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HIV Study Tutorial
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"cpas[1].log.1" attached to message "CPAS MS2 problem"

24 Feb 2006 21:08:31,570 DEBUG FastaDbLoader : Fri Feb 24 21:08:31 PST 2006 Entering insertIdentifiers, before collecting unparsed identifiers from temp table 24 Feb 2006 21:09:20,804 DEBUG FastaDbLoader : Fri Feb 24 21:09:20 PST 2006 In insertIdentifiers, before inserting parsed identifier batch into temp table 24 Feb 2006 21:09:24,773 DEBUG FastaDbLoader : Fri Feb 24 21:09:24 PST 2006 In insertIdentifiers,...

"Bovine_mini.fasta" attached to message "Error XTandem Search XInteract"

>gi|15674171|30S_ribosomal_pro gi|15674171|ref|NP_268346.1| 30S ribosomal protein S18 [Lactococcus lactis subsp. lactis]�gi|13878750|sp|Q9CDN0|RS18_LACLA 30S ribosomal protein S18�gi|25294831|pir||E86898 30S ribosomal protein S18 [imported] - Lactococcus lactis subsp. lactis (strain IL1403)�gi|12725253|gb|AAK06287.1|AE006448_5 30S ribosomal protein S18 [Lactococcus lactis subsp. lactis] [MASS=9371]...

"SmallCAT.log" attached to message "Mascot error in CPAS"

12 Mar 2008 13:31:29,876 INFO : Mascot search for SmallICAT.mzXML 12 Mar 2008 13:31:29,878 INFO : ======================================= 12 Mar 2008 13:31:29,945 INFO : MzXML2Search output 12 Mar 2008 13:31:29,952 INFO : ======================================= 12 Mar 2008 13:31:30,804 INFO : running: MzXML2Search -mgf SmallICAT.mzXML 12 Mar 2008 13:31:30,845 INFO : 12 Mar 2008 13:31:30,846 INFO...

"09FEB02_OT_57.log" attached to message "Java Heap Memory Errors"

03 Nov 2010 17:25:47,334 INFO : Starting to run task 'org.labkey.ms2.pipeline.mascot.MascotSearchTask' at location 'webserver' 03 Nov 2010 17:25:47,334 INFO : Copying E:\Sandy\Dhaval\Controls\@files\Control\09FEB02_OT_57.mzXML to E:\Sandy\Dhaval\Controls\@files\Control\mascot\PSD_protocol_Copy9\09FEB02_OT_57.work\09FEB02_OT_57.mzXML 03 Nov 2010 17:25:47,397 INFO : MzXML2Search output 03 Nov 2010...

"cpas.log" attached to message "error executing /_views/HomeTemplate.gm"

19 Jan 2006 15:00:05,481 DEBUG ModuleLoader : ModuleLoader init 19 Jan 2006 15:00:05,613 DEBUG CoreModule : Ensuring databases are present 19 Jan 2006 15:00:05,738 DEBUG CoreModule : Successful connection to cpasDataSource at jdbc:postgresql://localhost:5432/cpas 19 Jan 2006 15:00:05,810 INFO DbSchema : Loading DbSchema "core" from "PostgreSQL" at "jdbc:postgresql://localhost:5432...

"ms2.module" attached to message "Mascot error in CPAS"

META-INF/MANIFEST.MF Manifest-Version: 1.0 Ant-Version: Apache Ant 1.6.5 Created-By: 1.5.0_06-b05 (Sun Microsystems Inc.) ModuleClass: org.labkey.ms2.MS2Module SVNRevision: Not built from a Subversion source tree SVNURL: Not built from a Subversion source tree BuildUser: CheeHong BuildTime: March 15 2008, 1:09 AM BuildOS: Windows XP BuildPath: F:\\CPL\\tor\\stedi\\branches\\release2.3\\server\\modules\...

"ms2.module" attached to message "Mascot error in CPAS"

META-INF/MANIFEST.MF Manifest-Version: 1.0 Ant-Version: Apache Ant 1.6.5 Created-By: 1.5.0_06-b05 (Sun Microsystems Inc.) ModuleClass: org.labkey.ms2.MS2Module SVNRevision: Not built from a Subversion source tree SVNURL: Not built from a Subversion source tree BuildUser: CheeHong BuildTime: March 12 2008, 6:05 PM BuildOS: Windows XP BuildPath: F:\\CPL\\tor\\stedi\\branches\\release2.3\\server\\modules\...

"G24_MSMS_1614.9180_11.t2d.mzXML" attached to message "Help on t2d format"

QFF5B8UIsWsAAAAAAAAAAEBRea/7Spu8AAAAAAAAAABAUXpYNLgyggAAAAAAAAAAQFF7AHFRddkAAAAAAAAAAEBRe6ixFmXgQBCgoKAAAABAUXxQ9AcCskA0AAAAAAAAQFF8+TojTiJAKlpaYAAAAEBRfaGDa0TnQCG5ucAAAABAUX5Jz97qgj/rm5ugAAAAQFF+8h9+PWE/4ZGRoAAAAEBRf5pyST2eP84eHkAAAABAUYBCyD/rWj+0FBQgAAAAQFGA6yFiSGIAAAAAAAAAAEBRgZN9sFMjAAAAAAAAAABAUYI73SoKBAAAAAAAAAAAQFGC5D/PcI4AAAAAAAAAAEBRg4yloIUmAAAAAAAAAABAUYQ1Dp1H7AAAAAAAAAAAQFGE3XrFuPwAAAAAAAAAAEBRhYXqGdorAAAAAAAAAABAUYYuXJmoKQAAAAAAAAAAQFGG1tJFJoA...

"500_ Error Page .htm" attached to message "Server error upon automatic cohort creation"

Emory University Development LabKey Server DHO_Healthy Aging_Workspace ...

"FASTALoadError.log" attached to message "FASTA loading error"

09 May 2007 09:11:16,625 INFO : Sequest search for CNBr_Hse2 09 May 2007 09:11:16,625 INFO : ======================================= 09 May 2007 09:11:17,015 INFO : MzXML2Search output 09 May 2007 09:11:17,015 INFO : ======================================= 09 May 2007 09:11:17,625 INFO : running: MzXML2Search -dta -M2 -C1-2-3 -P10 07-0199.mzXML 09 May 2007 09:11:19,531 INFO : 09 May 2007 09:11:19,531...

"Log.txt" attached to message "Not able to build the latest (25373) development version"

dhcp157184:LabKey cytomatic$ svn update At revision 25378. dhcp157184:LabKey cytomatic$ cd server/ dhcp157184:server cytomatic$ ant clean Buildfile: /Library/LabKey/server/build.xml stop_tomcat: [echo] Stopping tomcat. clean_build: prepare: ensure-tomcat-shutdown: [javac] Compiling 2 source files to /Library/LabKey/server/test/build/classes [javac] Note: /Library/LabKey/server/test...

"CompareRuns_QueryBeta_2007-11-16 12_40_25.034.xls" attached to message "IPI repeated in Search Engine Comparison"

data Best Name Seq Id Description First IPI interact-GLHDLT5D.pep.xml (interact-GLHDLT5D.prot.xml) Group interact-GLHDLT5D.pep.xml (interact-GLHDLT5D.prot.xml) Prob interact-GLHDLT5D.pep.xml (interact-GLHDLT5D.prot.xml) Peptides interact-GLHDLT5C.pep.xml (interact-GLHDLT5C.prot.xml) Group interact-GLHDLT5C.pep.xml (interact-GLHDLT5C.prot.xml) Prob interact-GLHDLT5C.pep.xml (interact-GLHDLT5C.prot.xml)...

"o261_08mar17_02_sec9.log" attached to message "Xinteract being called with -d"..\..\.." errors out during XPressPeptideParser TPP xinteract ver 4.3.1"

25 Feb 2011 11:43:09,218 INFO : Mascot search for o261_08mar17_02_sec9 25 Feb 2011 11:43:09,218 INFO : ======================================= 25 Feb 2011 11:43:09,265 INFO : Starting to run task 'org.labkey.ms2.pipeline.FastaCheckTask' at location 'webserver-fasta-check' 25 Feb 2011 11:43:09,265 INFO : Check FASTA validity 25 Feb 2011 11:43:09,265 INFO : =======================================...

"logfile-error.txt" attached to message "NCBI database - annotatins problem?"

17 Dec 2010 16:53:15,752 INFO : Mascot search for 01 17 Dec 2010 16:53:15,752 INFO : ======================================= 17 Dec 2010 16:53:15,846 INFO : Starting to run task 'org.labkey.ms2.pipeline.FastaCheckTask' at location 'webserver-fasta-check' 17 Dec 2010 16:53:15,846 INFO : Check FASTA validity 17 Dec 2010 16:53:15,846 INFO : ======================================= 17 Dec 2010 16:53:15,846...

dataset5006.tsv

ParticipantId date QCStateLabel HIVWestern HIVStdAntibody HIVLoadIneq HIVLoadQuant HIVLoadQual HIVRapidTest HIVSourceLab 103866 2008-04-30 00:00:00.0 0 103866 2008-05-28 00:00:00.0 183255 103866 2008-06-25 00:00:00.0 38618 103866 2008-07-23 00:00:00.0 7774 103866 2008-08-20 00:00:00.0 3125 103866 2008-09-17 00:00:00.0 2489 103866 2008-11-12 00:00:00.0 ...

"MTP_A06.log" attached to message "Submitting search to Mascot server...Failed to find Mascot query file"

19 Jun 2009 11:51:49,085 INFO : Copying C:\Inetpub\wwwroot\ISB\data\LCMS_data\Argo_BS\RAW\MTP_A06.mzXML to C:\Inetpub\wwwroot\ISB\data\LCMS_data\Argo_BS\RAW\mascot\Argo_Mascot\MTP_A06.work\MTP_A06.mzXML 19 Jun 2009 11:52:23,225 INFO : MzXML2Search output 19 Jun 2009 11:52:24,507 INFO : ======================================= 19 Jun 2009 11:52:24,538 INFO : Working directory is C:\Inetpub\wwwroot\ISB\data\LCMS_data\Argo_BS\RAW\mascot\Argo_Mascot\MTP_A06.work...

"Integral_SCA#4.log.txt" attached to message "Problem with running sequest searching"

31 十月 2008 08:46:01,953 INFO : Sequest search for Integral_SCA#4 31 十月 2008 08:46:01,953 INFO : ======================================= 31 十月 2008 08:46:01,984 INFO : Check FASTA validity 31 十月 2008 08:46:01,984 INFO : ======================================= 31 十月 2008 08:46:01,984 INFO : Checking sequence file validity of C:\database\T.vaginalis_20050331.aa.fasta 31 十月 2008 08:46:04,937 INFO...

"mascot mod error Oct08.rtf" attached to message "problem with searching mascot with Mods"

20 Oct 2008 10:40:41,075 INFO : Mascot search for kjo63_08jul18_21_40prot_1to1_20uL 20 Oct 2008 10:40:41,075 INFO : ======================================= 20 Oct 2008 10:40:41,325 INFO : Check FASTA validity 20 Oct 2008 10:40:41,340 INFO : ======================================= 20 Oct 2008 10:40:41,356 INFO : 20 Oct 2008 10:40:49,981 INFO : MzXML2Search output 20 Oct 2008 10:40:49,981 INFO :...

"error.log" attached to message "Enzyme is not available in mascot seaching"

27 八月 2008 17:33:37,203 INFO : Check FASTA validity 27 八月 2008 17:33:37,203 INFO : ======================================= 27 八月 2008 17:33:37,203 INFO : 27 八月 2008 17:33:40,281 INFO : MzXML2Search output 27 八月 2008 17:33:40,281 INFO : ======================================= 27 八月 2008 17:33:40,281 INFO : running: MzXML2Search -mgf 080815_Yi_A_SCX_1.mzXML 27 八月 2008 17:33:40,546 INFO : 27...

"080207-2.log" attached to message "Basic Install Problem - Sequest Queue"

12 Feb 2009 16:02:21,640 INFO : Sequest search for 080207-2 12 Feb 2009 16:02:21,640 INFO : ======================================= 12 Feb 2009 16:02:22,171 INFO : Check FASTA validity 12 Feb 2009 16:02:22,171 INFO : ======================================= 12 Feb 2009 16:02:22,171 INFO : Checking sequence file validity of C:\database\uniprot-js614.fasta 12 Feb 2009 16:02:23,078 INFO : 12 Feb...