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From: Mark S. H. <mh...@ug...> - 2006-07-12 17:06:53
|
On Jul 12, 2006, at 12:28 PM, Pablo Mendes wrote: > > Hi Adhemar, > it seems you need the BlastAnal.pm package > > > Can't locate object method "new" via package > "Blast::BlastAnal" (perhaps you forgot to > > load "Blast::BlastAnal"?) at > It is available in a CBIL tar: > http://www.cbil.upenn.edu/downloads/CBIL/releases/ > > CBIL/Bio/lib/perl/Blast/BlastAnal.pm > You might want to change/add a "use lib" to > 'parseBlastFilesForSimilarity.pl' or to add the CBIL to your > "classpath", changing the $PERL5LIB variable. > (http://www.perl.com/doc/manual/html/pod/perlrun.html) > Add CBIL to your lib path as Pablo says. Also you probably need to change the line 'use Blast::BlastAnal;' in parseBlastFilesForSimilarity.pl to 'use CBIL::Bio::Blast::BlastAnal;' (Steve, I don't know the specific origin of parseBlastFilesForSimilarity.pl, it's pretty old and no longer (if it ever was) a supported GUS script. It is more or less functionally equivalent and maybe an ancestor to DJob's blastSimilarity script.) > > Good luck, > Pablo > ----- Original Message ----- > From: Adhemar Zerlotini Neto > To: gus...@li... > Sent: Wednesday, July 12, 2006 11:31 AM > Subject: [GUSDEV] Blast Similarities > > I'm trying to upload some blast results following a manual created > by Pablo, who works at Jessica's Lab. at UGA. > > The problem is that the perl script > 'parseBlastFilesForSimilarity.pl' isn't working. > > Here is the error: > > perl parseBlastFilesForSimilarity.pl --regex='(\S+)' > --outputFile=/home/japonicum/JaponicumDB/PROJECTS_INFO/BLAST/ > SJest.VS.SJcontigs/SJest.VS.SJcontigs.PARSED --dir=/home/japonicum/ > JaponicumDB/PROJECTS_INFO/BLAST/SJest.VS.SJcontigs/ > SJest.VS.SJcontigs.RESULTS Opening > /home/japonicum/JaponicumDB/PROJECTS_INFO/BLAST/SJest.VS.SJcontigs/ > SJest.VS.SJcontigs.PARSED /home/japonicum/JaponicumDB/PROJECTS_INFO/ > BLAST/SJest.VS.SJcontigs/SJest.VS.SJcontigs.PARSED is open > Cutoff parameters: > P value: 1e-05 > Length: 10 > Percent Identity: 20 > > > Analyzing > opening > /home/japonicum/JaponicumDB/PROJECTS_INFO/BLAST/SJest.VS.SJcontigs/ > SJest.VS.SJcontigs.PARSED Can't locate object method "new" via > package "Blast::BlastAnal" (perhaps you forgot to load > "Blast::BlastAnal"?) at > parseBlastFilesForSimilarity.pl line 81. > > > I would like to know how to fix this script or to download a new > version of the blast parse scripts. > > Thanks, > > Ad. > > > > > > ---------------------------------------------------------------------- > --- > Using Tomcat but need to do more? Need to support web services, > security? > Get stuff done quickly with pre-integrated technology to make your > job easier > Download IBM WebSphere Application Server v.1.0.1 based on Apache > Geronimo > http://sel.as-us.falkag.net/sel? > cmd=lnk&kid=120709&bid=263057&dat=121642 > > > _______________________________________________ > Gusdev-gusdev mailing list > Gus...@li... > https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev > > ---------------------------------------------------------------------- > --- > Using Tomcat but need to do more? Need to support web services, > security? > Get stuff done quickly with pre-integrated technology to make your > job easier > Download IBM WebSphere Application Server v.1.0.1 based on Apache > Geronimo > http://sel.as-us.falkag.net/sel? > cmd=lnk&kid=120709&bid=263057&dat=121642 > _______________________________________________ > Gusdev-gusdev mailing list > Gus...@li... > https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev |
From: <pi...@pc...> - 2006-07-12 17:02:05
|
One possibility: You might not be in the right group or group write is not set properly on the child table. If true, the plugin is not able to update the child row's taxon_id and therefore deleting that taxon row would violate a foreign key constraint. Check the core.groupinfo for which group you're in and the group_write field in the child table. Debbie Quoting Pablo Mendes <pa...@ug...>: > > Hi Adhemar, > it seems you need the BlastAnal.pm package > >> Can't locate object method "new" via package "Blast::BlastAnal" >> (perhaps you forgot to >> load "Blast::BlastAnal"?) at > > It is available in a CBIL tar: > http://www.cbil.upenn.edu/downloads/CBIL/releases/ > > CBIL/Bio/lib/perl/Blast/BlastAnal.pm > > You might want to change/add a "use lib" to > 'parseBlastFilesForSimilarity.pl' or to add the CBIL to your > "classpath", changing the $PERL5LIB variable. > (http://www.perl.com/doc/manual/html/pod/perlrun.html) > > > Good luck, > Pablo > ----- Original Message ----- > From: Adhemar Zerlotini Neto > To: gus...@li... > Sent: Wednesday, July 12, 2006 11:31 AM > Subject: [GUSDEV] Blast Similarities > > > I'm trying to upload some blast results following a manual created > by Pablo, who works at Jessica's Lab. at UGA. > > The problem is that the perl script > 'parseBlastFilesForSimilarity.pl' isn't working. > > Here is the error: > > perl parseBlastFilesForSimilarity.pl --regex='(\S+)' > > --outputFile=/home/japonicum/JaponicumDB/PROJECTS_INFO/BLAST/SJest.VS.SJcontigs/SJest.VS.SJcontigs.PARSED --dir=/home/japonicum/JaponicumDB/PROJECTS_INFO/BLAST/SJest.VS.SJcontigs/SJest.VS.SJcontigs.RESULTS > Opening > > /home/japonicum/JaponicumDB/PROJECTS_INFO/BLAST/SJest.VS.SJcontigs/SJest.VS.SJcontigs.PARSED /home/japonicum/JaponicumDB/PROJECTS_INFO/BLAST/SJest.VS.SJcontigs/SJest.VS.SJcontigs.PARSED is > open > Cutoff parameters: > P value: 1e-05 > Length: 10 > Percent Identity: 20 > > > Analyzing > opening > > /home/japonicum/JaponicumDB/PROJECTS_INFO/BLAST/SJest.VS.SJcontigs/SJest.VS.SJcontigs.PARSED Can't locate object method "new" via package "Blast::BlastAnal" (perhaps you forgot to load "Blast::BlastAnal"?) > at > parseBlastFilesForSimilarity.pl line 81. > > > I would like to know how to fix this script or to download a new > version of the blast parse scripts. > > Thanks, > > Ad. > > > > > > ------------------------------------------------------------------------------ > > > > ------------------------------------------------------------------------- > Using Tomcat but need to do more? Need to support web services, security? > Get stuff done quickly with pre-integrated technology to make your > job easier > Download IBM WebSphere Application Server v.1.0.1 based on Apache Geronimo > http://sel.as-us.falkag.net/sel?cmd=lnk&kid=120709&bid=263057&dat=121642 > > > > ------------------------------------------------------------------------------ > > > _______________________________________________ > Gusdev-gusdev mailing list > Gus...@li... > https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev > |
From: Pablo M. <pa...@ug...> - 2006-07-12 16:28:26
|
Hi Adhemar, it seems you need the BlastAnal.pm package=20 > Can't locate object method "new" via package "Blast::BlastAnal" = (perhaps you forgot to=20 > load "Blast::BlastAnal"?) at It is available in a CBIL tar: http://www.cbil.upenn.edu/downloads/CBIL/releases/ CBIL/Bio/lib/perl/Blast/BlastAnal.pm You might want to change/add a "use lib" to = 'parseBlastFilesForSimilarity.pl' or to add the CBIL to your = "classpath", changing the $PERL5LIB variable. (http://www.perl.com/doc/manual/html/pod/perlrun.html) Good luck, Pablo ----- Original Message -----=20 From: Adhemar Zerlotini Neto=20 To: gus...@li...=20 Sent: Wednesday, July 12, 2006 11:31 AM Subject: [GUSDEV] Blast Similarities I'm trying to upload some blast results following a manual created by = Pablo, who works at Jessica's Lab. at UGA. The problem is that the perl script 'parseBlastFilesForSimilarity.pl' = isn't working. Here is the error: perl parseBlastFilesForSimilarity.pl --regex=3D'(\S+)' = --outputFile=3D/home/japonicum/JaponicumDB/PROJECTS_INFO/BLAST/SJest.VS.S= Jcontigs/SJest.VS.SJcontigs.PARSED = --dir=3D/home/japonicum/JaponicumDB/PROJECTS_INFO/BLAST/SJest.VS.SJcontig= s/SJest.VS.SJcontigs.RESULTS Opening = /home/japonicum/JaponicumDB/PROJECTS_INFO/BLAST/SJest.VS.SJcontigs/SJest.= VS.SJcontigs.PARSED = /home/japonicum/JaponicumDB/PROJECTS_INFO/BLAST/SJest.VS.SJcontigs/SJest.= VS.SJcontigs.PARSED is open Cutoff parameters: P value: 1e-05 Length: 10 Percent Identity: 20 Analyzing opening = /home/japonicum/JaponicumDB/PROJECTS_INFO/BLAST/SJest.VS.SJcontigs/SJest.= VS.SJcontigs.PARSED Can't locate object method "new" via package = "Blast::BlastAnal" (perhaps you forgot to load "Blast::BlastAnal"?) at parseBlastFilesForSimilarity.pl line 81. I would like to know how to fix this script or to download a new = version of the blast parse scripts. Thanks, Ad. -------------------------------------------------------------------------= ----- = -------------------------------------------------------------------------= Using Tomcat but need to do more? Need to support web services, = security? Get stuff done quickly with pre-integrated technology to make your job = easier Download IBM WebSphere Application Server v.1.0.1 based on Apache = Geronimo = http://sel.as-us.falkag.net/sel?cmd=3Dlnk&kid=3D120709&bid=3D263057&dat=3D= 121642 -------------------------------------------------------------------------= ----- _______________________________________________ Gusdev-gusdev mailing list Gus...@li... https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev |
From: Kumar, S. <San...@ng...> - 2006-07-12 16:27:32
|
Hi Group, As Josef suggested in his previous mail, I deleted the entry on line number (given in the error message)from the merged.dmp. And when I ran the loading it certainly passed the previous error point. So, I think that the Josef's suggestion worked. But I am getting a new type of error message, provided below. Can some one pl. help me in understanding/resolving the error message. Thanks Sanjeev ------------------------------------------------------------------------ --------------------------------- ********select d.name,t2.name as superclass,t1.name as subclass from CORE.TableInfo t1,CORE.TableInfo t2, CORE.DatabaseInfo d where t 2.table_id =3D t1.view_on_table_id and t1.name not like '%Ver' and d.database_id =3D t2.database_id********select * from TESS.MoietyImp WHERE taxon_id =3D 525455 ********select * from DoTS.NASequenceImp WHERE taxon_id =3D 525455 Insufficient permission to retrieve GUS::Model::DoTS::NASequenceImp Child of GUS::Model::SRes::Taxon ********select * from DoTS.AASequenceImp WHERE taxon_id =3D 525455 ********select * from Study.BioMaterialImp WHERE taxon_id =3D 525455 Wed Jul 12 12:03:38 2006 Taxon_id =3D GUS::Model::SRes::Taxon=3DHASH(0xa166cf8) merged with Taxon_id =3D GUS::Model::SRes::Taxon=3DHAS H(0x9ee9e54) DBD::Oracle::db do failed: ORA-02292: integrity constraint (DOTS.NASEQUENCEIMP_FK02) violated - child record found (DBD ERROR: OCIStm tExecute) [for Statement "DELETE FROM SRes.Taxon WHERE taxon_id =3D 525455 "] at /home/oragus35/GUS/gus_home/lib/perl/GUS/ObjRelP/DbiDbHandle.pm line 119, <MERGED> line 5476. ERROR: SQL ERROR!! involving DELETE FROM SRes.Taxon WHERE taxon_id =3D 525455 at /home/oragus35/GUS/gus_home/lib/perl/GUS/ObjRelP/DbiDbHandle.pm line 166 =20 GUS::ObjRelP::DbiDbHandle::death('GUS::ObjRelP::DbiDbHandle=3DHASH(0x9e7c= b 84)', '\x{a} SQL ERROR!! involving\x{a} DELETE FROM S Res.Taxon \x{a}\x{9}WHERE tax...') called at /home/oragus35/GUS/gus_home/lib/perl/GUS/ObjRelP/DbiDbHandle.pm line 120 =20 GUS::ObjRelP::DbiDbHandle::sqlexecIns('GUS::ObjRelP::DbiDbHandle=3DHASH(0= x 9e7cb84)', 'DELETE FROM SRes.Taxon \x{a}\x{9}WHERE taxon_id =3D 525455 \x{a}') called at /home/oragus35/GUS/gus_home/lib/perl/GUS/ObjRelP/DbiRow.pm line 583 =20 GUS::ObjRelP::DbiRow::removeFromDB('GUS::Model::SRes::Taxon=3DHASH(0xa166= c f8)') called at /home/oragus35/GUS/gus_home/lib/perl/ GUS/Model/GusRow.pm line 1658 =20 GUS::Model::GusRow::submit('GUS::Model::SRes::Taxon=3DHASH(0xa166cf8)') called at /home/oragus35/GUS/gus_home/lib/perl/GUS/Supp orted/Plugin/LoadTaxon.pm line 196 =20 GUS::Supported::Plugin::LoadTaxon::updateTaxonAndChildRows('GUS::Support ed::Plugin::LoadTaxon=3DHASH(0x9defc2c)', 525455, 61030 7) called at /home/oragus35/GUS/gus_home/lib/perl/GUS/Supported/Plugin/LoadTaxon.pm line 155 =20 GUS::Supported::Plugin::LoadTaxon::mergeTaxons('GUS::Supported::Plugin:: LoadTaxon=3DHASH(0x9defc2c)') called at /home/oragus35/ GUS/gus_home/lib/perl/GUS/Supported/Plugin/LoadTaxon.pm line 114 =20 GUS::Supported::Plugin::LoadTaxon::run('GUS::Supported::Plugin::LoadTaxo n=3DHASH(0x9defc2c)', 'HASH(0xa08c2bc)') called at /hom e/oragus35/GUS/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line 469 eval {...} called at /home/oragus35/GUS/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line 461 =20 GUS::PluginMgr::GusApplication::doMajorMode_RunOrReport('GUS::PluginMgr: :GusApplication=3DHASH(0x994f180)', 'GUS::Supported::Pl ugin::LoadTaxon', 1) called at /home/oragus35/GUS/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line 380 =20 GUS::PluginMgr::GusApplication::doMajorMode_Run('GUS::PluginMgr::GusAppl ication=3DHASH(0x994f180)', 'GUS::Supported::Plugin::Lo adTaxon') called at /home/oragus35/GUS/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line 288 =20 GUS::PluginMgr::GusApplication::doMajorMode('GUS::PluginMgr::GusApplicat ion=3DHASH(0x994f180)', 'GUS::Supported::Plugin::LoadTa xon') called at /home/oragus35/GUS/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line 197 =20 GUS::PluginMgr::GusApplication::parseAndRun('GUS::PluginMgr::GusApplicat ion=3DHASH(0x994f180)', 'ARRAY(0x994f924)') called at / home/oragus35/GUS/gus_home/bin/ga line 11 STACK TRACE: at /home/oragus35/GUS/gus_home/lib/perl/GUS/ObjRelP/DbiDbHandle.pm line 166 =20 GUS::ObjRelP::DbiDbHandle::death('GUS::ObjRelP::DbiDbHandle=3DHASH(0x9e7c= b 84)', '\x{a} SQL ERROR!! involving\x{a} DELETE FROM S Res.Taxon \x{a}\x{9}WHERE tax...') called at /home/oragus35/GUS/gus_home/lib/perl/GUS/ObjRelP/DbiDbHandle.pm line 120 =20 GUS::ObjRelP::DbiDbHandle::sqlexecIns('GUS::ObjRelP::DbiDbHandle=3DHASH(0= x 9e7cb84)', 'DELETE FROM SRes.Taxon \x{a}\x{9}WHERE taxon_id =3D 525455 \x{a}') called at /home/oragus35/GUS/gus_home/lib/perl/GUS/ObjRelP/DbiRow.pm line 583 =20 GUS::ObjRelP::DbiRow::removeFromDB('GUS::Model::SRes::Taxon=3DHASH(0xa166= c f8)') called at /home/oragus35/GUS/gus_home/lib/perl/ GUS/Model/GusRow.pm line 1658 =20 GUS::Model::GusRow::submit('GUS::Model::SRes::Taxon=3DHASH(0xa166cf8)') called at /home/oragus35/GUS/gus_home/lib/perl/GUS/Supp orted/Plugin/LoadTaxon.pm line 196 =20 GUS::Supported::Plugin::LoadTaxon::updateTaxonAndChildRows('GUS::Support ed::Plugin::LoadTaxon=3DHASH(0x9defc2c)', 525455, 61030 7) called at /home/oragus35/GUS/gus_home/lib/perl/GUS/Supported/Plugin/LoadTaxon.pm line 155 =20 GUS::Supported::Plugin::LoadTaxon::mergeTaxons('GUS::Supported::Plugin:: LoadTaxon=3DHASH(0x9defc2c)') called at /home/oragus35/ GUS/gus_home/lib/perl/GUS/Supported/Plugin/LoadTaxon.pm line 114 =20 GUS::Supported::Plugin::LoadTaxon::run('GUS::Supported::Plugin::LoadTaxo n=3DHASH(0x9defc2c)', 'HASH(0xa08c2bc)') called at /hom e/oragus35/GUS/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line 469 eval {...} called at /home/oragus35/GUS/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line 461 =20 GUS::PluginMgr::GusApplication::doMajorMode_RunOrReport('GUS::PluginMgr: :GusApplication=3DHASH(0x994f180)', 'GUS::Supported::Pl ugin::LoadTaxon', 1) called at /home/oragus35/GUS/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line 380 =20 GUS::PluginMgr::GusApplication::doMajorMode_Run('GUS::PluginMgr::GusAppl ication=3DHASH(0x994f180)', 'GUS::Supported::Plugin::Lo adTaxon') called at /home/oragus35/GUS/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line 288 =20 GUS::PluginMgr::GusApplication::doMajorMode('GUS::PluginMgr::GusApplicat ion=3DHASH(0x994f180)', 'GUS::Supported::Plugin::LoadTa xon') called at /home/oragus35/GUS/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line 197 =20 GUS::PluginMgr::GusApplication::parseAndRun('GUS::PluginMgr::GusApplicat ion=3DHASH(0x994f180)', 'ARRAY(0x994f924)') called at / home/oragus35/GUS/gus_home/bin/ga line 11 Thanks Sanjeev -----Original Message----- From: Josef Jurek [mailto:ju...@cs...]=20 Sent: Wednesday, July 12, 2006 11:43 AM To: gus...@li...; Kumar, Sanjeev Cc: ju...@cs... Subject: Re: [GUSDEV] Out of Memory while loading Taxonomy data "Kumar, Sanjeev" <San...@ng...> writes: > > Hi Josef, > thanks for your quick response, let me look for the same entry and=20 > delete it and then retry the loading. >=20 > Thanks > Sanjeev Well, don't necessarily delete the "exact" entry, rather, delete the entry that is on the line number indicated by your error message. I would be interested if it is the same data or not though. Josef Josef Jurek, Ph.D. Daphne Preuss Laboratory Molecular Genetics and Cell Biology The University of Chicago ju...@cs... voice: (773) 702-9559 fax: (773) 702-6648 |
From: Steve F. <sfi...@pc...> - 2006-07-12 16:00:30
|
where did this script come from? i don't see it in the gus source tree. the problem is that the your PERL path doesn't include CBIL/lib/perl/Blast/ steve Adhemar Zerlotini Neto wrote: > I'm trying to upload some blast results following a manual created by > Pablo, who works at Jessica's Lab. at UGA. > > The problem is that the perl script 'parseBlastFilesForSimilarity.pl' > isn't working. > > Here is the error: > > perl parseBlastFilesForSimilarity.pl --regex='(\S+)' > --outputFile=/home/japonicum/JaponicumDB/PROJECTS_INFO/BLAST/SJest.VS.SJcontigs/SJest.VS.SJcontigs.PARSED > --dir=/home/japonicum/JaponicumDB/PROJECTS_INFO/BLAST/SJest.VS.SJcontigs/SJest.VS.SJcontigs.RESULTS > Opening > /home/japonicum/JaponicumDB/PROJECTS_INFO/BLAST/SJest.VS.SJcontigs/SJest.VS.SJcontigs.PARSED > /home/japonicum/JaponicumDB/PROJECTS_INFO/BLAST/SJest.VS.SJcontigs/SJest.VS.SJcontigs.PARSED > is open > Cutoff parameters: > P value: 1e-05 > Length: 10 > Percent Identity: 20 > > > Analyzing > opening > /home/japonicum/JaponicumDB/PROJECTS_INFO/BLAST/SJest.VS.SJcontigs/SJest.VS.SJcontigs.PARSED > Can't locate object method "new" via package "Blast::BlastAnal" > (perhaps you forgot to load "Blast::BlastAnal"?) at > parseBlastFilesForSimilarity.pl line 81. > > > I would like to know how to fix this script or to download a new > version of the blast parse scripts. > > Thanks, > > Ad. > > >------------------------------------------------------------------------ > > >------------------------------------------------------------------------- >Using Tomcat but need to do more? Need to support web services, security? >Get stuff done quickly with pre-integrated technology to make your job easier >Download IBM WebSphere Application Server v.1.0.1 based on Apache Geronimo >http://sel.as-us.falkag.net/sel?cmd=lnk&kid=120709&bid=263057&dat=121642 > > >------------------------------------------------------------------------ > >_______________________________________________ >Gusdev-gusdev mailing list >Gus...@li... >https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev > > |
From: <ju...@cs...> - 2006-07-12 15:43:17
|
"Kumar, Sanjeev" <San...@ng...> writes: > > Hi Josef, > thanks for your quick response, let me look for the same entry and > delete it and then retry the loading. > > Thanks > Sanjeev Well, don't necessarily delete the "exact" entry, rather, delete the entry that is on the line number indicated by your error message. I would be interested if it is the same data or not though. Josef Josef Jurek, Ph.D. Daphne Preuss Laboratory Molecular Genetics and Cell Biology The University of Chicago ju...@cs... voice: (773) 702-9559 fax: (773) 702-6648 |
From: Adhemar Z. N. <ad...@cp...> - 2006-07-12 15:34:56
|
<ad...@cp...>I'm trying to upload some blast results following a manual created by Pablo, who works at Jessica's Lab. at UGA.<br /><br />The problem is that the perl script 'parseBlastFilesForSimilarity.pl' isn't working.<br /><br />Here is the error:<br /><br /><font size="2" style="font-family: courier new,courier,monospace;">perl parseBlastFilesForSimilarity.pl --regex='(\S+)'<br />--outputFile=/home/japonicum/JaponicumDB/PROJECTS_INFO/BLAST/SJest.VS.SJcontigs/SJest.VS.SJcontigs.PARSED --dir=/home/japonicum/JaponicumDB/PROJECTS_INFO/BLAST/SJest.VS.SJcontigs/SJest.VS.SJcontigs.RESULTS Opening<br />/home/japonicum/JaponicumDB/PROJECTS_INFO/BLAST/SJest.VS.SJcontigs/SJest.VS.SJcontigs.PARSED /home/japonicum/JaponicumDB/PROJECTS_INFO/BLAST/SJest.VS.SJcontigs/SJest.VS.SJcontigs.PARSED is open<br />Cutoff parameters:<br /> P value: 1e-05<br /> Length: 10<br /> Percent Identity: 20<br /><br /><br />Analyzing<br />opening<br />/home/japonicum/JaponicumDB/PROJECTS_INFO/BLAST/SJest.VS.SJcontigs/SJest.VS.SJcontigs.PARSED Can't locate object method "new" via package "Blast::BlastAnal" (perhaps you forgot to load "Blast::BlastAnal"?) at<br />parseBlastFilesForSimilarity.pl line 81.</font><br /> <br /> <br />I would like to know how to fix this script or to download a new version of the blast parse scripts.<br /><br />Thanks,<br /><br />Ad.<br /><br /> <br /></ad...@cp...> |
From: Kumar, S. <San...@ng...> - 2006-07-12 15:29:31
|
Hi Ed, It is a GUS error. The error message is, Out of Memory! Issuing Rollback() for database handle being DESTROY'd without explicit disconnect(), <MERGED> line 3263 Issuing Rollback() for database handle being DESTROY'd without explicit disconnect(), <MERGED> line 3263 Thanks Sanjeev -----Original Message----- From: Ed Robinson [mailto:ero...@ug...]=20 Sent: Wednesday, July 12, 2006 11:05 AM To: Kumar, Sanjeev; gus...@li... Subject: Re: [GUSDEV] Out of Memory while loading Taxonomy data Can you send the actual error message? Is it a GUS error or an Oracle error. -ed ---- Original message ---- >Date: Wed, 12 Jul 2006 10:57:13 -0400 >From: "Kumar, Sanjeev" <San...@ng...> >Subject: [GUSDEV] Out of Memory while loading Taxonomy data >To: <gus...@li...> > >Hi Group, > I am getting 'out of memory' error while loading the Taxonomy data. > I remember Jian Lu got this error earlier, but I couldn't find any=20 >solution in the archive. > Pl. suggest me to resolve the issue. > >Thanks >Sanjeev > > >----------------------------------------------------------------------- >-- Using Tomcat but need to do more? Need to support web services,=20 >security? >Get stuff done quickly with pre-integrated technology to make your job=20 >easier Download IBM WebSphere Application Server v.1.0.1 based on=20 >Apache Geronimo >http://sel.as-us.falkag.net/sel?cmd=3Dlnk&kid=3D120709&bid=3D263057&dat=3D= 12164 >2 _______________________________________________ >Gusdev-gusdev mailing list >Gus...@li... >https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev ----------------- Ed Robinson Center for Tropical and Emerging Global Diseases University of Georgia, Athens, GA 30602 ero...@ug.../(706)542.1447/254.8883 |
From: <ju...@cs...> - 2006-07-12 15:28:18
|
"Kumar, Sanjeev" <San...@ng...> writes: > > I am getting 'out of memory' error while loading the Taxonomy data. > I remember Jian Lu got this error earlier, but I couldn't find any > solution in the archive. > Pl. suggest me to resolve the issue. I recently ran into this issue as well. I got the same error that was mentioned in the list archives, which looks something like this: Out of memory! Issuing rollback() for database handle being DESTROY'd without explicit disconnect(), <MERGED> line xxx. Issuing rollback() for database handle being DESTROY'd without explicit disconnect(), <MERGED> line xxx. and the line number will vary depending on what *.dmp files you use. What was happening was that in the merged.dmp file at line xxx was the entry: 88745 | 87265 | and this entry would cause LoadTaxon to run endlessly until the memory on my machine ran out. I deleted the line from merged.dmp and LoadTaxon would run successfully. Without investigating "why" this line in merged.dmp would cause this problem, I can think of two possible reasons: This line is an error/bug on NCBI's part. This line illustrates a case that the author(s) of LoadTaxon never considered. I look forward to other peoples comments. Josef Josef Jurek, Ph.D. Daphne Preuss Laboratory Molecular Genetics and Cell Biology The University of Chicago ju...@cs... voice: (773) 702-9559 fax: (773) 702-6648 |
From: Ed R. <ero...@ug...> - 2006-07-12 15:04:42
|
Can you send the actual error message? Is it a GUS error or an Oracle error. -ed ---- Original message ---- >Date: Wed, 12 Jul 2006 10:57:13 -0400 >From: "Kumar, Sanjeev" <San...@ng...> >Subject: [GUSDEV] Out of Memory while loading Taxonomy data >To: <gus...@li...> > >Hi Group, > I am getting 'out of memory' error while loading the Taxonomy data. > I remember Jian Lu got this error earlier, but I couldn't find any >solution in the archive. > Pl. suggest me to resolve the issue. > >Thanks >Sanjeev > > >------------------------------------------------------------------------- >Using Tomcat but need to do more? Need to support web services, security? >Get stuff done quickly with pre-integrated technology to make your job easier >Download IBM WebSphere Application Server v.1.0.1 based on Apache Geronimo >http://sel.as-us.falkag.net/sel?cmd=lnk&kid=120709&bid=263057&dat=121642 >_______________________________________________ >Gusdev-gusdev mailing list >Gus...@li... >https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev ----------------- Ed Robinson Center for Tropical and Emerging Global Diseases University of Georgia, Athens, GA 30602 ero...@ug.../(706)542.1447/254.8883 |
From: Kumar, S. <San...@ng...> - 2006-07-12 14:57:25
|
Hi Group, I am getting 'out of memory' error while loading the Taxonomy data. I remember Jian Lu got this error earlier, but I couldn't find any solution in the archive. Pl. suggest me to resolve the issue. Thanks Sanjeev |
From: marc j. <de...@ho...> - 2006-07-12 06:29:50
|
Hello, Where would I find GUS 3.0 documentation? I get the feeling that I'm looking at the wrong documentation. Also, where are the upgrade scripts to go from 3.0 to 3.5? Regards, Marc |
From: marc j. <de...@ho...> - 2006-07-12 06:01:43
|
Hello, I suspect that I'm not going about this the right way. I've got a valid GUS implementation, but due to hardware issues and backup issues I'm missing gus_home. I took a look at the build script, which is a wrapper for ant, and I found: my $cmd = "ant -f $projectHome/install/build.xml $doWhat -Dproj=$project -DtargetDir=$targetDir -Dcomp=$component -DprojectsDir=$projectHome $clean $skipJava $append $webPropFile $tag -logger org.apache.tools.ant.NoBannerLogger "; I'm guessing that I should *NOT* define $targetDir as $gus_home. In looking at the "Reinstalling the GUS application Framework" page, I see that I should 1 touch $PROJECT_HOME/Schema/gus_schema.xml 2. build GUS install -append I did not do #1 earlier. I'm a little uncomfortable though. #1 seems like it going to break what's already in the database. Can someone verify that that is so? Regards, Marc |
From: Ed R. <ero...@ug...> - 2006-07-10 14:38:48
|
The GB record lacks a gene feature but has mRNA and CDS features. The Unflattener, as it operates in ISF, infers a feature hierarchy. It can add mRNA and CDS records, but it assumes the existence of a gene feature. Since the file doesn't supply a gene feature, the Unflattener cannot build a valid hierarchy. How many files do you have like this? You can easily modify ISF to build different hierarchies, but the Unflattener always requires an explicit gene feature to start its hierachy. If you have a bunch of files, I would recommend writting a pre-parser to add gene features everytime you find a gene-less mRNA record. A simple BioPerl In and Out script with a conditional to add the gene feature to the std out every time you find an mRNA feature should do the trick. -ed ---- Original message ---- >Date: Fri, 7 Jul 2006 18:02:23 -0400 >From: "Kumar, Sanjeev" <San...@ng...> >Subject: Re: [GUSDEV] ISF error in loading influenza sequence >To: "Steve Fischer" <sfi...@pc...> >Cc: gus...@li... > >Hi Steve, > The file is small genBank file. Let me attach the file. > And the command I am using to load is as follows: >ga GUS::Supported::Plugin::InsertSequenceFeatures --seqFile $loadFile >--mapFile /home/oragus35/genbank2gus.xml --fileFormat 'genbank' >--extDbName $database --extDbRlsVer $dbVersion --soCvsVersion 3354 >--gusconfigfile /home/oragus35/GUS/gus.properties --commit >2>>$outputFile`; > >Thanks >Sanjeev > > >-----Original Message----- >From: Steve Fischer [mailto:sfi...@pc...] >Sent: Friday, July 07, 2006 5:54 PM >To: Kumar, Sanjeev >Cc: gus...@li... >Subject: Re: [GUSDEV] ISF error in loading influenza sequence > >sanjeev- > >how big is the file you are trying to load? i want to take a look at >it. is it in genbank? what is its accession? > >can you send the command line? > > >steve > >Kumar, Sanjeev wrote: >> Hi Group, >> I am getting following error when I am trying to load one >> influenza sequence using "InsertSequenceFeature' plugin. >> I am not able to figure out the reason of the failure. I need your > >> assistance, any help will be appreciated. >> The sequence file is attached. >> >> >> Thanks >> Sanjeev Kumar >> Northrop Grumman >> >> ERROR: >> >> ------------- EXCEPTION ------------- >> *MSG: structure_type 2 is currently unknown >> *STACK Bio::SeqFeature::Tools::Unflattener::unflatten_seq >> >/home/oragus35/perl/lib/site_perl/5.8.7/Bio/SeqFeature/Tools/Unflattener >.pm:1419 >> STACK GUS::Supported::Plugin::InsertSequenceFeatures::unflatten >> >/home/oragus35/GUS/gus_home/lib/perl/GUS/Supported/Plugin/InsertSequence >Features.pm:383 >> STACK GUS::Supported::Plugin::InsertSequenceFeatures::run >> >/home/oragus35/GUS/gus_home/lib/perl/GUS/Supported/Plugin/InsertSequence >Features.pm:358 >> STACK (eval) >> >/home/oragus35/GUS/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm:469 >> STACK GUS::PluginMgr::GusApplication::doMajorMode_RunOrReport >> >/home/oragus35/GUS/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm:461 >> STACK GUS::PluginMgr::GusApplication::doMajorMode_Run >> >/home/oragus35/GUS/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm:380 >> STACK GUS::PluginMgr::GusApplication::doMajorMode >> >/home/oragus35/GUS/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm:288 >> STACK GUS::PluginMgr::GusApplication::parseAndRun >> >/home/oragus35/GUS/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm:197 >> STACK toplevel /home/oragus35/GUS/gus_home/bin/ga:11 >> -------------------------------------- >> STACK TRACE: >> at /home/oragus35/perl/lib/site_perl/5.8.7/Bio/Root/Root.pm line >> 342 >> >> >Bio::Root::Root::throw('Bio::SeqFeature::Tools::Unflattener=HASH(0xa237d >08)', >> 'structure_type 2 is currently unknown') called at >> >/home/oragus35/perl/lib/site_perl/5.8.7/Bio/SeqFeature/Tools/Unflattener >.pm >> line 1419 >> >> >Bio::SeqFeature::Tools::Unflattener::unflatten_seq('Bio::SeqFeature::Too >ls::Unflattener=HASH(0xa237d08)', >> '-seq', 'Bio::Seq::RichSeq=HASH(0x9febe2c)', '-use_magic', 1) >> called at >> >/home/oragus35/GUS/gus_home/lib/perl/GUS/Supported/Plugin/InsertSequence >Features.pm >> line 383 >> >> >GUS::Supported::Plugin::InsertSequenceFeatures::unflatten('GUS::Supporte >d::Plugin::InsertSequenceFeatures=HASH(0x9414bf0)', >> 'Bio::Seq::RichSeq=HASH(0x9febe2c)') called at >> >/home/oragus35/GUS/gus_home/lib/perl/GUS/Supported/Plugin/InsertSequence >Features.pm >> line 358 >> >> >GUS::Supported::Plugin::InsertSequenceFeatures::run('GUS::Supported::Plu >gin::InsertSequenceFeatures=HASH(0x9414bf0)', >> 'HASH(0x9ef7284)') called at >> >/home/oragus35/GUS/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm >> line 469 >> eval {...} called at >> >/home/oragus35/GUS/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm >> line 461 >> >> >GUS::PluginMgr::GusApplication::doMajorMode_RunOrReport('GUS::PluginMgr: >:GusApplication=HASH(0x8f74180)', >> 'GUS::Supported::Plugin::InsertSequenceFeatures', 1) called at >> >/home/oragus35/GUS/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm >> line 380 >> >> >GUS::PluginMgr::GusApplication::doMajorMode_Run('GUS::PluginMgr::GusAppl >ication=HASH(0x8f74180)', >> 'GUS::Supported::Plugin::InsertSequenceFeatures') called at >> >/home/oragus35/GUS/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm >> line 288 >> >> >GUS::PluginMgr::GusApplication::doMajorMode('GUS::PluginMgr::GusApplicat >ion=HASH(0x8f74180)', >> 'GUS::Supported::Plugin::InsertSequenceFeatures') called at >> >/home/oragus35/GUS/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm >> line 197 >> >> >GUS::PluginMgr::GusApplication::parseAndRun('GUS::PluginMgr::GusApplicat >ion=HASH(0x8f74180)', >> 'ARRAY(0x8f74924)') called at /home/oragus35/GUS/gus_home/bin/ga >> line 11 >> >> >> >> >> ---------------------------------------------------------------------- >> -- >> >> Using Tomcat but need to do more? Need to support web services, >security? >> Get stuff done quickly with pre-integrated technology to make your job > >> easier Download IBM WebSphere Application Server v.1.0.1 based on >> Apache Geronimo >> http://sel.as-us.falkag.net/sel?cmd=lnk&kid=120709&bid=263057&dat=1216 >> 42 >> ---------------------------------------------------------------------- >> -- >> >> _______________________________________________ >> Gusdev-gusdev mailing list >> Gus...@li... >> https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev >> >________________ >FLBHAOA.gbf (8k bytes) >________________ >Using Tomcat but need to do more? Need to support web services, security? >Get stuff done quickly with pre-integrated technology to make your job easier >Download IBM WebSphere Application Server v.1.0.1 based on Apache Geronimo >http://sel.as-us.falkag.net/sel?cmd=lnk&kid=120709&bid=263057&dat=121642 >________________ >_______________________________________________ >Gusdev-gusdev mailing list >Gus...@li... >https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev ----------------- Ed Robinson Center for Tropical and Emerging Global Diseases University of Georgia, Athens, GA 30602 ero...@ug.../(706)542.1447/254.8883 |
From: Mark S. H. <mh...@ug...> - 2006-07-07 22:25:52
|
See http://lists.open-bio.org/pipermail/bioperl-l/2006-January/020687.html where this error was diagnosed as a BioPerl Unflattener issue. Even if it does not directly solve your problem perhaps you can take comfort in knowing you are not alone. :-( -Mark Mark Heiges CryptoDB.org Center for Tropical and Emerging Global Diseases University of Georgia, Athens, GA 30602 TEL: +1 (706) 542-1447 On Jul 7, 2006, at 5:39 PM, Kumar, Sanjeev wrote: > Hi Group, > I am getting following error when I am trying to load one > influenza sequence using "InsertSequenceFeature' plugin. > I am not able to figure out the reason of the failure. I need > your assistance, any help will be appreciated. > The sequence file is attached. > > > Thanks > Sanjeev Kumar > Northrop Grumman > > ERROR: > ------------- EXCEPTION ------------- > MSG: structure_type 2 is currently unknown > STACK Bio::SeqFeature::Tools::Unflattener::unflatten_seq /home/ > oragus35/perl/lib/site_perl/5.8.7/Bio/SeqFeature/Tools/ > Unflattener.pm:1419 > STACK GUS::Supported::Plugin::InsertSequenceFeatures::unflatten / > home/oragus35/GUS/gus_home/lib/perl/GUS/Supported/Plugin/ > InsertSequenceFeatures.pm:383 > STACK GUS::Supported::Plugin::InsertSequenceFeatures::run /home/ > oragus35/GUS/gus_home/lib/perl/GUS/Supported/Plugin/ > InsertSequenceFeatures.pm:358 > STACK (eval) /home/oragus35/GUS/gus_home/lib/perl/GUS/PluginMgr/ > GusApplication.pm:469 > STACK GUS::PluginMgr::GusApplication::doMajorMode_RunOrReport /home/ > oragus35/GUS/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm:461 > STACK GUS::PluginMgr::GusApplication::doMajorMode_Run /home/ > oragus35/GUS/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm:380 > STACK GUS::PluginMgr::GusApplication::doMajorMode /home/oragus35/ > GUS/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm:288 > STACK GUS::PluginMgr::GusApplication::parseAndRun /home/oragus35/ > GUS/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm:197 > STACK toplevel /home/oragus35/GUS/gus_home/bin/ga:11 > -------------------------------------- > STACK TRACE: > at /home/oragus35/perl/lib/site_perl/5.8.7/Bio/Root/Root.pm line 342 > Bio::Root::Root::throw > ('Bio::SeqFeature::Tools::Unflattener=HASH(0xa237d08)', > 'structure_type 2 is currently unknown') called at /home/oragus35/ > perl/lib/site_perl/5.8.7/Bio/SeqFeature/Tools/Unflattener.pm line 1419 > Bio::SeqFeature::Tools::Unflattener::unflatten_seq > ('Bio::SeqFeature::Tools::Unflattener=HASH(0xa237d08)', '-seq', > 'Bio::Seq::RichSeq=HASH(0x9febe2c)', '-use_magic', 1) called at / > home/oragus35/GUS/gus_home/lib/perl/GUS/Supported/Plugin/ > InsertSequenceFeatures.pm line 383 > GUS::Supported::Plugin::InsertSequenceFeatures::unflatten > ('GUS::Supported::Plugin::InsertSequenceFeatures=HASH(0x9414bf0)', > 'Bio::Seq::RichSeq=HASH(0x9febe2c)') called at /home/oragus35/GUS/ > gus_home/lib/perl/GUS/Supported/Plugin/InsertSequenceFeatures.pm > line 358 > GUS::Supported::Plugin::InsertSequenceFeatures::run > ('GUS::Supported::Plugin::InsertSequenceFeatures=HASH(0x9414bf0)', > 'HASH(0x9ef7284)') called at /home/oragus35/GUS/gus_home/lib/perl/ > GUS/PluginMgr/GusApplication.pm line 469 > eval {...} called at /home/oragus35/GUS/gus_home/lib/perl/ > GUS/PluginMgr/GusApplication.pm line 461 > GUS::PluginMgr::GusApplication::doMajorMode_RunOrReport > ('GUS::PluginMgr::GusApplication=HASH(0x8f74180)', > 'GUS::Supported::Plugin::InsertSequenceFeatures', 1) called at / > home/oragus35/GUS/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm > line 380 > GUS::PluginMgr::GusApplication::doMajorMode_Run > ('GUS::PluginMgr::GusApplication=HASH(0x8f74180)', > 'GUS::Supported::Plugin::InsertSequenceFeatures') called at /home/ > oragus35/GUS/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line > 288 > GUS::PluginMgr::GusApplication::doMajorMode > ('GUS::PluginMgr::GusApplication=HASH(0x8f74180)', > 'GUS::Supported::Plugin::InsertSequenceFeatures') called at /home/ > oragus35/GUS/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm line > 197 > GUS::PluginMgr::GusApplication::parseAndRun > ('GUS::PluginMgr::GusApplication=HASH(0x8f74180)', 'ARRAY > (0x8f74924)') called at /home/oragus35/GUS/gus_home/bin/ga line 11 > > > > <FLBHAOA.gbf> > Using Tomcat but need to do more? Need to support web services, > security? > Get stuff done quickly with pre-integrated technology to make your > job easier > Download IBM WebSphere Application Server v.1.0.1 based on Apache > Geronimo > http://sel.as-us.falkag.net/sel? > cmd=lnk&kid=120709&bid=263057&dat=121642______________________________ > _________________ > Gusdev-gusdev mailing list > Gus...@li... > https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev |
From: Kumar, S. <San...@ng...> - 2006-07-07 22:02:34
|
Hi Steve, The file is small genBank file. Let me attach the file. And the command I am using to load is as follows: ga GUS::Supported::Plugin::InsertSequenceFeatures --seqFile $loadFile --mapFile /home/oragus35/genbank2gus.xml --fileFormat 'genbank' --extDbName $database --extDbRlsVer $dbVersion --soCvsVersion 3354 --gusconfigfile /home/oragus35/GUS/gus.properties --commit 2>>$outputFile`; Thanks Sanjeev -----Original Message----- From: Steve Fischer [mailto:sfi...@pc...]=20 Sent: Friday, July 07, 2006 5:54 PM To: Kumar, Sanjeev Cc: gus...@li... Subject: Re: [GUSDEV] ISF error in loading influenza sequence sanjeev- how big is the file you are trying to load? i want to take a look at it. is it in genbank? what is its accession? can you send the command line? steve Kumar, Sanjeev wrote: > Hi Group, > I am getting following error when I am trying to load one=20 > influenza sequence using "InsertSequenceFeature' plugin. > I am not able to figure out the reason of the failure. I need your > assistance, any help will be appreciated. > The sequence file is attached. > =20 > =20 > Thanks > Sanjeev Kumar > Northrop Grumman > =20 > ERROR: > > ------------- EXCEPTION ------------- > *MSG: structure_type 2 is currently unknown > *STACK Bio::SeqFeature::Tools::Unflattener::unflatten_seq > /home/oragus35/perl/lib/site_perl/5.8.7/Bio/SeqFeature/Tools/Unflattener .pm:1419 > STACK GUS::Supported::Plugin::InsertSequenceFeatures::unflatten > /home/oragus35/GUS/gus_home/lib/perl/GUS/Supported/Plugin/InsertSequence Features.pm:383 > STACK GUS::Supported::Plugin::InsertSequenceFeatures::run > /home/oragus35/GUS/gus_home/lib/perl/GUS/Supported/Plugin/InsertSequence Features.pm:358 > STACK (eval) > /home/oragus35/GUS/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm:469 > STACK GUS::PluginMgr::GusApplication::doMajorMode_RunOrReport > /home/oragus35/GUS/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm:461 > STACK GUS::PluginMgr::GusApplication::doMajorMode_Run > /home/oragus35/GUS/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm:380 > STACK GUS::PluginMgr::GusApplication::doMajorMode > /home/oragus35/GUS/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm:288 > STACK GUS::PluginMgr::GusApplication::parseAndRun > /home/oragus35/GUS/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm:197 > STACK toplevel /home/oragus35/GUS/gus_home/bin/ga:11 > -------------------------------------- > STACK TRACE: > at /home/oragus35/perl/lib/site_perl/5.8.7/Bio/Root/Root.pm line=20 > 342 > =20 > Bio::Root::Root::throw('Bio::SeqFeature::Tools::Unflattener=3DHASH(0xa237= d 08)', > 'structure_type 2 is currently unknown') called at > /home/oragus35/perl/lib/site_perl/5.8.7/Bio/SeqFeature/Tools/Unflattener .pm > line 1419 > =20 > Bio::SeqFeature::Tools::Unflattener::unflatten_seq('Bio::SeqFeature::Too ls::Unflattener=3DHASH(0xa237d08)', > '-seq', 'Bio::Seq::RichSeq=3DHASH(0x9febe2c)', '-use_magic', 1) > called at > /home/oragus35/GUS/gus_home/lib/perl/GUS/Supported/Plugin/InsertSequence Features.pm > line 383 > =20 > GUS::Supported::Plugin::InsertSequenceFeatures::unflatten('GUS::Supporte d::Plugin::InsertSequenceFeatures=3DHASH(0x9414bf0)', > 'Bio::Seq::RichSeq=3DHASH(0x9febe2c)') called at > /home/oragus35/GUS/gus_home/lib/perl/GUS/Supported/Plugin/InsertSequence Features.pm > line 358 > =20 > GUS::Supported::Plugin::InsertSequenceFeatures::run('GUS::Supported::Plu gin::InsertSequenceFeatures=3DHASH(0x9414bf0)', > 'HASH(0x9ef7284)') called at > /home/oragus35/GUS/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm > line 469 > eval {...} called at > /home/oragus35/GUS/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm > line 461 > =20 > GUS::PluginMgr::GusApplication::doMajorMode_RunOrReport('GUS::PluginMgr: :GusApplication=3DHASH(0x8f74180)', > 'GUS::Supported::Plugin::InsertSequenceFeatures', 1) called at > /home/oragus35/GUS/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm > line 380 > =20 > GUS::PluginMgr::GusApplication::doMajorMode_Run('GUS::PluginMgr::GusAppl ication=3DHASH(0x8f74180)', > 'GUS::Supported::Plugin::InsertSequenceFeatures') called at > /home/oragus35/GUS/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm > line 288 > =20 > GUS::PluginMgr::GusApplication::doMajorMode('GUS::PluginMgr::GusApplicat ion=3DHASH(0x8f74180)', > 'GUS::Supported::Plugin::InsertSequenceFeatures') called at > /home/oragus35/GUS/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm > line 197 > =20 > GUS::PluginMgr::GusApplication::parseAndRun('GUS::PluginMgr::GusApplicat ion=3DHASH(0x8f74180)', > 'ARRAY(0x8f74924)') called at /home/oragus35/GUS/gus_home/bin/ga > line 11 > =20 > > =20 > =20 > ---------------------------------------------------------------------- > -- > > Using Tomcat but need to do more? Need to support web services, security? > Get stuff done quickly with pre-integrated technology to make your job > easier Download IBM WebSphere Application Server v.1.0.1 based on=20 > Apache Geronimo > = http://sel.as-us.falkag.net/sel?cmd=3Dlnk&kid=3D120709&bid=3D263057&dat=3D= 1216 > 42 > ---------------------------------------------------------------------- > -- > > _______________________________________________ > Gusdev-gusdev mailing list > Gus...@li... > https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev > =20 |
From: Steve F. <sfi...@pc...> - 2006-07-07 21:53:27
|
sanjeev- how big is the file you are trying to load? i want to take a look at it. is it in genbank? what is its accession? can you send the command line? steve Kumar, Sanjeev wrote: > Hi Group, > I am getting following error when I am trying to load one > influenza sequence using "InsertSequenceFeature' plugin. > I am not able to figure out the reason of the failure. I need your > assistance, any help will be appreciated. > The sequence file is attached. > > > Thanks > Sanjeev Kumar > Northrop Grumman > > ERROR: > > ------------- EXCEPTION ------------- > *MSG: structure_type 2 is currently unknown > *STACK Bio::SeqFeature::Tools::Unflattener::unflatten_seq > /home/oragus35/perl/lib/site_perl/5.8.7/Bio/SeqFeature/Tools/Unflattener.pm:1419 > STACK GUS::Supported::Plugin::InsertSequenceFeatures::unflatten > /home/oragus35/GUS/gus_home/lib/perl/GUS/Supported/Plugin/InsertSequenceFeatures.pm:383 > STACK GUS::Supported::Plugin::InsertSequenceFeatures::run > /home/oragus35/GUS/gus_home/lib/perl/GUS/Supported/Plugin/InsertSequenceFeatures.pm:358 > STACK (eval) > /home/oragus35/GUS/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm:469 > STACK GUS::PluginMgr::GusApplication::doMajorMode_RunOrReport > /home/oragus35/GUS/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm:461 > STACK GUS::PluginMgr::GusApplication::doMajorMode_Run > /home/oragus35/GUS/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm:380 > STACK GUS::PluginMgr::GusApplication::doMajorMode > /home/oragus35/GUS/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm:288 > STACK GUS::PluginMgr::GusApplication::parseAndRun > /home/oragus35/GUS/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm:197 > STACK toplevel /home/oragus35/GUS/gus_home/bin/ga:11 > -------------------------------------- > STACK TRACE: > at /home/oragus35/perl/lib/site_perl/5.8.7/Bio/Root/Root.pm line 342 > > Bio::Root::Root::throw('Bio::SeqFeature::Tools::Unflattener=HASH(0xa237d08)', > 'structure_type 2 is currently unknown') called at > /home/oragus35/perl/lib/site_perl/5.8.7/Bio/SeqFeature/Tools/Unflattener.pm > line 1419 > > Bio::SeqFeature::Tools::Unflattener::unflatten_seq('Bio::SeqFeature::Tools::Unflattener=HASH(0xa237d08)', > '-seq', 'Bio::Seq::RichSeq=HASH(0x9febe2c)', '-use_magic', 1) > called at > /home/oragus35/GUS/gus_home/lib/perl/GUS/Supported/Plugin/InsertSequenceFeatures.pm > line 383 > > GUS::Supported::Plugin::InsertSequenceFeatures::unflatten('GUS::Supported::Plugin::InsertSequenceFeatures=HASH(0x9414bf0)', > 'Bio::Seq::RichSeq=HASH(0x9febe2c)') called at > /home/oragus35/GUS/gus_home/lib/perl/GUS/Supported/Plugin/InsertSequenceFeatures.pm > line 358 > > GUS::Supported::Plugin::InsertSequenceFeatures::run('GUS::Supported::Plugin::InsertSequenceFeatures=HASH(0x9414bf0)', > 'HASH(0x9ef7284)') called at > /home/oragus35/GUS/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm > line 469 > eval {...} called at > /home/oragus35/GUS/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm > line 461 > > GUS::PluginMgr::GusApplication::doMajorMode_RunOrReport('GUS::PluginMgr::GusApplication=HASH(0x8f74180)', > 'GUS::Supported::Plugin::InsertSequenceFeatures', 1) called at > /home/oragus35/GUS/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm > line 380 > > GUS::PluginMgr::GusApplication::doMajorMode_Run('GUS::PluginMgr::GusApplication=HASH(0x8f74180)', > 'GUS::Supported::Plugin::InsertSequenceFeatures') called at > /home/oragus35/GUS/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm > line 288 > > GUS::PluginMgr::GusApplication::doMajorMode('GUS::PluginMgr::GusApplication=HASH(0x8f74180)', > 'GUS::Supported::Plugin::InsertSequenceFeatures') called at > /home/oragus35/GUS/gus_home/lib/perl/GUS/PluginMgr/GusApplication.pm > line 197 > > GUS::PluginMgr::GusApplication::parseAndRun('GUS::PluginMgr::GusApplication=HASH(0x8f74180)', > 'ARRAY(0x8f74924)') called at /home/oragus35/GUS/gus_home/bin/ga > line 11 > > > > > ------------------------------------------------------------------------ > > Using Tomcat but need to do more? Need to support web services, security? > Get stuff done quickly with pre-integrated technology to make your job easier > Download IBM WebSphere Application Server v.1.0.1 based on Apache Geronimo > http://sel.as-us.falkag.net/sel?cmd=lnk&kid=120709&bid=263057&dat=121642 > ------------------------------------------------------------------------ > > _______________________________________________ > Gusdev-gusdev mailing list > Gus...@li... > https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev > |
From: marc j. <de...@ho...> - 2006-07-07 18:51:57
|
Hello, 1. I didn't not see your response angel. Could you try again. 2. I believe you asked for some info. [ I sent a message to s specific user and he indicated you had responded. ] I used the command: build GUS install -append. According to the install doc this should not touch the database. My output is: build GUS install -append ant -f /opt/gus/project_home/install/build.xml install -Dproj=GUS -DtargetDir=/opt/gus/gus_home -Dcomp= -DprojectsDir=/opt/gus/project_home -Dappend=true -logger org.apache.tools.ant.NoBannerLogger | grep ']' BUILD FAILED /opt/gus/project_home/install/build.xml:26: The following error occurred while executing this line: java.io.FileNotFoundException: /opt/gus/project_home/GUS/build.xml (No such file or directory) of course there is no /opt/gus/project_home/GUS/build.xml restoring that from tape now. Regards, Marc |
From: Debora C. <deb...@gm...> - 2006-07-07 03:21:29
|
Hi all ! I'm trying to install GUS on Oracle 10g Express Edition, but I'm getting an error. /home/djs/GUS/project_home/GusSchema/build.xml:62: java.lan.IllegalArgumentException: No enum const class org.gudb.admin.model.Cikumn$ColumnType.Date. Please help me ! Thanks Debora |
From: Angel P. <an...@ma...> - 2006-07-06 14:17:50
|
FIRST -- You probably do not want to mess with your data, so I suggest that you disable all read-write-dba access for your login while you do this. SECOND -- rule out the obvious for us and make sure: - you have write access to the target dir, - the gus properties file is filled out currectly, all env are correct. THIRD -- try it again and give us (copy/paste) the command line and any error messages you get. Cheers, Angel On Thursday 06 July 2006 09:51, marc jackson wrote: > Hello, > > > We have a small problem. The GUS database is still working, but gus_home > is no longer available. > I tried doing a "build" with the flag append, but it's failing. What is > the best way to re-make gus_home? > > Regards, > > Marc > > > > Using Tomcat but need to do more? Need to support web services, security? > Get stuff done quickly with pre-integrated technology to make your job > easier Download IBM WebSphere Application Server v.1.0.1 based on Apache > Geronimo > http://sel.as-us.falkag.net/sel?cmd=lnk&kid=120709&bid=263057&dat=121642 > _______________________________________________ > Gusdev-gusdev mailing list > Gus...@li... > https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev -- Angel Pizarro Director, Bioinformatics Facility Institute for Translational Medicine and Therapeutics University of Pennsylvania 806 BRB II/III 421 Curie Blvd. Philadelphia, PA 19104-6160 P: 215-573-3736 F: 215-573-9004 E: an...@ma... |
From: marc j. <de...@ho...> - 2006-07-06 13:51:28
|
Hello, We have a small problem. The GUS database is still working, but gus_home is no longer available. I tried doing a "build" with the flag append, but it's failing. What is the best way to re-make gus_home? Regards, Marc |
From: Elisabetta M. <man...@pc...> - 2006-06-24 00:59:03
|
Hi Michael, I don't think you got a bad download. There are plugins that have been placed into the repository subsequently to the GUS 3.5 release. Those that came with the 3.5 release should all be plugins that have been tested to work with 3.5. Of those which entered the repository after the release, some might work with 3.5, but some might require higher versions of the schema. Elisabetta --- On Thu, 22 Jun 2006 mro...@cs... wrote: > Folks: > > I need some help. > > We installed gusDB 3.5 (current version), with it we got 19 plugins, > however at location: > > https://www.cbil.upenn.edu/svn/gus/GusAppFramework/trunk/Supported/plugin/perl/ > > I found 36 plugins. > > Are these 36 plugins for comming version 4.0 or could it be that I got a > bad download, or maybe these are patches to be applied to the current > version? > > The plugins that are in common in both sections have different sizes > except for 2 of them. > > > Cheers, > Michael Robinson > Bioinformatics Research Group (BioRG) > Florida International University > Miami FL 33199 > > > > Using Tomcat but need to do more? Need to support web services, security? > Get stuff done quickly with pre-integrated technology to make your job easier > Download IBM WebSphere Application Server v.1.0.1 based on Apache Geronimo > http://sel.as-us.falkag.net/sel?cmd=lnk&kid=120709&bid=263057&dat=121642 > _______________________________________________ > Gusdev-gusdev mailing list > Gus...@li... > https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev > |
From: <mro...@cs...> - 2006-06-22 22:02:10
|
Folks: I need some help. We installed gusDB 3.5 (current version), with it we got 19 plugins, however at location: https://www.cbil.upenn.edu/svn/gus/GusAppFramework/trunk/Supported/plugin= /perl/ I found 36 plugins. Are these 36 plugins for comming version 4.0 or could it be that I got a bad download, or maybe these are patches to be applied to the current version? The plugins that are in common in both sections have different sizes except for 2 of them. Cheers, Michael Robinson Bioinformatics Research Group (BioRG) Florida International University Miami FL 33199 |
From: <mro...@cs...> - 2006-06-13 19:17:38
|
Thank you very much. It worked perfectly, I just adjusted the regular expressions to match my data. My data was a fasta data file and this was the adjustment: --regexSourceId '>(\S+)\s' Is there a place where I can obtain samples of how to run all Plugins? Thanks again Michael Robinson Bioinformatics Research Group (BioRG) Florida International University Miami FL 33199 > Send Gusdev-gusdev mailing list submissions to > gus...@li... > > To subscribe or unsubscribe via the World Wide Web, visit > https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev > or, via email, send a message with subject or body 'help' to > gus...@li... > > You can reach the person managing the list at > gus...@li... > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of Gusdev-gusdev digest..." > > > Today's Topics: > > 1. LoadFastaSequences.pm (mro...@cs...) > 2. Re: LoadFastaSequences.pm (Mark S. Heiges) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Mon, 12 Jun 2006 20:18:48 -0400 (EDT) > From: mro...@cs... > Subject: [GUSDEV] LoadFastaSequences.pm > To: gus...@li... > Message-ID: <196...@ww...> > Content-Type: text/plain;charset=3Diso-8859-1 > > Folks: > > I am trying to run the LoadFastaSequences.pm plugin to add a sequence. > > The results from running LoadFastaSequences.pm --help are not very clea= r > to me. > > According to the instructions only 3 attributes are required, but I fou= nd > that it is not so, Gus wants data for other attributes, I am up to 7 so > far and is asking for more. > > Does anybody have a detailed listing with examples, of how Gus wants th= e > attributes when running the LoadFastaSequences.pm plugin? > > Cheers, > Michael Robinson > Bioinformatics Research Group (BioRG) > Florida International University > Miami FL 33199 > > > > > > ------------------------------ > > Message: 2 > Date: Mon, 12 Jun 2006 20:42:34 -0400 > From: "Mark S. Heiges" <mh...@ug...> > Subject: Re: [GUSDEV] LoadFastaSequences.pm > To: GUS-Dev gusdev-gusdev <gus...@li...> > Message-ID: <1B6...@ug...> > Content-Type: text/plain; charset=3DUS-ASCII; delsp=3Dyes; format=3Dflo= wed > > Here is one example. > > ga GUS::Supported::Plugin::LoadFastaSequences \ > --externalDatabaseName 'C. parvum ORF50' \ > --externalDatabaseVersion '2006-01-24' \ > --sequenceFile /home/mheiges/CparvumORF50.fsa \ > --regexSourceId '^>([^\t]+)\t[^\t]+\t[^\t]+$' \ > --regexSecondaryId '^>[^\t]+\t([^\t]+)\t[^\t]+$' \ > --regexChromosome '^>[^\t]+\t[^\t]+\t([^\t]+)$' \ > --tableName 'DoTS::TranslatedAASequence' \ > --commit > > > regexSecondaryId and regexChromosome are optional. > > > On Jun 12, 2006, at 8:18 PM, mro...@cs... wrote: > >> Folks: >> >> I am trying to run the LoadFastaSequences.pm plugin to add a sequence. >> >> The results from running LoadFastaSequences.pm --help are not very >> clear >> to me. >> >> According to the instructions only 3 attributes are required, but I >> found >> that it is not so, Gus wants data for other attributes, I am up to >> 7 so >> far and is asking for more. >> >> Does anybody have a detailed listing with examples, of how Gus >> wants the >> attributes when running the LoadFastaSequences.pm plugin? >> >> Cheers, >> Michael Robinson >> Bioinformatics Research Group (BioRG) >> Florida International University >> Miami FL 33199 >> >> >> >> >> _______________________________________________ >> Gusdev-gusdev mailing list >> Gus...@li... >> https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev > > > > > ------------------------------ > > > > ------------------------------ > > _______________________________________________ > Gusdev-gusdev mailing list > Gus...@li... > https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev > > > End of Gusdev-gusdev Digest, Vol 1, Issue 797 > ********************************************* > |
From: Mark S. H. <mh...@ug...> - 2006-06-13 00:42:40
|
Here is one example. ga GUS::Supported::Plugin::LoadFastaSequences \ --externalDatabaseName 'C. parvum ORF50' \ --externalDatabaseVersion '2006-01-24' \ --sequenceFile /home/mheiges/CparvumORF50.fsa \ --regexSourceId '^>([^\t]+)\t[^\t]+\t[^\t]+$' \ --regexSecondaryId '^>[^\t]+\t([^\t]+)\t[^\t]+$' \ --regexChromosome '^>[^\t]+\t[^\t]+\t([^\t]+)$' \ --tableName 'DoTS::TranslatedAASequence' \ --commit regexSecondaryId and regexChromosome are optional. On Jun 12, 2006, at 8:18 PM, mro...@cs... wrote: > Folks: > > I am trying to run the LoadFastaSequences.pm plugin to add a sequence. > > The results from running LoadFastaSequences.pm --help are not very > clear > to me. > > According to the instructions only 3 attributes are required, but I > found > that it is not so, Gus wants data for other attributes, I am up to > 7 so > far and is asking for more. > > Does anybody have a detailed listing with examples, of how Gus > wants the > attributes when running the LoadFastaSequences.pm plugin? > > Cheers, > Michael Robinson > Bioinformatics Research Group (BioRG) > Florida International University > Miami FL 33199 > > > > > _______________________________________________ > Gusdev-gusdev mailing list > Gus...@li... > https://lists.sourceforge.net/lists/listinfo/gusdev-gusdev |