15 Nov 2011 10:56:33,081 INFO : X! Tandem search for MM_clICAT13 15 Nov 2011 10:56:33,082 INFO : ======================================= 15 Nov 2011 10:56:33,082 INFO : MM_clICAT13.mzXML 15 Nov 2011 10:56:33,753 INFO : Starting to run task 'org.labkey.ms2.pipeline.FastaCheckTask' at location 'webserver-fasta-check' 15 Nov 2011 10:56:33,766 INFO : Check FASTA validity 15 Nov 2011 10:56:33,766 INFO : ======================================= 15 Nov 2011 10:56:33,775 INFO : Checking sequence file validity of /extra/labkey/files/home/CPAS/demo/@files/databases/yeast.nci.20070223.fasta 15 Nov 2011 10:56:34,156 INFO : 15 Nov 2011 10:56:34,157 INFO : Successfully completed task 'org.labkey.ms2.pipeline.FastaCheckTask' 15 Nov 2011 10:56:34,447 INFO : Starting to run task 'org.labkey.ms2.pipeline.tandem.XTandemSearchTask' at location 'webserver' 15 Nov 2011 10:56:34,536 INFO : tandem.exe output 15 Nov 2011 10:56:34,536 INFO : ======================================= 15 Nov 2011 10:56:34,537 INFO : Working directory is /extra/labkey/files/home/CPAS/demo/@files/Peroxisomal_ICAT/xtandem/k_Yeast_ICAT/MM_clICAT13.work 15 Nov 2011 10:56:34,538 INFO : running: /labkey/tools/bin/tandem.exe input.xml 15 Nov 2011 10:56:34,965 INFO : 15 Nov 2011 10:56:34,966 INFO : X! TANDEM 2 (2007.07.01.3) 15 Nov 2011 10:56:34,966 INFO : 15 Nov 2011 10:56:36,543 INFO : Loading spectra ... loaded. 15 Nov 2011 10:56:36,544 INFO : Spectra matching criteria = 4799 15 Nov 2011 10:56:36,544 INFO : Pluggable scoring enabled. 15 Nov 2011 10:56:36,544 INFO : Starting threads . started. 15 Nov 2011 10:56:36,544 INFO : Computing models: 15 Nov 2011 10:57:25,176 INFO : Spectrum sequences modelled = 7 ks 15 Nov 2011 10:57:25,191 INFO : Model refinement: 15 Nov 2011 10:57:25,191 INFO : Creating report: 15 Nov 2011 10:57:25,308 INFO : initial calculations ..... done. 15 Nov 2011 10:57:25,308 INFO : sorting ..... done. 15 Nov 2011 10:57:25,449 INFO : finding repeats ..... done. 15 Nov 2011 10:57:25,453 INFO : evaluating results ..... done. 15 Nov 2011 10:57:25,465 INFO : calculating expectations ..... done. 15 Nov 2011 10:57:25,610 INFO : writing results ..... done. 15 Nov 2011 10:57:25,665 INFO : 15 Nov 2011 10:57:25,665 INFO : Valid models = 92 15 Nov 2011 10:57:25,668 INFO : 15 Nov 2011 10:57:25,668 INFO : 15 Nov 2011 10:57:25,676 INFO : Moving /extra/labkey/files/home/CPAS/demo/@files/Peroxisomal_ICAT/xtandem/k_Yeast_ICAT/MM_clICAT13.work/input.xml to /extra/labkey/files/home/CPAS/demo/@files/Peroxisomal_ICAT/xtandem/k_Yeast_ICAT/MM_clICAT13.input.xml 15 Nov 2011 10:57:25,684 INFO : Tandem2XML output 15 Nov 2011 10:57:25,684 INFO : ======================================= 15 Nov 2011 10:57:25,685 INFO : Working directory is /extra/labkey/files/home/CPAS/demo/@files/Peroxisomal_ICAT/xtandem/k_Yeast_ICAT/MM_clICAT13.work 15 Nov 2011 10:57:25,685 INFO : running: /labkey/tools/bin/Tandem2XML MM_clICAT13.xtan.xml MM_clICAT13_raw.pep.xml 15 Nov 2011 10:57:26,282 INFO : Moving /extra/labkey/files/home/CPAS/demo/@files/Peroxisomal_ICAT/xtandem/k_Yeast_ICAT/MM_clICAT13.work/MM_clICAT13.xtan.xml to /extra/labkey/files/home/CPAS/demo/@files/Peroxisomal_ICAT/xtandem/k_Yeast_ICAT/MM_clICAT13.xtan.xml 15 Nov 2011 10:57:26,282 INFO : Moving /extra/labkey/files/home/CPAS/demo/@files/Peroxisomal_ICAT/xtandem/k_Yeast_ICAT/MM_clICAT13.work/MM_clICAT13_raw.pep.xml to /extra/labkey/files/home/CPAS/demo/@files/Peroxisomal_ICAT/xtandem/k_Yeast_ICAT/MM_clICAT13_raw.pep.xml 15 Nov 2011 10:57:26,283 INFO : Successfully completed task 'org.labkey.ms2.pipeline.tandem.XTandemSearchTask' 15 Nov 2011 10:57:26,351 INFO : Starting to run task 'org.labkey.ms2.pipeline.TPPTask' at location 'webserver' 15 Nov 2011 10:57:26,448 INFO : xinteract output 15 Nov 2011 10:57:26,449 INFO : ======================================= 15 Nov 2011 10:57:26,449 INFO : Working directory is /extra/labkey/files/home/CPAS/demo/@files/Peroxisomal_ICAT/xtandem/k_Yeast_ICAT/MM_clICAT13.work 15 Nov 2011 10:57:26,449 INFO : running: /labkey/tools/bin/xinteract -x20 -Opt -nR -X-nC,9.0 -d"../../.." -NMM_clICAT13.pep.xml ../MM_clICAT13_raw.pep.xml 15 Nov 2011 10:57:26,494 INFO : 15 Nov 2011 10:57:26,494 INFO : /labkey/tools/bin/xinteract (TPP v4.3 JETSTREAM rev 1, Build 201102211837 (linux)) 15 Nov 2011 10:57:26,495 INFO : 15 Nov 2011 10:57:26,495 INFO : running: "InteractParser 'MM_clICAT13.pep.xml' '../MM_clICAT13_raw.pep.xml' -L'7'" 15 Nov 2011 10:57:26,865 INFO : file 1: ../MM_clICAT13_raw.pep.xml 15 Nov 2011 10:57:27,151 INFO : processed altogether 4206 results 15 Nov 2011 10:57:27,394 INFO : command completed in 1 sec 15 Nov 2011 10:57:27,394 INFO : 15 Nov 2011 10:57:27,394 INFO : running: "PeptideProphetParser 'MM_clICAT13.pep.xml' EXTRAITRS=20" 15 Nov 2011 10:57:27,566 INFO : (X! Tandem (k-score)) (icat) 15 Nov 2011 10:57:27,566 INFO : init with X! Tandem (k-score) trypsin 15 Nov 2011 10:57:27,695 INFO : MS Instrument info: Manufacturer: ThermoFinnigan, Model: LTQ, Ionization: ESI, Analyzer: Ion Trap, Detector: EMT 15 Nov 2011 10:57:27,695 INFO : 15 Nov 2011 10:57:27,696 INFO : PeptideProphet (TPP v4.3 JETSTREAM rev 1, Build 201102211837 (linux)) AKeller@ISB 15 Nov 2011 10:57:27,696 INFO : read in 465 1+, 1730 2+, 1910 3+, 0 4+, 0 5+, 0 6+, and 0 7+ spectra. 15 Nov 2011 10:57:27,696 INFO : Initialising statistical models ... 15 Nov 2011 10:57:27,696 INFO : negmean = -0.829845 15 Nov 2011 10:57:27,696 INFO : negmean = -1.4397 15 Nov 2011 10:57:27,697 INFO : negmean = -1.04047 15 Nov 2011 10:57:27,697 INFO : negmean = -0.2 15 Nov 2011 10:57:27,697 INFO : negmean = -0.2 15 Nov 2011 10:57:27,697 INFO : negmean = -0.2 15 Nov 2011 10:57:27,697 INFO : negmean = -0.2 15 Nov 2011 10:57:27,807 INFO : Iterations: .........10.........20......... 15 Nov 2011 10:57:27,808 INFO : WARNING: Mixture model quality test failed for charge (3+). 15 Nov 2011 10:57:27,810 INFO : model complete after 30 iterations 15 Nov 2011 10:57:28,081 INFO : command completed in 1 sec 15 Nov 2011 10:57:28,081 INFO : 15 Nov 2011 10:57:28,082 INFO : running: "ProphetModels.pl -i MM_clICAT13.pep.xml" 15 Nov 2011 10:57:29,414 INFO : Analyzing MM_clICAT13.pep.xml ... 15 Nov 2011 10:57:29,415 INFO : Parsing search results "/extra/labkey/files/home/CPAS/demo/@files/Peroxisomal_ICAT/MM_clICAT13 (X! Tandem (k-score))"... 15 Nov 2011 10:57:29,415 INFO : => Total of 207 hits. 15 Nov 2011 10:57:32,098 INFO : Warning: empty y range [0:0], adjusting to [0:1] 15 Nov 2011 10:57:32,110 INFO : Warning: empty y range [0:0], adjusting to [0:1] 15 Nov 2011 10:57:32,314 INFO : 15 Nov 2011 10:57:32,314 INFO : plot "MM_clICAT13.pep_IPPROB.tsv" using 2:1 title "iProphet" with line lc 2 , x notitle with line lt 0 lc -1 15 Nov 2011 10:57:32,314 INFO : ^ 15 Nov 2011 10:57:32,314 INFO : "MM_clICAT13.pep_IPPROB.gp", line 16: warning: Skipping data file with no valid points 15 Nov 2011 10:57:32,351 INFO : command completed in 4 sec 15 Nov 2011 10:57:32,352 INFO : 15 Nov 2011 10:57:32,352 INFO : running: "XPressPeptideParser 'MM_clICAT13.pep.xml' -nC,9.0 -d"../../.."" 15 Nov 2011 10:57:33,820 INFO : ........command completed in 1 sec 15 Nov 2011 10:57:33,821 INFO : 15 Nov 2011 10:57:33,821 INFO : running: "ProteinProphet 'MM_clICAT13.pep.xml' 'MM_clICAT13.prot.xml' XML NOPLOT" 15 Nov 2011 10:57:34,084 INFO : ProteinProphet (C++) by Insilicos LLC and LabKey Software, after the original Perl by A. Keller (TPP v4.3 JETSTREAM rev 1, Build 201102211837 (linux)) 15 Nov 2011 10:57:34,153 INFO : (xml input) (report Protein Length) (using degen pep info) 15 Nov 2011 10:57:34,154 INFO : . . . reading in /extra/labkey/files/home/CPAS/demo/@files/Peroxisomal_ICAT/xtandem/k_Yeast_ICAT/MM_clICAT13.work/MM_clICAT13.pep.xml. . . 15 Nov 2011 10:57:34,162 INFO : . . . read in 76 1+, 131 2+, 0 3+, 0 4+, 0 5+, 0 6+, 0 7+ spectra with min prob 0.05 15 Nov 2011 10:57:34,386 INFO : INFO: mu=9.58194e-06, db_size=6682437 15 Nov 2011 10:57:34,409 INFO : command completed in 1 sec 15 Nov 2011 10:57:34,410 INFO : 15 Nov 2011 10:57:34,410 INFO : running: "ProtProphModels.pl -i MM_clICAT13.prot.xml" 15 Nov 2011 10:57:34,518 INFO : Analyzing MM_clICAT13.prot.xml ... 15 Nov 2011 10:57:34,529 INFO : command completed in 0 sec 15 Nov 2011 10:57:34,529 INFO : 15 Nov 2011 10:57:34,529 INFO : running: "XPressProteinRatioParser 'MM_clICAT13.prot.xml'" 15 Nov 2011 10:57:34,688 INFO : XPressProteinRatioParser (TPP v4.3 JETSTREAM rev 1, Build 201102211837 (linux)) 15 Nov 2011 10:57:34,719 INFO : command completed in 0 sec 15 Nov 2011 10:57:34,719 INFO : InteractParser 'MM_clICAT13.pep.xml' '../MM_clICAT13_raw.pep.xml' -L'7' 1 sec 15 Nov 2011 10:57:34,719 INFO : PeptideProphetParser 'MM_clICAT13.pep.xml' EXTRAITRS=20 1 sec 15 Nov 2011 10:57:34,719 INFO : ProphetModels.pl -i MM_clICAT13.pep.xml 4 sec 15 Nov 2011 10:57:34,719 INFO : XPressPeptideParser 'MM_clICAT13.pep.xml' -nC,9.0 -d"../../.." 1 sec 15 Nov 2011 10:57:34,719 INFO : ProteinProphet 'MM_clICAT13.pep.xml' 'MM_clICAT13.prot.xml' XML NOPLOT 1 sec 15 Nov 2011 10:57:34,719 INFO : ProtProphModels.pl -i MM_clICAT13.prot.xml 0 sec 15 Nov 2011 10:57:34,720 INFO : XPressProteinRatioParser 'MM_clICAT13.prot.xml' 0 sec 15 Nov 2011 10:57:34,720 INFO : job completed in 8 sec 15 Nov 2011 10:57:34,725 INFO : Moving /extra/labkey/files/home/CPAS/demo/@files/Peroxisomal_ICAT/xtandem/k_Yeast_ICAT/MM_clICAT13.work/MM_clICAT13.pep.xml to /extra/labkey/files/home/CPAS/demo/@files/Peroxisomal_ICAT/xtandem/k_Yeast_ICAT/MM_clICAT13.pep.xml 15 Nov 2011 10:57:34,769 INFO : Moving /extra/labkey/files/home/CPAS/demo/@files/Peroxisomal_ICAT/xtandem/k_Yeast_ICAT/MM_clICAT13.work/MM_clICAT13.prot.xml to /extra/labkey/files/home/CPAS/demo/@files/Peroxisomal_ICAT/xtandem/k_Yeast_ICAT/MM_clICAT13.prot.xml 15 Nov 2011 10:57:34,770 INFO : Moving /extra/labkey/files/home/CPAS/demo/@files/Peroxisomal_ICAT/xtandem/k_Yeast_ICAT/MM_clICAT13.work/MM_clICAT13.pep_FVAL_2.png to /extra/labkey/files/home/CPAS/demo/@files/Peroxisomal_ICAT/xtandem/k_Yeast_ICAT/MM_clICAT13.pep_FVAL_2.png 15 Nov 2011 10:57:34,770 INFO : Moving /extra/labkey/files/home/CPAS/demo/@files/Peroxisomal_ICAT/xtandem/k_Yeast_ICAT/MM_clICAT13.work/MM_clICAT13.pep_PPPROB.png to /extra/labkey/files/home/CPAS/demo/@files/Peroxisomal_ICAT/xtandem/k_Yeast_ICAT/MM_clICAT13.pep_PPPROB.png 15 Nov 2011 10:57:34,771 INFO : Moving /extra/labkey/files/home/CPAS/demo/@files/Peroxisomal_ICAT/xtandem/k_Yeast_ICAT/MM_clICAT13.work/MM_clICAT13.pep_FVAL_4.png to /extra/labkey/files/home/CPAS/demo/@files/Peroxisomal_ICAT/xtandem/k_Yeast_ICAT/MM_clICAT13.pep_FVAL_4.png 15 Nov 2011 10:57:34,771 INFO : Moving /extra/labkey/files/home/CPAS/demo/@files/Peroxisomal_ICAT/xtandem/k_Yeast_ICAT/MM_clICAT13.work/MM_clICAT13.pep_FVAL_5.png to /extra/labkey/files/home/CPAS/demo/@files/Peroxisomal_ICAT/xtandem/k_Yeast_ICAT/MM_clICAT13.pep_FVAL_5.png 15 Nov 2011 10:57:34,771 INFO : Moving /extra/labkey/files/home/CPAS/demo/@files/Peroxisomal_ICAT/xtandem/k_Yeast_ICAT/MM_clICAT13.work/MM_clICAT13.pep_FVAL_3.png to /extra/labkey/files/home/CPAS/demo/@files/Peroxisomal_ICAT/xtandem/k_Yeast_ICAT/MM_clICAT13.pep_FVAL_3.png 15 Nov 2011 10:57:34,771 INFO : Moving /extra/labkey/files/home/CPAS/demo/@files/Peroxisomal_ICAT/xtandem/k_Yeast_ICAT/MM_clICAT13.work/MM_clICAT13.pep_IPPROB.png to /extra/labkey/files/home/CPAS/demo/@files/Peroxisomal_ICAT/xtandem/k_Yeast_ICAT/MM_clICAT13.pep_IPPROB.png 15 Nov 2011 10:57:34,772 INFO : Moving /extra/labkey/files/home/CPAS/demo/@files/Peroxisomal_ICAT/xtandem/k_Yeast_ICAT/MM_clICAT13.work/MM_clICAT13.pep_FVAL_1.png to /extra/labkey/files/home/CPAS/demo/@files/Peroxisomal_ICAT/xtandem/k_Yeast_ICAT/MM_clICAT13.pep_FVAL_1.png 15 Nov 2011 10:57:34,775 INFO : Successfully completed task 'org.labkey.ms2.pipeline.TPPTask' 15 Nov 2011 10:57:34,915 INFO : Starting to run task 'org.labkey.api.exp.pipeline.XarGeneratorId:expGeneratorSearch' at location 'webserver' 15 Nov 2011 10:57:34,916 INFO : Investigating files involved in experiment run 15 Nov 2011 10:57:34,917 INFO : File investigation complete 15 Nov 2011 10:57:35,206 DEBUG: Checking urn:lsid:cpas.fhcrc.org:Protocol.Folder-464:MS2.XTandemSearch to see if it is a match 15 Nov 2011 10:57:35,257 DEBUG: Wrong number of steps in existing protocol, expected 15 but was 14 15 Nov 2011 10:57:35,263 DEBUG: Checking urn:lsid:cpas.fhcrc.org:Protocol.Folder-464:MS2.XTandemSearch:2 to see if it is a match 15 Nov 2011 10:57:35,266 DEBUG: Wrong number of steps in existing protocol, expected 15 but was 0 15 Nov 2011 10:57:38,473 INFO : Existing action set with parent protocol LSID 'urn:lsid:cpas.fhcrc.org:Protocol.Folder-464:MS2.XTandemSearch:3' is referenced by other experiment runs, so it cannot be updated 15 Nov 2011 10:57:38,480 INFO : Existing protocol with LSID 'urn:lsid:cpas.fhcrc.org:Protocol.Folder-464:MS2.XTandemSearch:3' is referenced by other experiment runs, so it cannot be updated 15 Nov 2011 10:57:38,491 INFO : Existing protocol with LSID 'urn:lsid:cpas.fhcrc.org:Protocol.Folder-464:Check+FASTA' is referenced by other experiment runs, so it cannot be updated 15 Nov 2011 10:57:38,497 INFO : Existing protocol with LSID 'urn:lsid:cpas.fhcrc.org:Protocol.Folder-464:msPrefix' is referenced by other experiment runs, so it cannot be updated 15 Nov 2011 10:57:38,505 INFO : Existing protocol with LSID 'urn:lsid:cpas.fhcrc.org:Protocol.Folder-464:msPicture' is referenced by other experiment runs, so it cannot be updated 15 Nov 2011 10:57:38,513 INFO : Existing protocol with LSID 'urn:lsid:cpas.fhcrc.org:Protocol.Folder-464:X%21Tandem' is referenced by other experiment runs, so it cannot be updated 15 Nov 2011 10:57:38,524 INFO : Existing protocol with LSID 'urn:lsid:cpas.fhcrc.org:Protocol.Folder-464:Tandem2XML' is referenced by other experiment runs, so it cannot be updated 15 Nov 2011 10:57:38,531 INFO : Existing protocol with LSID 'urn:lsid:cpas.fhcrc.org:Protocol.Folder-464:PeptideProphet' is referenced by other experiment runs, so it cannot be updated 15 Nov 2011 10:57:38,539 INFO : Existing protocol with LSID 'urn:lsid:cpas.fhcrc.org:Protocol.Folder-464:Peptide+Quantitation' is referenced by other experiment runs, so it cannot be updated 15 Nov 2011 10:57:38,548 INFO : Existing protocol with LSID 'urn:lsid:cpas.fhcrc.org:Protocol.Folder-464:ProteinProphet' is referenced by other experiment runs, so it cannot be updated 15 Nov 2011 10:57:38,555 INFO : Existing protocol with LSID 'urn:lsid:cpas.fhcrc.org:Protocol.Folder-464:Protein+Quantitation' is referenced by other experiment runs, so it cannot be updated 15 Nov 2011 10:57:38,562 INFO : Existing protocol with LSID 'urn:lsid:cpas.fhcrc.org:Protocol.Folder-464:MS2.XTandemSearch.Output:3' is referenced by other experiment runs, so it cannot be updated 15 Nov 2011 10:57:38,577 INFO : Protocol with LSID 'urn:lsid:cpas.fhcrc.org:Protocol.Folder-464:MS2.XTandemSearch:3' matches a protocol with the same LSID that has already been loaded. 15 Nov 2011 10:57:38,592 INFO : Protocol with LSID 'urn:lsid:cpas.fhcrc.org:Protocol.Folder-464:Check+FASTA' matches a protocol with the same LSID that has already been loaded. 15 Nov 2011 10:57:38,605 INFO : Protocol with LSID 'urn:lsid:cpas.fhcrc.org:Protocol.Folder-464:msPrefix' matches a protocol with the same LSID that has already been loaded. 15 Nov 2011 10:57:38,616 INFO : Protocol with LSID 'urn:lsid:cpas.fhcrc.org:Protocol.Folder-464:msPicture' matches a protocol with the same LSID that has already been loaded. 15 Nov 2011 10:57:38,631 INFO : Protocol with LSID 'urn:lsid:cpas.fhcrc.org:Protocol.Folder-464:X%21Tandem' matches a protocol with the same LSID that has already been loaded. 15 Nov 2011 10:57:38,642 INFO : Protocol with LSID 'urn:lsid:cpas.fhcrc.org:Protocol.Folder-464:Tandem2XML' matches a protocol with the same LSID that has already been loaded. 15 Nov 2011 10:57:38,652 INFO : Protocol with LSID 'urn:lsid:cpas.fhcrc.org:Protocol.Folder-464:PeptideProphet' matches a protocol with the same LSID that has already been loaded. 15 Nov 2011 10:57:38,664 INFO : Protocol with LSID 'urn:lsid:cpas.fhcrc.org:Protocol.Folder-464:Peptide+Quantitation' matches a protocol with the same LSID that has already been loaded. 15 Nov 2011 10:57:38,677 INFO : Protocol with LSID 'urn:lsid:cpas.fhcrc.org:Protocol.Folder-464:ProteinProphet' matches a protocol with the same LSID that has already been loaded. 15 Nov 2011 10:57:38,690 INFO : Protocol with LSID 'urn:lsid:cpas.fhcrc.org:Protocol.Folder-464:Protein+Quantitation' matches a protocol with the same LSID that has already been loaded. 15 Nov 2011 10:57:38,702 INFO : Protocol with LSID 'urn:lsid:cpas.fhcrc.org:Protocol.Folder-464:MS2.XTandemSearch.Output:3' matches a protocol with the same LSID that has already been loaded. 15 Nov 2011 10:57:38,702 INFO : Protocol import complete 15 Nov 2011 10:57:38,702 INFO : 15 Nov 2011 10:57:38,821 INFO : Protocol action set import complete 15 Nov 2011 10:57:38,822 INFO : 15 Nov 2011 10:57:38,832 INFO : Found an existing entry for Data LSID urn:lsid:cpas.fhcrc.org:Data.Folder-464-Xar-0fb68037-f1d1-102e-95f1-987439a61584:MM_clICAT13.input.xml, not reloading its values from scratch 15 Nov 2011 10:57:38,835 INFO : Finished loading Data with LSID 'urn:lsid:cpas.fhcrc.org:Data.Folder-464-Xar-0fb68037-f1d1-102e-95f1-987439a61584:MM_clICAT13.input.xml' 15 Nov 2011 10:57:38,922 INFO : Found an existing entry for Data LSID urn:lsid:cpas.fhcrc.org:UploadedFile.Folder-464:6e8658bf-6acf-102e-ad11-56716a13a170, not reloading its values from scratch 15 Nov 2011 10:57:38,922 INFO : Finished loading Data with LSID 'urn:lsid:cpas.fhcrc.org:UploadedFile.Folder-464:6e8658bf-6acf-102e-ad11-56716a13a170' 15 Nov 2011 10:57:38,928 INFO : Found an existing entry for Data LSID urn:lsid:cpas.fhcrc.org:Data.Folder-464-Xar-0fb68037-f1d1-102e-95f1-987439a61584:tandem.xml, not reloading its values from scratch 15 Nov 2011 10:57:38,928 INFO : Finished loading Data with LSID 'urn:lsid:cpas.fhcrc.org:Data.Folder-464-Xar-0fb68037-f1d1-102e-95f1-987439a61584:tandem.xml' 15 Nov 2011 10:57:38,932 INFO : Found an existing entry for Data LSID urn:lsid:cpas.fhcrc.org:UploadedFile.Folder-464:6e8658db-6acf-102e-ad11-56716a13a170, not reloading its values from scratch 15 Nov 2011 10:57:38,932 INFO : Finished loading Data with LSID 'urn:lsid:cpas.fhcrc.org:UploadedFile.Folder-464:6e8658db-6acf-102e-ad11-56716a13a170' 15 Nov 2011 10:57:38,932 INFO : Starting input import complete 15 Nov 2011 10:57:38,932 INFO : 15 Nov 2011 10:57:38,933 WARN : Experiment run already exists, it will NOT be reimported, LSID 'urn:lsid:cpas.fhcrc.org:Run.Folder-464:0fb6803b-f1d1-102e-95f1-987439a61584' 15 Nov 2011 10:57:38,939 INFO : Experiment run import complete, LSID 'urn:lsid:cpas.fhcrc.org:Run.Folder-464:0fb6803b-f1d1-102e-95f1-987439a61584' 15 Nov 2011 10:57:38,939 INFO : 15 Nov 2011 10:57:38,954 INFO : Trying to load data file file:/extra/labkey/files/home/CPAS/demo/@files/Peroxisomal_ICAT/xtandem/k_Yeast_ICAT/MM_clICAT13.input.xml into the system 15 Nov 2011 10:57:38,956 INFO : No ExperimentDataHandler registered for data file file:/extra/labkey/files/home/CPAS/demo/@files/Peroxisomal_ICAT/xtandem/k_Yeast_ICAT/MM_clICAT13.input.xml, no special loading will be done on this file. 15 Nov 2011 10:57:38,956 INFO : Finished trying to load data file file:/extra/labkey/files/home/CPAS/demo/@files/Peroxisomal_ICAT/xtandem/k_Yeast_ICAT/MM_clICAT13.input.xml into the system 15 Nov 2011 10:57:38,956 INFO : Trying to load data file file:/extra/labkey/files/home/CPAS/demo/@files/Peroxisomal_ICAT/MM_clICAT13.mzXML into the system 15 Nov 2011 10:57:38,956 INFO : No ExperimentDataHandler registered for data file file:/extra/labkey/files/home/CPAS/demo/@files/Peroxisomal_ICAT/MM_clICAT13.mzXML, no special loading will be done on this file. 15 Nov 2011 10:57:38,956 INFO : Finished trying to load data file file:/extra/labkey/files/home/CPAS/demo/@files/Peroxisomal_ICAT/MM_clICAT13.mzXML into the system 15 Nov 2011 10:57:38,956 INFO : Trying to load data file file:/extra/labkey/files/home/CPAS/demo/@files/Peroxisomal_ICAT/xtandem/k_Yeast_ICAT/tandem.xml into the system 15 Nov 2011 10:57:38,958 INFO : No ExperimentDataHandler registered for data file file:/extra/labkey/files/home/CPAS/demo/@files/Peroxisomal_ICAT/xtandem/k_Yeast_ICAT/tandem.xml, no special loading will be done on this file. 15 Nov 2011 10:57:38,958 INFO : Finished trying to load data file file:/extra/labkey/files/home/CPAS/demo/@files/Peroxisomal_ICAT/xtandem/k_Yeast_ICAT/tandem.xml into the system 15 Nov 2011 10:57:38,958 INFO : Trying to load data file file:/extra/labkey/files/home/CPAS/demo/@files/databases/yeast.nci.20070223.fasta into the system 15 Nov 2011 10:57:38,959 INFO : No ExperimentDataHandler registered for data file file:/extra/labkey/files/home/CPAS/demo/@files/databases/yeast.nci.20070223.fasta, no special loading will be done on this file. 15 Nov 2011 10:57:38,959 INFO : Finished trying to load data file file:/extra/labkey/files/home/CPAS/demo/@files/databases/yeast.nci.20070223.fasta into the system 15 Nov 2011 10:57:38,959 INFO : Trying to load data file file:/extra/labkey/files/home/CPAS/demo/@files/Peroxisomal_ICAT/xtandem/k_Yeast_ICAT/MM_clICAT13.pep_FVAL_1.png into the system 15 Nov 2011 10:57:38,960 INFO : No ExperimentDataHandler registered for data file file:/extra/labkey/files/home/CPAS/demo/@files/Peroxisomal_ICAT/xtandem/k_Yeast_ICAT/MM_clICAT13.pep_FVAL_1.png, no special loading will be done on this file. 15 Nov 2011 10:57:38,960 INFO : Finished trying to load data file file:/extra/labkey/files/home/CPAS/demo/@files/Peroxisomal_ICAT/xtandem/k_Yeast_ICAT/MM_clICAT13.pep_FVAL_1.png into the system 15 Nov 2011 10:57:38,960 INFO : Trying to load data file file:/extra/labkey/files/home/CPAS/demo/@files/Peroxisomal_ICAT/xtandem/k_Yeast_ICAT/MM_clICAT13.pep_IPPROB.png into the system 15 Nov 2011 10:57:38,960 INFO : No ExperimentDataHandler registered for data file file:/extra/labkey/files/home/CPAS/demo/@files/Peroxisomal_ICAT/xtandem/k_Yeast_ICAT/MM_clICAT13.pep_IPPROB.png, no special loading will be done on this file. 15 Nov 2011 10:57:38,960 INFO : Finished trying to load data file file:/extra/labkey/files/home/CPAS/demo/@files/Peroxisomal_ICAT/xtandem/k_Yeast_ICAT/MM_clICAT13.pep_IPPROB.png into the system 15 Nov 2011 10:57:38,960 INFO : Trying to load data file file:/extra/labkey/files/home/CPAS/demo/@files/Peroxisomal_ICAT/xtandem/k_Yeast_ICAT/MM_clICAT13.pep_FVAL_3.png into the system 15 Nov 2011 10:57:38,961 INFO : No ExperimentDataHandler registered for data file file:/extra/labkey/files/home/CPAS/demo/@files/Peroxisomal_ICAT/xtandem/k_Yeast_ICAT/MM_clICAT13.pep_FVAL_3.png, no special loading will be done on this file. 15 Nov 2011 10:57:38,961 INFO : Finished trying to load data file file:/extra/labkey/files/home/CPAS/demo/@files/Peroxisomal_ICAT/xtandem/k_Yeast_ICAT/MM_clICAT13.pep_FVAL_3.png into the system 15 Nov 2011 10:57:38,961 INFO : Trying to load data file file:/extra/labkey/files/home/CPAS/demo/@files/Peroxisomal_ICAT/xtandem/k_Yeast_ICAT/MM_clICAT13.pep_FVAL_5.png into the system 15 Nov 2011 10:57:38,961 INFO : No ExperimentDataHandler registered for data file file:/extra/labkey/files/home/CPAS/demo/@files/Peroxisomal_ICAT/xtandem/k_Yeast_ICAT/MM_clICAT13.pep_FVAL_5.png, no special loading will be done on this file. 15 Nov 2011 10:57:38,961 INFO : Finished trying to load data file file:/extra/labkey/files/home/CPAS/demo/@files/Peroxisomal_ICAT/xtandem/k_Yeast_ICAT/MM_clICAT13.pep_FVAL_5.png into the system 15 Nov 2011 10:57:38,961 INFO : Trying to load data file file:/extra/labkey/files/home/CPAS/demo/@files/Peroxisomal_ICAT/xtandem/k_Yeast_ICAT/MM_clICAT13.pep_FVAL_4.png into the system 15 Nov 2011 10:57:38,962 INFO : No ExperimentDataHandler registered for data file file:/extra/labkey/files/home/CPAS/demo/@files/Peroxisomal_ICAT/xtandem/k_Yeast_ICAT/MM_clICAT13.pep_FVAL_4.png, no special loading will be done on this file. 15 Nov 2011 10:57:38,962 INFO : Finished trying to load data file file:/extra/labkey/files/home/CPAS/demo/@files/Peroxisomal_ICAT/xtandem/k_Yeast_ICAT/MM_clICAT13.pep_FVAL_4.png into the system 15 Nov 2011 10:57:38,962 INFO : Trying to load data file file:/extra/labkey/files/home/CPAS/demo/@files/Peroxisomal_ICAT/xtandem/k_Yeast_ICAT/MM_clICAT13.pep_PPPROB.png into the system 15 Nov 2011 10:57:38,962 INFO : No ExperimentDataHandler registered for data file file:/extra/labkey/files/home/CPAS/demo/@files/Peroxisomal_ICAT/xtandem/k_Yeast_ICAT/MM_clICAT13.pep_PPPROB.png, no special loading will be done on this file. 15 Nov 2011 10:57:38,962 INFO : Finished trying to load data file file:/extra/labkey/files/home/CPAS/demo/@files/Peroxisomal_ICAT/xtandem/k_Yeast_ICAT/MM_clICAT13.pep_PPPROB.png into the system 15 Nov 2011 10:57:38,963 INFO : Trying to load data file file:/extra/labkey/files/home/CPAS/demo/@files/Peroxisomal_ICAT/xtandem/k_Yeast_ICAT/MM_clICAT13.pep_FVAL_2.png into the system 15 Nov 2011 10:57:38,963 INFO : No ExperimentDataHandler registered for data file file:/extra/labkey/files/home/CPAS/demo/@files/Peroxisomal_ICAT/xtandem/k_Yeast_ICAT/MM_clICAT13.pep_FVAL_2.png, no special loading will be done on this file. 15 Nov 2011 10:57:38,963 INFO : Finished trying to load data file file:/extra/labkey/files/home/CPAS/demo/@files/Peroxisomal_ICAT/xtandem/k_Yeast_ICAT/MM_clICAT13.pep_FVAL_2.png into the system 15 Nov 2011 10:57:38,963 INFO : Trying to load data file file:/extra/labkey/files/home/CPAS/demo/@files/Peroxisomal_ICAT/xtandem/k_Yeast_ICAT/MM_clICAT13.prot.xml into the system 15 Nov 2011 10:57:39,063 INFO : Starting to load ProteinProphet file /extra/labkey/files/home/CPAS/demo/@files/Peroxisomal_ICAT/xtandem/k_Yeast_ICAT/MM_clICAT13.prot.xml 15 Nov 2011 10:57:39,405 INFO : Resolved referenced PepXML file to /extra/labkey/files/home/CPAS/demo/@files/Peroxisomal_ICAT/xtandem/k_Yeast_ICAT/MM_clICAT13.pep.xml 15 Nov 2011 10:57:39,418 INFO : Starting import from MM_clICAT13.pep.xml 15 Nov 2011 10:57:39,623 INFO : Starting to clear out any previously imported data for MM_clICAT13.pep.xml 15 Nov 2011 10:57:40,643 INFO : 1.02 seconds to clear out any previously imported data for MM_clICAT13.pep.xml 15 Nov 2011 10:57:40,643 INFO : Starting to import FASTA file /extra/labkey/files/home/CPAS/demo/@files/databases/yeast.nci.20070223.fasta 15 Nov 2011 10:57:40,716 INFO : FASTA file "/extra/labkey/files/home/CPAS/demo/@files/databases/yeast.nci.20070223.fasta" not imported, but another file, '/usr/local/labkey/CPASDemo/databases/yeast.nci.20070223.fasta', has the same checksum 15 Nov 2011 10:57:40,810 INFO : 0.17 seconds to import FASTA file /extra/labkey/files/home/CPAS/demo/@files/databases/yeast.nci.20070223.fasta 15 Nov 2011 10:57:40,811 INFO : Starting to import peptide search results from file /extra/labkey/files/home/CPAS/demo/@files/Peroxisomal_ICAT/MM_clICAT13.mzXML 15 Nov 2011 10:57:40,812 INFO : Importing MS/MS results is 0% complete 15 Nov 2011 10:57:40,816 INFO : Starting to parse /extra/labkey/files/home/CPAS/demo/@files/Peroxisomal_ICAT/MM_clICAT13.mzXML to get scan counts 15 Nov 2011 10:57:42,892 INFO : Finished parsing /extra/labkey/files/home/CPAS/demo/@files/Peroxisomal_ICAT/MM_clICAT13.mzXML to get scan counts 15 Nov 2011 10:57:43,218 INFO : Importing MS/MS results is 1% complete 15 Nov 2011 10:57:43,339 INFO : Importing MS/MS results is 2% complete 15 Nov 2011 10:57:43,519 INFO : Importing MS/MS results is 3% complete 15 Nov 2011 10:57:43,605 INFO : Importing MS/MS results is 4% complete 15 Nov 2011 10:57:43,757 INFO : Importing MS/MS results is 5% complete 15 Nov 2011 10:57:43,802 INFO : Importing MS/MS results is 6% complete 15 Nov 2011 10:57:43,872 INFO : Importing MS/MS results is 7% complete 15 Nov 2011 10:57:43,889 INFO : Importing MS/MS results is 8% complete 15 Nov 2011 10:57:43,905 INFO : Importing MS/MS results is 9% complete 15 Nov 2011 10:57:43,932 INFO : Importing MS/MS results is 10% complete 15 Nov 2011 10:57:43,977 INFO : Importing MS/MS results is 11% complete 15 Nov 2011 10:57:43,996 INFO : Importing MS/MS results is 12% complete 15 Nov 2011 10:57:44,035 INFO : Importing MS/MS results is 13% complete 15 Nov 2011 10:57:44,116 INFO : Importing MS/MS results is 14% complete 15 Nov 2011 10:57:44,142 INFO : Importing MS/MS results is 15% complete 15 Nov 2011 10:57:44,187 INFO : Importing MS/MS results is 16% complete 15 Nov 2011 10:57:44,228 INFO : Importing MS/MS results is 17% complete 15 Nov 2011 10:57:44,260 INFO : Importing MS/MS results is 18% complete 15 Nov 2011 10:57:44,285 INFO : Importing MS/MS results is 19% complete 15 Nov 2011 10:57:44,326 INFO : Importing MS/MS results is 20% complete 15 Nov 2011 10:57:44,373 INFO : Importing MS/MS results is 21% complete 15 Nov 2011 10:57:44,534 INFO : Importing MS/MS results is 22% complete 15 Nov 2011 10:57:44,583 INFO : Importing MS/MS results is 23% complete 15 Nov 2011 10:57:44,706 INFO : Importing MS/MS results is 24% complete 15 Nov 2011 10:57:44,720 INFO : Importing MS/MS results is 25% complete 15 Nov 2011 10:57:44,818 INFO : Importing MS/MS results is 26% complete 15 Nov 2011 10:57:44,841 INFO : Importing MS/MS results is 27% complete 15 Nov 2011 10:57:44,860 INFO : Importing MS/MS results is 28% complete 15 Nov 2011 10:57:44,893 INFO : Importing MS/MS results is 29% complete 15 Nov 2011 10:57:44,917 INFO : Importing MS/MS results is 30% complete 15 Nov 2011 10:57:44,940 INFO : Importing MS/MS results is 31% complete 15 Nov 2011 10:57:44,959 INFO : Importing MS/MS results is 32% complete 15 Nov 2011 10:57:44,976 INFO : Importing MS/MS results is 33% complete 15 Nov 2011 10:57:44,997 INFO : Importing MS/MS results is 34% complete 15 Nov 2011 10:57:45,059 INFO : Importing MS/MS results is 35% complete 15 Nov 2011 10:57:45,114 INFO : Importing MS/MS results is 36% complete 15 Nov 2011 10:57:45,168 INFO : Importing MS/MS results is 37% complete 15 Nov 2011 10:57:45,218 INFO : Importing MS/MS results is 38% complete 15 Nov 2011 10:57:45,264 INFO : Importing MS/MS results is 39% complete 15 Nov 2011 10:57:45,278 INFO : Importing MS/MS results is 40% complete 15 Nov 2011 10:57:45,355 INFO : Importing MS/MS results is 41% complete 15 Nov 2011 10:57:45,411 INFO : Importing MS/MS results is 42% complete 15 Nov 2011 10:57:45,493 INFO : Importing MS/MS results is 43% complete 15 Nov 2011 10:57:45,515 INFO : Importing MS/MS results is 44% complete 15 Nov 2011 10:57:45,543 INFO : Importing MS/MS results is 45% complete 15 Nov 2011 10:57:45,588 INFO : Importing MS/MS results is 46% complete 15 Nov 2011 10:57:45,639 INFO : Importing MS/MS results is 47% complete 15 Nov 2011 10:57:45,658 INFO : Importing MS/MS results is 48% complete 15 Nov 2011 10:57:45,732 INFO : Importing MS/MS results is 49% complete 15 Nov 2011 10:57:45,785 INFO : Importing MS/MS results is 50% complete 15 Nov 2011 10:57:45,854 INFO : Importing MS/MS results is 51% complete 15 Nov 2011 10:57:45,879 INFO : Importing MS/MS results is 52% complete 15 Nov 2011 10:57:45,926 INFO : Importing MS/MS results is 53% complete 15 Nov 2011 10:57:45,948 INFO : Importing MS/MS results is 54% complete 15 Nov 2011 10:57:45,961 INFO : Importing MS/MS results is 55% complete 15 Nov 2011 10:57:45,982 INFO : Importing MS/MS results is 56% complete 15 Nov 2011 10:57:46,033 INFO : Importing MS/MS results is 57% complete 15 Nov 2011 10:57:46,047 INFO : Importing MS/MS results is 58% complete 15 Nov 2011 10:57:46,076 INFO : Importing MS/MS results is 59% complete 15 Nov 2011 10:57:46,124 INFO : Importing MS/MS results is 60% complete 15 Nov 2011 10:57:46,170 INFO : Importing MS/MS results is 61% complete 15 Nov 2011 10:57:46,246 INFO : Importing MS/MS results is 62% complete 15 Nov 2011 10:57:46,283 INFO : Importing MS/MS results is 63% complete 15 Nov 2011 10:57:46,350 INFO : Importing MS/MS results is 64% complete 15 Nov 2011 10:57:46,373 INFO : Importing MS/MS results is 65% complete 15 Nov 2011 10:57:46,434 INFO : Importing MS/MS results is 66% complete 15 Nov 2011 10:57:46,457 INFO : Importing MS/MS results is 67% complete 15 Nov 2011 10:57:46,475 INFO : Importing MS/MS results is 68% complete 15 Nov 2011 10:57:46,501 INFO : Importing MS/MS results is 69% complete 15 Nov 2011 10:57:46,552 INFO : Importing MS/MS results is 70% complete 15 Nov 2011 10:57:46,580 INFO : Importing MS/MS results is 71% complete 15 Nov 2011 10:57:46,606 INFO : Importing MS/MS results is 72% complete 15 Nov 2011 10:57:46,673 INFO : Importing MS/MS results is 73% complete 15 Nov 2011 10:57:46,719 INFO : Importing MS/MS results is 74% complete 15 Nov 2011 10:57:46,781 INFO : Importing MS/MS results is 75% complete 15 Nov 2011 10:57:46,801 INFO : Importing MS/MS results is 76% complete 15 Nov 2011 10:57:46,915 INFO : Importing MS/MS results is 77% complete 15 Nov 2011 10:57:46,951 INFO : Importing MS/MS results is 78% complete 15 Nov 2011 10:57:46,968 INFO : Importing MS/MS results is 79% complete 15 Nov 2011 10:57:46,992 INFO : Importing MS/MS results is 80% complete 15 Nov 2011 10:57:47,032 INFO : Importing MS/MS results is 81% complete 15 Nov 2011 10:57:47,056 INFO : Importing MS/MS results is 82% complete 15 Nov 2011 10:57:47,094 INFO : Importing MS/MS results is 83% complete 15 Nov 2011 10:57:47,121 INFO : Importing MS/MS results is 84% complete 15 Nov 2011 10:57:47,155 INFO : Importing MS/MS results is 85% complete 15 Nov 2011 10:57:47,222 INFO : Importing MS/MS results is 86% complete 15 Nov 2011 10:57:47,237 INFO : Importing MS/MS results is 87% complete 15 Nov 2011 10:57:47,260 INFO : Importing MS/MS results is 88% complete 15 Nov 2011 10:57:47,296 INFO : Importing MS/MS results is 89% complete 15 Nov 2011 10:57:47,338 INFO : Importing MS/MS results is 90% complete 15 Nov 2011 10:57:47,352 INFO : Importing MS/MS results is 91% complete 15 Nov 2011 10:57:47,400 INFO : Importing MS/MS results is 92% complete 15 Nov 2011 10:57:47,456 INFO : Importing MS/MS results is 93% complete 15 Nov 2011 10:57:47,511 INFO : Importing MS/MS results is 94% complete 15 Nov 2011 10:57:47,546 INFO : Importing MS/MS results is 95% complete 15 Nov 2011 10:57:47,609 INFO : Importing MS/MS results is 96% complete 15 Nov 2011 10:57:47,664 INFO : Importing MS/MS results is 97% complete 15 Nov 2011 10:57:47,716 INFO : Importing MS/MS results is 98% complete 15 Nov 2011 10:57:47,802 INFO : Importing MS/MS results is 99% complete 15 Nov 2011 10:57:47,868 INFO : Importing MS/MS results is 100% complete 15 Nov 2011 10:57:47,907 INFO : Spectra were not imported: pep.xml file included "pipeline, import spectra = no" or "pipeline, load spectra = no" setting. 15 Nov 2011 10:57:47,932 INFO : 7.12 seconds to import peptide search results from file /extra/labkey/files/home/CPAS/demo/@files/Peroxisomal_ICAT/MM_clICAT13.mzXML 15 Nov 2011 10:57:47,932 INFO : Starting to update SeqId column 15 Nov 2011 10:57:48,372 INFO : 0.44 seconds to update SeqId column 15 Nov 2011 10:57:48,372 INFO : Starting to update SequencePosition column 15 Nov 2011 10:57:48,492 INFO : 0.12 seconds to update SequencePosition column 15 Nov 2011 10:57:48,493 INFO : Starting to update peptide and spectrum counts 15 Nov 2011 10:57:48,646 INFO : 0.15 seconds to update peptide and spectrum counts 15 Nov 2011 10:57:48,647 INFO : ======================================== 15 Nov 2011 10:57:48,647 INFO : Summary of all timed tasks: 15 Nov 2011 10:57:48,647 INFO : 15 Nov 2011 10:57:48,662 INFO : 1.02 seconds to clear out any previously imported data 15 Nov 2011 10:57:48,662 INFO : 0.17 seconds to import FASTA file 15 Nov 2011 10:57:48,662 INFO : 7.12 seconds to import peptide search results 15 Nov 2011 10:57:48,662 INFO : 0.44 seconds to update SeqId column 15 Nov 2011 10:57:48,662 INFO : 0.12 seconds to update SequencePosition column 15 Nov 2011 10:57:48,662 INFO : 0.15 seconds to update peptide and spectrum counts 15 Nov 2011 10:57:48,662 INFO : 15 Nov 2011 10:57:48,662 INFO : 9.02 seconds to import "MM_clICAT13.pep.xml" 15 Nov 2011 10:57:48,663 INFO : ======================================== 15 Nov 2011 10:57:50,325 INFO : Starting to move data into ms2.PeptidesMemberships 15 Nov 2011 10:57:50,479 INFO : Finished with moving data into ms2.PeptidesMemberships after 154 ms 15 Nov 2011 10:57:50,479 INFO : Starting to move data into ms2.ProteinGroupMemberships 15 Nov 2011 10:57:51,108 INFO : Finished with moving data into ms2.ProteinGroupMemberships after 629 ms 15 Nov 2011 10:57:51,139 INFO : ProteinProphet file import finished successfully, 128 protein groups loaded 15 Nov 2011 10:57:51,155 INFO : ProteinProphet import took 12 seconds. 15 Nov 2011 10:57:51,155 INFO : Finished trying to load data file file:/extra/labkey/files/home/CPAS/demo/@files/Peroxisomal_ICAT/xtandem/k_Yeast_ICAT/MM_clICAT13.prot.xml into the system 15 Nov 2011 10:57:51,155 INFO : Trying to load data file file:/extra/labkey/files/home/CPAS/demo/@files/Peroxisomal_ICAT/xtandem/k_Yeast_ICAT/MM_clICAT13.pep.xml into the system 15 Nov 2011 10:57:51,252 INFO : Finished trying to load data file file:/extra/labkey/files/home/CPAS/demo/@files/Peroxisomal_ICAT/xtandem/k_Yeast_ICAT/MM_clICAT13.pep.xml into the system 15 Nov 2011 10:57:51,252 INFO : Trying to load data file file:/extra/labkey/files/home/CPAS/demo/@files/Peroxisomal_ICAT/xtandem/k_Yeast_ICAT/MM_clICAT13.xtan.xml into the system 15 Nov 2011 10:57:51,253 INFO : No ExperimentDataHandler registered for data file file:/extra/labkey/files/home/CPAS/demo/@files/Peroxisomal_ICAT/xtandem/k_Yeast_ICAT/MM_clICAT13.xtan.xml, no special loading will be done on this file. 15 Nov 2011 10:57:51,253 INFO : Finished trying to load data file file:/extra/labkey/files/home/CPAS/demo/@files/Peroxisomal_ICAT/xtandem/k_Yeast_ICAT/MM_clICAT13.xtan.xml into the system 15 Nov 2011 10:57:51,253 INFO : Trying to load data file file:/extra/labkey/files/home/CPAS/demo/@files/Peroxisomal_ICAT/xtandem/k_Yeast_ICAT/MM_clICAT13.pep.xml into the system 15 Nov 2011 10:57:51,326 INFO : Finished trying to load data file file:/extra/labkey/files/home/CPAS/demo/@files/Peroxisomal_ICAT/xtandem/k_Yeast_ICAT/MM_clICAT13.pep.xml into the system 15 Nov 2011 10:57:51,327 INFO : Trying to load data file file:/extra/labkey/files/home/CPAS/demo/@files/Peroxisomal_ICAT/xtandem/k_Yeast_ICAT/MM_clICAT13.pep.xml into the system 15 Nov 2011 10:57:51,422 INFO : Finished trying to load data file file:/extra/labkey/files/home/CPAS/demo/@files/Peroxisomal_ICAT/xtandem/k_Yeast_ICAT/MM_clICAT13.pep.xml into the system 15 Nov 2011 10:57:51,422 INFO : Trying to load data file file:/extra/labkey/files/home/CPAS/demo/@files/Peroxisomal_ICAT/MM_clICAT13.mzXML into the system 15 Nov 2011 10:57:51,423 INFO : No ExperimentDataHandler registered for data file file:/extra/labkey/files/home/CPAS/demo/@files/Peroxisomal_ICAT/MM_clICAT13.mzXML, no special loading will be done on this file. 15 Nov 2011 10:57:51,423 INFO : Finished trying to load data file file:/extra/labkey/files/home/CPAS/demo/@files/Peroxisomal_ICAT/MM_clICAT13.mzXML into the system 15 Nov 2011 10:57:51,423 INFO : Trying to load data file file:/extra/labkey/files/home/CPAS/demo/@files/Peroxisomal_ICAT/xtandem/k_Yeast_ICAT/MM_clICAT13_raw.pep.xml into the system 15 Nov 2011 10:57:51,423 WARN : Unable to find the data file /extra/labkey/files/home/CPAS/demo/@files/Peroxisomal_ICAT/xtandem/k_Yeast_ICAT/MM_clICAT13_raw.pep.xml on disk. 15 Nov 2011 10:57:51,423 INFO : Trying to load data file file:/extra/labkey/files/home/CPAS/demo/@files/Peroxisomal_ICAT/xtandem/k_Yeast_ICAT/MM_clICAT13.xtan.xml into the system 15 Nov 2011 10:57:51,424 INFO : No ExperimentDataHandler registered for data file file:/extra/labkey/files/home/CPAS/demo/@files/Peroxisomal_ICAT/xtandem/k_Yeast_ICAT/MM_clICAT13.xtan.xml, no special loading will be done on this file. 15 Nov 2011 10:57:51,424 INFO : Finished trying to load data file file:/extra/labkey/files/home/CPAS/demo/@files/Peroxisomal_ICAT/xtandem/k_Yeast_ICAT/MM_clICAT13.xtan.xml into the system 15 Nov 2011 10:57:51,424 INFO : Trying to load data file file:/extra/labkey/files/home/CPAS/demo/@files/Peroxisomal_ICAT/xtandem/k_Yeast_ICAT/MM_clICAT13.input.xml into the system 15 Nov 2011 10:57:51,424 INFO : No ExperimentDataHandler registered for data file file:/extra/labkey/files/home/CPAS/demo/@files/Peroxisomal_ICAT/xtandem/k_Yeast_ICAT/MM_clICAT13.input.xml, no special loading will be done on this file. 15 Nov 2011 10:57:51,424 INFO : Finished trying to load data file file:/extra/labkey/files/home/CPAS/demo/@files/Peroxisomal_ICAT/xtandem/k_Yeast_ICAT/MM_clICAT13.input.xml into the system 15 Nov 2011 10:57:51,424 INFO : Trying to load data file file:/extra/labkey/files/home/CPAS/demo/@files/databases/yeast.nci.20070223.fasta into the system 15 Nov 2011 10:57:51,424 INFO : No ExperimentDataHandler registered for data file file:/extra/labkey/files/home/CPAS/demo/@files/databases/yeast.nci.20070223.fasta, no special loading will be done on this file. 15 Nov 2011 10:57:51,424 INFO : Finished trying to load data file file:/extra/labkey/files/home/CPAS/demo/@files/databases/yeast.nci.20070223.fasta into the system 15 Nov 2011 10:57:51,425 INFO : Trying to load data file file:/extra/labkey/files/home/CPAS/demo/@files/Peroxisomal_ICAT/MM_clICAT13.mzXML into the system 15 Nov 2011 10:57:51,425 INFO : No ExperimentDataHandler registered for data file file:/extra/labkey/files/home/CPAS/demo/@files/Peroxisomal_ICAT/MM_clICAT13.mzXML, no special loading will be done on this file. 15 Nov 2011 10:57:51,425 INFO : Finished trying to load data file file:/extra/labkey/files/home/CPAS/demo/@files/Peroxisomal_ICAT/MM_clICAT13.mzXML into the system 15 Nov 2011 10:57:51,425 INFO : Trying to load data file file:/extra/labkey/files/home/CPAS/demo/@files/databases/yeast.nci.20070223.fasta into the system 15 Nov 2011 10:57:51,426 INFO : No ExperimentDataHandler registered for data file file:/extra/labkey/files/home/CPAS/demo/@files/databases/yeast.nci.20070223.fasta, no special loading will be done on this file. 15 Nov 2011 10:57:51,426 INFO : Finished trying to load data file file:/extra/labkey/files/home/CPAS/demo/@files/databases/yeast.nci.20070223.fasta into the system 15 Nov 2011 10:57:51,426 INFO : Trying to load data file file:/extra/labkey/files/home/CPAS/demo/@files/Peroxisomal_ICAT/xtandem/k_Yeast_ICAT/MM_clICAT13.input.xml into the system 15 Nov 2011 10:57:51,426 INFO : No ExperimentDataHandler registered for data file file:/extra/labkey/files/home/CPAS/demo/@files/Peroxisomal_ICAT/xtandem/k_Yeast_ICAT/MM_clICAT13.input.xml, no special loading will be done on this file. 15 Nov 2011 10:57:51,426 INFO : Finished trying to load data file file:/extra/labkey/files/home/CPAS/demo/@files/Peroxisomal_ICAT/xtandem/k_Yeast_ICAT/MM_clICAT13.input.xml into the system 15 Nov 2011 10:57:51,426 INFO : Trying to load data file file:/extra/labkey/files/home/CPAS/demo/@files/databases/yeast.nci.20070223.fasta into the system 15 Nov 2011 10:57:51,427 INFO : No ExperimentDataHandler registered for data file file:/extra/labkey/files/home/CPAS/demo/@files/databases/yeast.nci.20070223.fasta, no special loading will be done on this file. 15 Nov 2011 10:57:51,427 INFO : Finished trying to load data file file:/extra/labkey/files/home/CPAS/demo/@files/databases/yeast.nci.20070223.fasta into the system 15 Nov 2011 10:57:51,427 INFO : Trying to load data file file:/extra/labkey/files/home/CPAS/demo/@files/Peroxisomal_ICAT/MM_clICAT13.mzXML into the system 15 Nov 2011 10:57:51,428 INFO : No ExperimentDataHandler registered for data file file:/extra/labkey/files/home/CPAS/demo/@files/Peroxisomal_ICAT/MM_clICAT13.mzXML, no special loading will be done on this file. 15 Nov 2011 10:57:51,428 INFO : Finished trying to load data file file:/extra/labkey/files/home/CPAS/demo/@files/Peroxisomal_ICAT/MM_clICAT13.mzXML into the system 15 Nov 2011 10:57:51,428 INFO : Trying to load data file file:/extra/labkey/files/home/CPAS/demo/@files/Peroxisomal_ICAT/xtandem/k_Yeast_ICAT/tandem.xml into the system 15 Nov 2011 10:57:51,428 INFO : No ExperimentDataHandler registered for data file file:/extra/labkey/files/home/CPAS/demo/@files/Peroxisomal_ICAT/xtandem/k_Yeast_ICAT/tandem.xml, no special loading will be done on this file. 15 Nov 2011 10:57:51,428 INFO : Finished trying to load data file file:/extra/labkey/files/home/CPAS/demo/@files/Peroxisomal_ICAT/xtandem/k_Yeast_ICAT/tandem.xml into the system 15 Nov 2011 10:57:51,429 INFO : Successfully completed task 'org.labkey.api.exp.pipeline.XarGeneratorId:expGeneratorSearch'