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HIV Study Tutorial
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"cpas.log.1" attached to message "500: Unexpected server error"

03 Feb 2006 10:46:57,287 ERROR Global : Unhandled exception caught in Global.app: 500: Unexpected server error java.lang.RuntimeException: java.lang.reflect.InvocationTargetException at org.fhcrc.cpas.util.BoundMap.get(BoundMap.java:89) at org.fhcrc.cpas.view.GroovyView.createModelBinding(GroovyView.java:475) at org.fhcrc.cpas.view.GroovyView.renderView(GroovyView.java:447) at org.fhcrc.cpas.view.WebPartView.render(WebPartView.java:123)...

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

Emory University Development LabKey Server DHO_Healthy Aging_Workspace ...

HIV Test Results.xls

data Participant ID Group Assignment Country Gender Start Date Height Source Lsid Date Day HIV Western Blot Standard HIV Antibody Viral Load > = < Viral Load Quantified (copies/ml) Viral Load Qualitative Result HIV Rapid Blood Test Source of HIV Tests 103866 Group 1: Acute HIV-1 USA m 2008-04-21 69 2009-05-27 401 3 103866 Group 1: Acute HIV-1 USA m 2008-04-21 69 2009-06-24 429 15 103866...

"050727-Brachypodium-SDS-spot_418.xtan.xml" attached to message "FATAL: Upload FAILED"

Rs_BP|59353pri:N|_4 3e-19 UniRef90_Q948Y7 VMP3 protein related cluster QQTPTKTPRT GHSAIVQRWW RCSIQCHGRQ AGFCRTGDVR RQGSVNGSRE **DRRRRRGK WRGRAWRRGR AGGARGMAAW IGGARREGCR RGGATAESSR GGGGGGARER RPGGM*ARRG MRRAGSLWRG TVGGRGAAGR AAAGSGRGGG CRRRGRPRRS *RAPRGAPPG RSPPRWPQP* WRTPRP*RRP SRRAGGWPRP *GGRRRGVLS VALCPDEG 050727-Brachypodium-SDS-spot_418.mzXML scan 415 (charge 2) 1315.6...

Luminex_Assay_200-2015-06-09-1231.tsv

container date wellRole fiBackgroundNegative stdCurve fiOORIndicator specimenID type singlePointControl excluded samplingErrors protocol regressionType outlier resVar fiBackground fiBackgroundString dilution name extraSpecimenInfo stdDevOORIndicator expConc stdDev maxStandardRecovery obsConc fi obsConcOORIndicator minStandardRecovery obsConcString beadCount description lsid dataId fiString obsOverExp...

Luminex_Assay_200-2015-06-09-1230.tsv

container date wellRole fiBackgroundNegative stdCurve fiOORIndicator specimenID type singlePointControl excluded samplingErrors protocol regressionType outlier resVar fiBackground fiBackgroundString dilution name extraSpecimenInfo stdDevOORIndicator expConc stdDev maxStandardRecovery obsConc fi obsConcOORIndicator minStandardRecovery obsConcString beadCount description lsid dataId fiString obsOverExp...

Luminex_Assay_200-2015-06-09-1226.tsv

container date wellRole fiBackgroundNegative stdCurve fiOORIndicator specimenID type singlePointControl excluded samplingErrors protocol regressionType outlier resVar fiBackground fiBackgroundString dilution name extraSpecimenInfo stdDevOORIndicator expConc stdDev maxStandardRecovery obsConc fi obsConcOORIndicator minStandardRecovery obsConcString beadCount description lsid dataId fiString obsOverExp...

"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...

"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 ...

"catalina.out" attached to message "Labkey error"

Jun 12, 2015 3:31:55 PM org.apache.catalina.startup.VersionLoggerListener log INFO: Server version: Apache Tomcat/7.0.62 Jun 12, 2015 3:31:55 PM org.apache.catalina.startup.VersionLoggerListener log INFO: Server built: May 7 2015 17:14:55 UTC Jun 12, 2015 3:31:55 PM org.apache.catalina.startup.VersionLoggerListener log INFO: Server number: 7.0.62.0 Jun 12, 2015 3:31:55 PM org.apache.catalina.startup.VersionLoggerListener...

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

MIME-Version: 1.0 (Generated by Mascot version 1.0) Content-Type: multipart/mixed; boundary=gc0p4Jq0M2Yt08jU534c0p --gc0p4Jq0M2Yt08jU534c0p Content-Type: application/x-Mascot; name="parameters" LICENSE=Licensed to: NIH Central Mascot Server (263-MD-216066), (6 processors). MP= NM= COM=Conversion of E:\Sandy\Dhaval\Controls\@files\Control\mascot\PSD_protocol_Copy9\09FEB02_OT_57.work\09FEB02_OT_57.mzXML...

2020.12.03.408500v1.full.pdf

See discussions, stats, and author profiles for this publication at: https://www.researchgate.net/publication/346632754 An Integrated Clinical, Omic, and Image Atlas of an Evolving Metastatic Breast Cancer Preprint · December 2020 DOI: 10.1101/2020.12.03.408500 CITATIONS 0 READS 5 38 authors, including: Some of the authors of this publication are also working on these related projects: ...

"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...

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

30 八月 2008 20:43:36,171 INFO : Check FASTA validity 30 八月 2008 20:43:36,171 INFO : ======================================= 30 八月 2008 20:43:36,171 INFO : 30 八月 2008 20:43:37,156 INFO : MzXML2Search output 30 八月 2008 20:43:37,156 INFO : ======================================= 30 八月 2008 20:43:37,156 INFO : running: MzXML2Search -mgf 080815_Yi_A_SCX_10.mzXML 30 八月 2008 20:43:39,218 INFO : 30...