.mail-archive.com/gmod-gbrowse@.../msg00080.html. >>>> But I am not sure. >>>> If this problem can be solved by adding data to chado analysisfeatures, >>>> what data should I load? >>>> Thanks, >>>> >>>> Li >>>> >>>> gmod_bulk_load_gff3.pl --organism yeast --gfffile >>>> saccharomyces_cerevisiae.sorted.gff >>>> (Re)creating the uniquename cache in the database... >>>> Creating table... >>>> Populating table... >>>> Creating indexes...Done. >>>> >>>> Preparing data for inserting into the Chado database >>>> (This may take a while ...) >>>> Operation "ne": no method found, >>>> left argument in overloaded package Bio::Annotation::SimpleValue, >>>> right argument has no overloaded magic at >>>> /usr/local/bin/gmod_bulk_load_gff3.pl line 811, <GEN0> line 1. >>>> >>>> >>>> >>>> >>>> ---------------------------------------------- >>>> Li Jin >>>> Computer and Information Sciences Department >>>> University of Delaware >>>> Newark, DE 19716 >>>> >>>> >>>> >>>> On Mon, 28 Jan 2008, Scott Cain wrote: >>>> >>>> >>>> >>>>> Hi Li, >>>>> >>>>> My first guess is that your bioperl isn't up to date. Did you get it >>>>> from svn or did you download a release? The most recent release is not >>>>> new enough; you need to get bioperl-live from svn: >>>>> >>>>> http://www.bioperl.org/wiki/Using_Subversion#Instructions_for_downloading_any_BioPerl_repository_using_anonymous_SVN >>>>> >>>>> Scott >>>>> >>>>> On Sat, 2008-01-26 at 23:49 -0500, Li Jin wrote: >>>>>> Dear gmod developer, >>>>>> >>>>>> I am using gmod_bulk_load_gff3.pl to load gff file into Chado DB. But I >>>>>> get the follwoing error message. Could you please help to figure it out? >>>>>> >>>>>> Preparing data for inserting into the Chado database >>>>>> (This may take a while ...) >>>>>> Can't locate object method "database" via package >>>>>> "Bio::Annotation::SimpleValue" at >>>>>> /usr/local/lib/perl5/site_perl/5.8.3/Bio/GMOD/DB/Adapter.pm line >>>>>> 3061, <GEN0> line 1. >>>>>> Issuing rollback() for database handle being DESTROY'd without >>>>>> explicit disconnect(). >>>>>> >>>>>> Thanks, >>>>>> >>>>>> Li >>>>>> >>>>>> >>>>>> >>>>>> ---------------------------------------------- >>>>>> Li Jin >>>>>> Computer and Information Sciences Department >>>>>> University of Delaware >>>>>> Newark, DE 19716 >>>>>> >>>>>> >>>>>> ------------------------------------------------------------------------- >>>>>> This SF.net email is sponsored by: Microsoft >>>>>> Defy all challenges. Microsoft(R) Visual Studio 2008. >>>>>> http://clk.atdmt.com/MRT/go/vse0120000070mrt/direct/01/ >>>>>> _______________________________________________ >>>>>> Gmod-devel mailing list >>>>>> Gmod-devel@... >>>>>> https://lists.sourceforge.net/lists/listinfo/gmod-devel >>>>> -- >>>>> ------------------------------------------------------------------------ >>>>> Scott Cain, Ph. D. cain@... >>>>> GMOD Coordinator (http://www.gmod.org/) 216-392-3087 >>>>> Cold Spring Harbor Laboratory >>>>> >>>>> >>>> >>> > -- > ------------------------------------------------------------------------ > Scott Cain, Ph. D. cain.cshl@... > GMOD Coordinator (http://www.gmod.org/) 216-392-3087 > Cold Spring Harbor Laboratory > > > ------------------------------------------------------------------------- Check out the new SourceForge.net Marketplace. It's the best place to buy or sell services for just about anything Open Source. http://ad.doubleclick.net/clk;164216239;13503038;w?http://sf.net/marketplace _______________________________________________ Gmod-devel mailing list Gmod-devel@... https://lists.sourceforge.net/lists/listinfo/gmod-devel |
|
|
Re: question about gmod_bulk_load_gff3.pl
by Scott Cain-3
::
Rate this Message:
Hi Li,
CentOS4 is not required, in fact I use Ubuntu on a regular basis along with CentOS 4.5. I've worked with Pg 7.4, 8.1 and 8.2. The main reason I can think of for using CentOS is to make installing GMODWeb easier (there are RPMs for Fedora and CentOS). Otherwise, it doesn't matter much which distro you use. Scott On Fri, 2008-04-04 at 10:38 -0400, Li Jin wrote: > Hi, Scott, > Thank you! I believe the second step is still running on my pc. > Now our group is going to install GMOD on a new machine of 16G memory. I > believe GMOD will like our new machine. > Our administrator asked if GMOD requires CentOS4 because the default > version of postgres with centos4 is 7.4. > I would like to make sure with you about Centos4 and postgres8.1. > Thanks, > > Li > > > > > On Tue, 1 Apr 2008, Scott Cain wrote: > > > Hi Li, > > > > 128M is not much. I would guess that you are swapping a lot. Did you > > look at `top` to see what processes are running? There are two steps > > performed to load ontologies after the file is downloaded. First it is > > converted to oboxml using go2fmt.pl from go-perl. The resulting oboxml > > file will go in tmp/go/go.oboxml (assuming you accepted the default > > directory when you ran perl Makefile.PL). If you look at the end of > > that file with `tail tmp/go/go.oboxml`, you should see </chado> on the > > last line. > > > > The other step is to load the oboxml into chado using stag-storenode.pl. > > That can run quite a while. One way to see if it is still running is to > > go into the database with psql and execute the query > > > > select count(*) from cvterm; > > > > and then wait a little while and execute it again to see if the count is > > increasing. > > > > I am a little concerned that your OS will run out of memory and the > > database server will be killed by the OS to keep the OS from crashing, > > but until that happens, there isn't much reason to make it stop. > > > > Scott > > > > On Mon, 2008-03-31 at 22:47 -0400, Li Jin wrote: > >> Hi, Scott, > >> > >> You are correct. The problem I ever met disappered. > >> But I have another problem relating Gene Ontology. I have loaded gene > >> ontology for one day, but the process is still working, not done. The > >> machine seems writing a lot to hard disk. Is it because the memory is too > >> small? My personal PC only has 128M memory. I am wondering how big memory > >> is required at least? > >> > >> Thank you so much! > >> > >> Li > >> > >> On Sun, 30 Mar 2008, Scott Cain wrote: > >> > >>> Hi Li, > >>> > >>> I still think you need to get bioperl-live from svn; take a look at > >>> this page for directions: > >>> > >>> http://www.bioperl.org/wiki/Using_Subversion#Instructions_for_downloading_any_BioPerl_repository_using_anonymous_SVN > >>> > >>> You will probably want to get gmod 1.0 when it gets released tomorrow (!) > >>> > >>> Scott > >>> > >>> > >>> On Sat, Mar 29, 2008 at 5:12 PM, Li Jin <jin@...> wrote: > >>>> Hi, Scott, > >>>> I reinstalled my OS system from Redhat to CentOS. > >>>> When I tried to load gff3 file to chado, I got the following error. It > >>>> looks similar as the problem > >>>> http://www.mail-archive.com/gmod-gbrowse@.../msg00080.html. > >>>> But I am not sure. > >>>> If this problem can be solved by adding data to chado analysisfeatures, > >>>> what data should I load? > >>>> Thanks, > >>>> > >>>> Li > >>>> > >>>> gmod_bulk_load_gff3.pl --organism yeast --gfffile > >>>> saccharomyces_cerevisiae.sorted.gff > >>>> (Re)creating the uniquename cache in the database... > >>>> Creating table... > >>>> Populating table... > >>>> Creating indexes...Done. > >>>> > >>>> Preparing data for inserting into the Chado database > >>>> (This may take a while ...) > >>>> Operation "ne": no method found, > >>>> left argument in overloaded package Bio::Annotation::SimpleValue, > >>>> right argument has no overloaded magic at > >>>> /usr/local/bin/gmod_bulk_load_gff3.pl line 811, <GEN0> line 1. > >>>> > >>>> > >>>> > >>>> > >>>> ---------------------------------------------- > >>>> Li Jin > >>>> Computer and Information Sciences Department > >>>> University of Delaware > >>>> Newark, DE 19716 > >>>> > >>>> > >>>> > >>>> On Mon, 28 Jan 2008, Scott Cain wrote: > >>>> > >>>> > >>>> > >>>>> Hi Li, > >>>>> > >>>>> My first guess is that your bioperl isn't up to date. Did you get it > >>>>> from svn or did you download a release? The most recent release is not > >>>>> new enough; you need to get bioperl-live from svn: > >>>>> > >>>>> http://www.bioperl.org/wiki/Using_Subversion#Instructions_for_downloading_any_BioPerl_repository_using_anonymous_SVN > >>>>> > >>>>> Scott > >>>>> > >>>>> On Sat, 2008-01-26 at 23:49 -0500, Li Jin wrote: > >>>>>> Dear gmod developer, > >>>>>> > >>>>>> I am using gmod_bulk_load_gff3.pl to load gff file into Chado DB. But I > >>>>>> get the follwoing error message. Could you please help to figure it out? > >>>>>> > >>>>>> Preparing data for inserting into the Chado database > >>>>>> (This may take a while ...) > >>>>>> Can't locate object method "database" via package > >>>>>> "Bio::Annotation::SimpleValue" at > >>>>>> /usr/local/lib/perl5/site_perl/5.8.3/Bio/GMOD/DB/Adapter.pm line > >>>>>> 3061, <GEN0> line 1. > >>>>>> Issuing rollback() for database handle being DESTROY'd without > >>>>>> explicit disconnect(). > >>>>>> > >>>>>> Thanks, > >>>>>> > >>>>>> Li > >>>>>> > >>>>>> > >>>>>> > >>>>>> ---------------------------------------------- > >>>>>> Li Jin > >>>>>> Computer and Information Sciences Department > >>>>>> University of Delaware > >>>>>> Newark, DE 19716 > >>>>>> > >>>>>> > >>>>>> ------------------------------------------------------------------------- > >>>>>> This SF.net email is sponsored by: Microsoft > >>>>>> Defy all challenges. Microsoft(R) Visual Studio 2008. > >>>>>> http://clk.atdmt.com/MRT/go/vse0120000070mrt/direct/01/ > >>>>>> _______________________________________________ > >>>>>> Gmod-devel mailing list > >>>>>> Gmod-devel@... > >>>>>> https://lists.sourceforge.net/lists/listinfo/gmod-devel > >>>>> -- > >>>>> ------------------------------------------------------------------------ > >>>>> Scott Cain, Ph. D. cain@... > >>>>> GMOD Coordinator (http://www.gmod.org/) 216-392-3087 > >>>>> Cold Spring Harbor Laboratory > >>>>> > >>>>> > >>>> > >>> > > -- > > ------------------------------------------------------------------------ > > Scott Cain, Ph. D. cain.cshl@... > > GMOD Coordinator (http://www.gmod.org/) 216-392-3087 > > Cold Spring Harbor Laboratory > > > > > > > > ------------------------------------------------------------------------- > Check out the new SourceForge.net Marketplace. > It's the best place to buy or sell services for > just about anything Open Source. > http://ad.doubleclick.net/clk;164216239;13503038;w?http://sf.net/marketplace > _______________________________________________ > Gmod-devel mailing list > Gmod-devel@... > https://lists.sourceforge.net/lists/listinfo/gmod-devel ------------------------------------------------------------------------ Scott Cain, Ph. D. cain.cshl@... GMOD Coordinator (http://www.gmod.org/) 216-392-3087 Cold Spring Harbor Laboratory ------------------------------------------------------------------------- Check out the new SourceForge.net Marketplace. It's the best place to buy or sell services for just about anything Open Source. http://ad.doubleclick.net/clk;164216239;13503038;w?http://sf.net/marketplace _______________________________________________ Gmod-devel mailing list Gmod-devel@... https://lists.sourceforge.net/lists/listinfo/gmod-devel |
|
|
Re: question about gmod_bulk_load_gff3.pl
by Li Jin
::
Rate this Message:
Hi, Scott,
Could you let me know if you compile PostgreSQL from source? Thanks, Li On Fri, 4 Apr 2008, Scott Cain wrote: > Hi Li, > > CentOS4 is not required, in fact I use Ubuntu on a regular basis along > with CentOS 4.5. I've worked with Pg 7.4, 8.1 and 8.2. The main reason > I can think of for using CentOS is to make installing GMODWeb easier > (there are RPMs for Fedora and CentOS). Otherwise, it doesn't matter > much which distro you use. > > Scott > > On Fri, 2008-04-04 at 10:38 -0400, Li Jin wrote: >> Hi, Scott, >> Thank you! I believe the second step is still running on my pc. >> Now our group is going to install GMOD on a new machine of 16G memory. I >> believe GMOD will like our new machine. >> Our administrator asked if GMOD requires CentOS4 because the default >> version of postgres with centos4 is 7.4. >> I would like to make sure with you about Centos4 and postgres8.1. >> Thanks, >> >> Li >> >> >> >> >> On Tue, 1 Apr 2008, Scott Cain wrote: >> >>> Hi Li, >>> >>> 128M is not much. I would guess that you are swapping a lot. Did you >>> look at `top` to see what processes are running? There are two steps >>> performed to load ontologies after the file is downloaded. First it is >>> converted to oboxml using go2fmt.pl from go-perl. The resulting oboxml >>> file will go in tmp/go/go.oboxml (assuming you accepted the default >>> directory when you ran perl Makefile.PL). If you look at the end of >>> that file with `tail tmp/go/go.oboxml`, you should see </chado> on the >>> last line. >>> >>> The other step is to load the oboxml into chado using stag-storenode.pl. >>> That can run quite a while. One way to see if it is still running is to >>> go into the database with psql and execute the query >>> >>> select count(*) from cvterm; >>> >>> and then wait a little while and execute it again to see if the count is >>> increasing. >>> >>> I am a little concerned that your OS will run out of memory and the >>> database server will be killed by the OS to keep the OS from crashing, >>> but until that happens, there isn't much reason to make it stop. >>> >>> Scott >>> >>> On Mon, 2008-03-31 at 22:47 -0400, Li Jin wrote: >>>> Hi, Scott, >>>> >>>> You are correct. The problem I ever met disappered. >>>> But I have another problem relating Gene Ontology. I have loaded gene >>>> ontology for one day, but the process is still working, not done. The >>>> machine seems writing a lot to hard disk. Is it because the memory is too >>>> small? My personal PC only has 128M memory. I am wondering how big memory >>>> is required at least? >>>> >>>> Thank you so much! >>>> >>>> Li >>>> >>>> On Sun, 30 Mar 2008, Scott Cain wrote: >>>> >>>>> Hi Li, >>>>> >>>>> I still think you need to get bioperl-live from svn; take a look at >>>>> this page for directions: >>>>> >>>>> http://www.bioperl.org/wiki/Using_Subversion#Instructions_for_downloading_any_BioPerl_repository_using_anonymous_SVN >>>>> >>>>> You will probably want to get gmod 1.0 when it gets released tomorrow (!) >>>>> >>>>> Scott >>>>> >>>>> >>>>> On Sat, Mar 29, 2008 at 5:12 PM, Li Jin <jin@...> wrote: >>>>>> Hi, Scott, >>>>>> I reinstalled my OS system from Redhat to CentOS. >>>>>> When I tried to load gff3 file to chado, I got the following error. It >>>>>> looks similar as the problem >>>>>> http://www.mail-archive.com/gmod-gbrowse@.../msg00080.html. >>>>>> But I am not sure. >>>>>> If this problem can be solved by adding data to chado analysisfeatures, >>>>>> what data should I load? >>>>>> Thanks, >>>>>> >>>>>> Li >>>>>> >>>>>> gmod_bulk_load_gff3.pl --organism yeast --gfffile >>>>>> saccharomyces_cerevisiae.sorted.gff >>>>>> (Re)creating the uniquename cache in the database... >>>>>> Creating table... >>>>>> Populating table... >>>>>> Creating indexes...Done. >>>>>> >>>>>> Preparing data for inserting into the Chado database >>>>>> (This may take a while ...) >>>>>> Operation "ne": no method found, >>>>>> left argument in overloaded package Bio::Annotation::SimpleValue, >>>>>> right argument has no overloaded magic at >>>>>> /usr/local/bin/gmod_bulk_load_gff3.pl line 811, <GEN0> line 1. >>>>>> >>>>>> >>>>>> >>>>>> >>>>>> ---------------------------------------------- >>>>>> Li Jin >>>>>> Computer and Information Sciences Department >>>>>> University of Delaware >>>>>> Newark, DE 19716 >>>>>> >>>>>> >>>>>> >>>>>> On Mon, 28 Jan 2008, Scott Cain wrote: >>>>>> >>>>>> >>>>>> >>>>>>> Hi Li, >>>>>>> >>>>>>> My first guess is that your bioperl isn't up to date. Did you get it >>>>>>> from svn or did you download a release? The most recent release is not >>>>>>> new enough; you need to get bioperl-live from svn: >>>>>>> >>>>>>> http://www.bioperl.org/wiki/Using_Subversion#Instructions_for_downloading_any_BioPerl_repository_using_anonymous_SVN >>>>>>> >>>&g |
