Download peptideshaker

Author: o | 2025-04-24

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Download file PeptideShaker-.zip - PeptideShaker

DevelopmentJmol Version: 12.0.43 2011-05-03 14:21java.vendor: Oracle Corporationjava.version: 1.8.0_102os.name: Windows 8.1memory: 51.1/163.1processors available: 12useCommandThread: falsePeptideShaker processing failed. See the PeptideShaker log for details.java.lang.IllegalArgumentException: Object 20160704_19_D_04.mgf_cus_File230635 Spectrum47895 scans: 26334 [S:\p2069\Proteomics\FUSION_1\seeschwalbe_20160704_MS_brain_HILIC_D\20160704_19_D_04.raw] corresponding to entry GRAY_MS_GRAY_MS_0_id_ccs_"20160704_19_D_04.mgf_assumptions"_ccs_20160704_19_D_04.mgf_cus_File230635 Spectrum47895 scans: 26334 [S:\p2069\Proteomics\FUSION_1\seeschwalbe_20160704_MS_brain_HILIC_D\20160704_19_D_04.raw] not found in cache when saving.at com.compomics.util.db.ObjectsCache.saveObjects(ObjectsCache.java:408)at com.compomics.util.db.ObjectsCache.saveObjects(ObjectsCache.java:342)at com.compomics.util.db.ObjectsCache.updateCacheSynchronized(ObjectsCache.java:585)at com.compomics.util.db.ObjectsCache.updateCache(ObjectsCache.java:562)at com.compomics.util.db.ObjectsCache.addObject(ObjectsCache.java:315)at com.compomics.util.db.ObjectsDB.loadObjects(ObjectsDB.java:689)at com.compomics.util.experiment.identification.IdentificationDB.loadSpectrumMatches(IdentificationDB.java:856)at com.compomics.util.experiment.identification.Identification.loadSpectrumMatches(Identification.java:241)at com.compomics.util.experiment.identification.matches_iterators.PsmIterator.checkBuffer(PsmIterator.java:280)at com.compomics.util.experiment.identification.matches_iterators.PsmIterator.next(PsmIterator.java:241)at eu.isas.peptideshaker.PeptideShaker.attachAssumptionsProbabilities(PeptideShaker.java:687)at eu.isas.peptideshaker.PeptideShaker.processIdentifications(PeptideShaker.java:330)at eu.isas.peptideshaker.fileimport.FileImporter$IdProcessorFromFile.importFiles(FileImporter.java:559)at eu.isas.peptideshaker.fileimport.FileImporter$IdProcessorFromFile.doInBackground(FileImporter.java:442)at javax.swing.SwingWorker$1.call(Unknown Source)at java.util.concurrent.FutureTask.run(Unknown Source)at javax.swing.SwingWorker.run(Unknown Source)at java.util.concurrent.ThreadPoolExecutor.runWorker(Unknown Source)at java.util.concurrent.ThreadPoolExecutor$Worker.run(Unknown Source)at java.lang.Thread.run(Unknown Source)Free memory: 1121204296Mon Nov 14 10:23:25 CET 2016: PeptideShaker version 1.13.6.Memory given to the Java virtual machine: 3817865216.Total amount of memory in the Java virtual machine: 128974848.Free memory: 99234896.Java version: 1.8.0_102.PeptideShaker processing failed. See the PeptideShaker log for details.java.lang.IllegalArgumentException: Object 20160704_19_D_04.mgf_cus_File230635 Spectrum47943 scans: 26386 [S:\p2069\Proteomics\FUSION_1\seeschwalbe_20160704_MS_brain_HILIC_D\20160704_19_D_04.raw] corresponding to entry test_test_0_id_ccs_"20160704_19_D_04.mgf_assumptions"_ccs_20160704_19_D_04.mgf_cus_File230635 Spectrum47943 scans: 26386 [S:\p2069\Proteomics\FUSION_1\seeschwalbe_20160704_MS_brain_HILIC_D\20160704_19_D_04.raw] not found in cache when saving.at com.compomics.util.db.ObjectsCache.saveObjects(ObjectsCache.java:408)at com.compomics.util.db.ObjectsCache.saveObjects(ObjectsCache.java:342)at com.compomics.util.db.ObjectsCache.updateCacheSynchronized(ObjectsCache.java:585)at com.compomics.util.db.ObjectsCache.updateCache(ObjectsCache.java:562)at com.compomics.util.db.ObjectsCache.addObject(ObjectsCache.java:315)at com.compomics.util.db.ObjectsDB.insertObject(ObjectsDB.java:299)at com.compomics.util.experiment.identification.IdentificationDB.addProteinMatchParameter(IdentificationDB.java:1256)at com.compomics.util.experiment.identification.Identification.addProteinMatchParameter(Identification.java:654)at eu.isas.peptideshaker.validation.MatchesValidator.fillProteinMap(MatchesValidator.java:1205)at eu.isas.peptideshaker.PeptideShaker.processIdentifications(PeptideShaker.java:447)at eu.isas.peptideshaker.fileimport.FileImporter$IdProcessorFromFile.importFiles(FileImporter.java:559)at eu.isas.peptideshaker.fileimport.FileImporter$IdProcessorFromFile.doInBackground(FileImporter.java:442)at javax.swing.SwingWorker$1.call(Unknown Source)at java.util.concurrent.FutureTask.run(Unknown Source)at javax.swing.SwingWorker.run(Unknown Source)at java.util.concurrent.ThreadPoolExecutor.runWorker(Unknown Source)at java.util.concurrent.ThreadPoolExecutor$Worker.run(Unknown Source)at java.lang.Thread.run(Unknown Source)Free memory: 840606056Mon Nov 14 10:42:19 CET 2016: PeptideShaker version 1.13.6.Memory given to the Java virtual machine: 3817865216.Total amount of memory in the Java virtual machine: 128974848.Free memory: 99894272.Java version: 1.8.0_102.Mon Nov 14 11:54:42 CET 2016: PeptideShaker version 1.13.6.Memory given to the Java virtual machine: 3817865216.Total amount of memory in the Java virtual machine: 128974848.Free memory: 95303872.Java version: 1.8.0_102.1714 script command tokens(C) 2009 Jmol DevelopmentJmol Version: 12.0.43 2011-05-03 14:21java.vendor: Oracle Corporationjava.version: 1.8.0_102os.name: Windows 8.1memory: 48.3/163.1processors available: 12useCommandThread: falsejava.lang.IllegalArgumentException: Object 20160704_03_C_01.mgf_cus_File18780 Spectrum57718 scans: 33903 [S:\p2069\Proteomics\FUSION_1\seeschwalbe_20160704_MS_brain_HILIC_C\20160704_03_C_01.raw] corresponding to entry Test_test_0_id_ccs_"20160704_03_C_01.mgf_assumptions"_ccs_20160704_03_C_01.mgf_cus_File18780 Spectrum57718 scans: 33903 [S:\p2069\Proteomics\FUSION_1\seeschwalbe_20160704_MS_brain_HILIC_C\20160704_03_C_01.raw] not found in cache when saving.at com.compomics.util.db.ObjectsCache.saveObjects(ObjectsCache.java:408)at com.compomics.util.db.ObjectsCache.saveObjects(ObjectsCache.java:342)at com.compomics.util.db.ObjectsCache.updateCacheSynchronized(ObjectsCache.java:585)at com.compomics.util.db.ObjectsCache.updateCache(ObjectsCache.java:562)at com.compomics.util.db.ObjectsCache.addObject(ObjectsCache.java:315)at com.compomics.util.db.ObjectsDB.loadObjects(ObjectsDB.java:689)at com.compomics.util.experiment.identification.IdentificationDB.loadSpectrumMatches(IdentificationDB.java:856)at com.compomics.util.experiment.identification.Identification.loadSpectrumMatches(Identification.java:241)at com.compomics.util.experiment.identification.matches_iterators.PsmIterator.checkBuffer(PsmIterator.java:280)at com.compomics.util.experiment.identification.matches_iterators.PsmIterator.next(PsmIterator.java:241)at eu.isas.peptideshaker.gui.tablemodels.PsmTableModel.loadDataForRows(PsmTableModel.java:351)at com.compomics.util.gui.tablemodels.SelfUpdatingTableModel$LoadingRunnable.run(SelfUpdatingTableModel.java:486)at java.lang.Thread.run(Unknown Source)Tue Nov 15 13:24:10 CET 2016: PeptideShaker version 1.13.6.Memory given to the Java virtual machine: 3817865216.Total amount of memory in the Java virtual machine: 128974848.Free memory: 95354632.Java version: 1.8.0_102.1714 script command tokens(C) 2009 Jmol DevelopmentJmol Version: 12.0.43 2011-05-03 14:21java.vendor: Oracle

StephanHolgerD/peptideshaker: Docker PeptideShake SearchGui

[S:\p2069\Proteomics\FUSION_1\seeschwalbe_20160704_MS_brain_HILIC_C\20160704_12_C_04.raw] corresponding to entry GRAY_HD_GRAY_HD_0_id_ccs_"20160704_12_C_04.mgf_assumptions"ccs_20160704_12_C_04.mgf_cus_File230304 Spectrum29926 scans: 16690 [S:\p2069\Proteomics\FUSION_1\seeschwalbe_20160704_MS_brain_HILIC_C\20160704_12_C_04.raw] not found in cache when saving.at com.compomics.util.db.ObjectsCache.saveObjects(ObjectsCache.java:408)at com.compomics.util.db.ObjectsCache.saveObjects(ObjectsCache.java:342)at com.compomics.util.db.ObjectsCache.updateCacheSynchronized(ObjectsCache.java:585)at com.compomics.util.db.ObjectsCache.updateCache(ObjectsCache.java:562)at com.compomics.util.db.ObjectsCache.addObject(ObjectsCache.java:315)at com.compomics.util.db.ObjectsDB.loadObjects(ObjectsDB.java:689)at com.compomics.util.experiment.identification.IdentificationDB.loadAssumptions(IdentificationDB.java:714)at com.compomics.util.experiment.identification.Identification.loadAssumptions(Identification.java:174)at com.compomics.util.experiment.identification.matches_iterators.PsmIterator.checkBuffer(PsmIterator.java:298)at com.compomics.util.experiment.identification.matches_iterators.PsmIterator.next(PsmIterator.java:241)at eu.isas.peptideshaker.PeptideShaker.attachAssumptionsProbabilities(PeptideShaker.java:687)at eu.isas.peptideshaker.PeptideShaker.processIdentifications(PeptideShaker.java:330)at eu.isas.peptideshaker.fileimport.FileImporter$IdProcessorFromFile.importFiles(FileImporter.java:559)at eu.isas.peptideshaker.fileimport.FileImporter$IdProcessorFromFile.doInBackground(FileImporter.java:442)at javax.swing.SwingWorker$1.call(Unknown Source)at java.util.concurrent.FutureTask.run(Unknown Source)at javax.swing.SwingWorker.run(Unknown Source)at java.util.concurrent.ThreadPoolExecutor.runWorker(Unknown Source)at java.util.concurrent.ThreadPoolExecutor$Worker.run(Unknown Source)at java.lang.Thread.run(Unknown Source)Free memory: 531727768java.io.EOFException: no more data available - expected end tags to close start tag from line 3375096 and start tag from line 3374999 and start tag from line 3374998 and start tag from line 3 and start tag from line 2, parser stopped on TEXT seen ...at org.xmlpull.mxp1.MXParser.fillBuf(MXParser.java:2919)at org.xmlpull.mxp1.MXParser.more(MXParser.java:2928)at org.xmlpull.mxp1.MXParser.parseAttribute(MXParser.java:1967)at org.xmlpull.mxp1.MXParser.parseStartTag(MXParser.java:1740)at org.xmlpull.mxp1.MXParser.nextImpl(MXParser.java:1095)at org.xmlpull.mxp1.MXParser.next(MXParser.java:1061)at com.compomics.util.experiment.io.identifications.idfilereaders.PepxmlIdfileReader.parseFile(PepxmlIdfileReader.java:142)at com.compomics.util.experiment.io.identifications.idfilereaders.PepxmlIdfileReader.getAllSpectrumMatches(PepxmlIdfileReader.java:691)at eu.isas.peptideshaker.fileimport.FileImporter$IdProcessorFromFile.importPsms(FileImporter.java:692)at eu.isas.peptideshaker.fileimport.FileImporter$IdProcessorFromFile.importFiles(FileImporter.java:488)at eu.isas.peptideshaker.fileimport.FileImporter$IdProcessorFromFile.doInBackground(FileImporter.java:442)at javax.swing.SwingWorker$1.call(Unknown Source)at java.util.concurrent.FutureTask.run(Unknown Source)at javax.swing.SwingWorker.run(Unknown Source)at java.util.concurrent.ThreadPoolExecutor.runWorker(Unknown Source)at java.util.concurrent.ThreadPoolExecutor$Worker.run(Unknown Source)at java.lang.Thread.run(Unknown Source)PeptideShaker processing failed. See the PeptideShaker log for details.java.lang.IllegalArgumentException: Object 20160704_12_C_04.mgf_cus_File230304 Spectrum11511 scans: 6471 [S:\p2069\Proteomics\FUSION_1\seeschwalbe_20160704_MS_brain_HILIC_C\20160704_12_C_04.raw] corresponding to entry GRAY_HD_GRAY_HD_0_id_ccs"20160704_12_C_04.mgf_assumptions"_ccs_20160704_12_C_04.mgf_cus_File230304 Spectrum11511 scans: 6471 [S:\p2069\Proteomics\FUSION_1\seeschwalbe_20160704_MS_brain_HILIC_C\20160704_12_C_04.raw] not found in cache when saving.at com.compomics.util.db.ObjectsCache.saveObjects(ObjectsCache.java:408)at com.compomics.util.db.ObjectsCache.saveObjects(ObjectsCache.java:342)at com.compomics.util.db.ObjectsCache.updateCacheSynchronized(ObjectsCache.java:585)at com.compomics.util.db.ObjectsCache.updateCache(ObjectsCache.java:562)at com.compomics.util.db.ObjectsCache.addObject(ObjectsCache.java:315)at com.compomics.util.db.ObjectsDB.loadObjects(ObjectsDB.java:689)at com.compomics.util.experiment.identification.IdentificationDB.loadAssumptions(IdentificationDB.java:714)at com.compomics.util.experiment.identification.Identification.loadAssumptions(Identification.java:174)at com.compomics.util.experiment.identification.matches_iterators.PsmIterator.checkBuffer(PsmIterator.java:298)at com.compomics.util.experiment.identification.matches_iterators.PsmIterator.next(PsmIterator.java:241)at eu.isas.peptideshaker.PeptideShaker.attachAssumptionsProbabilities(PeptideShaker.java:687)at eu.isas.peptideshaker.PeptideShaker.processIdentifications(PeptideShaker.java:330)at eu.isas.peptideshaker.fileimport.FileImporter$IdProcessorFromFile.importFiles(FileImporter.java:559)at eu.isas.peptideshaker.fileimport.FileImporter$IdProcessorFromFile.doInBackground(FileImporter.java:442)at javax.swing.SwingWorker$1.call(Unknown Source)at java.util.concurrent.FutureTask.run(Unknown Source)at javax.swing.SwingWorker.run(Unknown Source)at java.util.concurrent.ThreadPoolExecutor.runWorker(Unknown Source)at java.util.concurrent.ThreadPoolExecutor$Worker.run(Unknown Source)at java.lang.Thread.run(Unknown Source)Free memory: 675726576Fri Nov 11 09:00:21 CET 2016: PeptideShaker version 1.13.6.Memory given to the Java virtual machine: 3817865216.Total amount of memory in the Java virtual machine: 128974848.Free memory: 95229960.Java version: 1.8.0_102.1714 script command tokens(C) 2009 Jmol DevelopmentJmol Version: 12.0.43 2011-05-03 14:21java.vendor: Oracle Corporationjava.version: 1.8.0_102os.name: Windows 8.1memory: 47.2/163.1processors available: 12useCommandThread: falsejava.io.EOFException: no more data available - expected end tags to close start tag from line 3375096 and start tag from line 3374999 and start tag from line 3374998 and start tag from line 3 and start tag from line 2, parser stopped on TEXT seen ...at org.xmlpull.mxp1.MXParser.fillBuf(MXParser.java:2919)at org.xmlpull.mxp1.MXParser.more(MXParser.java:2928)at org.xmlpull.mxp1.MXParser.parseAttribute(MXParser.java:1967)at org.xmlpull.mxp1.MXParser.parseStartTag(MXParser.java:1740)at org.xmlpull.mxp1.MXParser.nextImpl(MXParser.java:1095)at org.xmlpull.mxp1.MXParser.next(MXParser.java:1061)at com.compomics.util.experiment.io.identifications.idfilereaders.PepxmlIdfileReader.parseFile(PepxmlIdfileReader.java:142)at com.compomics.util.experiment.io.identifications.idfilereaders.PepxmlIdfileReader.getAllSpectrumMatches(PepxmlIdfileReader.java:691)at eu.isas.peptideshaker.fileimport.FileImporter$IdProcessorFromFile.importPsms(FileImporter.java:692)at eu.isas.peptideshaker.fileimport.FileImporter$IdProcessorFromFile.importFiles(FileImporter.java:488)at eu.isas.peptideshaker.fileimport.FileImporter$IdProcessorFromFile.doInBackground(FileImporter.java:442)at javax.swing.SwingWorker$1.call(Unknown Source)at java.util.concurrent.FutureTask.run(Unknown Source)at javax.swing.SwingWorker.run(Unknown Source)at java.util.concurrent.ThreadPoolExecutor.runWorker(Unknown Source)at java.util.concurrent.ThreadPoolExecutor$Worker.run(Unknown Source)at java.lang.Thread.run(Unknown Source)PeptideShaker processing failed. See the PeptideShaker log for details.java.lang.IllegalArgumentException: Object 20160704_12_C_04.mgf_cus_File230304 Spectrum31110 scans: 16890 [S:\p2069\Proteomics\FUSION_1\seeschwalbe_20160704_MS_brain_HILIC_C\20160704_12_C_04.raw] corresponding to entry Gray_HD_Gray_HD_0_id_ccs_"20160704_12_C_04.mgf_assumptions"ccs_20160704_12_C_04.mgf_cus_File230304

PeptideShaker - PeptideShaker is a user friendly tool for shotgun

The download jar file contains the following class files or Java source files.1.Download jodd-petite-3.4.5.jar2.Download jodd-proxetta-3.4.4-sources.jar3.Download jodd-proxetta-3.4.4.jar4.Download jodd-proxetta-3.4.5-sources.jar5.Download jodd-proxetta-3.4.5.jar6.Download jodd-lagarto-3.4.3-sources.jar7.Download jodd-lagarto-3.4.3.jar8.Download jodd-lagarto-3.4.4-sources.jar9.Download jodd-lagarto-3.4.4.jar10.Download jodd-lagarto-3.4.5-sources.jar11.Download jodd-lagarto-3.4.5.jar12.Download jodd-lagarto-web-3.4.3-sources.jar13.Download jodd-lagarto-web-3.4.3.jar14.Download jodd-lagarto-web-3.4.4-sources.jar15.Download jodd-lagarto-web-3.4.4.jar16.Download jodd-lagarto-web-3.4.5-sources.jar17.Download jodd-lagarto-web-3.4.5.jar18.Download jodd-petite-3.4.3-sources.jar19.Download jodd-petite-3.4.3.jar20.Download jodd-petite-3.4.4-sources.jar21.Download jodd-petite-3.4.4.jar22.Download jodd-proxetta-3.4.3-sources.jar23.Download jodd-proxetta-3.4.3.jar24.Download jodd-joy-3.4.3-sources.jar25.Download jodd-joy-3.4.3.jar26.Download jodd-vtor-3.4.3-sources.jar27.Download jodd-vtor-3.4.3.jar28.Download jodd-vtor-3.4.4-sources.jar29.Download jodd-vtor-3.4.4.jar30.Download jodd-vtor-3.4.5-sources.jar31.Download jodd-vtor-3.4.5.jar32.Download jodd-bean-3.4.4-sources.jar33.Download jodd-bean-3.4.4.jar34.Download jodd-bean-3.4.5-sources.jar35.Download jodd-bean-3.4.5.jar36.Download jodd-wot-3.2.5-sources.jar37.Download jodd-wot-3.2.5.jar38.Download jodd-mail-3.4.0-sources.jar39.Download jodd-mail-3.4.0.jar40.Download jodd-mail-3.4.1-sources.jar41.Download jodd-mail-3.4.1.jar42.Download jodd-mail-3.4.2-sources.jar43.Download jodd-mail-3.4.2.jar44.Download jodd-mail-3.4.3-sources.jar45.Download jodd-mail-3.4.3.jar46.Download jodd-mail-3.4.4-sources.jar47.Download jodd-mail-3.4.4.jar48.Download jodd-mail-3.4.5-sources.jar49.Download jodd-mail-3.4.5.jar50.Download jodd-servlet-3.4.3-sources.jar51.Download jodd-servlet-3.4.3.jar52.Download jodd-servlet-3.4.4-sources.jar53.Download jodd-servlet-3.4.4.jar54.Download jodd-servlet-3.4.5-sources.jar55.Download jodd-servlet-3.4.5.jar56.Download jodd-core-3.4.2-sources.jar57.Download jodd-core-3.4.2.jar58.Download jodd-core-3.4.3-sources.jar59.Download jodd-core-3.4.3.jar60.Download jodd-core-3.4.4-sources.jar61.Download jodd-core-3.4.4.jar62.Download jodd-core-3.4.5-sources.jar63.Download jodd-core-3.4.5.jar64.Download jodd-swingspy-3.4.3-sources.jar65.Download jodd-swingspy-3.4.3.jar66.Download jodd-swingspy-3.4.4-sources.jar67.Download jodd-swingspy-3.4.4.jar68.Download jodd-swingspy-3.4.5-sources.jar69.Download jodd-swingspy-3.4.5.jar70.Download jodd-upload-3.4.3-sources.jar71.Download jodd-upload-3.4.3.jar72.Download jodd-upload-3.4.4-sources.jar73.Download jodd-upload-3.4.4.jar74.Download jodd-upload-3.4.5-sources.jar75.Download jodd-upload-3.4.5.jar76.Download jodd-props-3.4.3-sources.jar77.Download jodd-props-3.4.3.jar78.Download jodd-props-3.4.4-sources.jar79.Download 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PeptideShaker Overview What makes PeptideShaker special?

Hello, I have a project with 11 mgf files searched with 4 search engines run by SearchGUI. I am not able to load those results in peptide shaker. Below is the Error log I copied out of the Bug Report Window.Do you have any advice how to proceed? Thank you.Thu Nov 10 08:40:53 CET 2016: PeptideShaker version 1.13.6.Memory given to the Java virtual machine: 3817865216.Total amount of memory in the Java virtual machine: 128974848.Free memory: 95162336.Java version: 1.8.0_102.1714 script command tokens(C) 2009 Jmol DevelopmentJmol Version: 12.0.43 2011-05-03 14:21java.vendor: Oracle Corporationjava.version: 1.8.0_102os.name: Windows 8.1memory: 49.8/163.1processors available: 12useCommandThread: falsejava.io.EOFException: no more data available - expected end tags to close start tag from line 95379 and start tag from line 95371 and start tag from line 95267 and start tag from line 95266 and start tag from line 3 and start tag from line 2, parser stopped on TEXT seen ...\r\n at org.xmlpull.mxp1.MXParser.fillBuf(MXParser.java:2919)at org.xmlpull.mxp1.MXParser.more(MXParser.java:2928)at org.xmlpull.mxp1.MXParser.parseStartTag(MXParser.java:1679)at org.xmlpull.mxp1.MXParser.nextImpl(MXParser.java:1095)at org.xmlpull.mxp1.MXParser.next(MXParser.java:1061)at com.compomics.util.experiment.io.identifications.idfilereaders.PepxmlIdfileReader.parseSearchHit(PepxmlIdfileReader.java:450)at com.compomics.util.experiment.io.identifications.idfilereaders.PepxmlIdfileReader.parseFile(PepxmlIdfileReader.java:179)at com.compomics.util.experiment.io.identifications.idfilereaders.PepxmlIdfileReader.getAllSpectrumMatches(PepxmlIdfileReader.java:691)at eu.isas.peptideshaker.fileimport.FileImporter$IdProcessorFromFile.importPsms(FileImporter.java:692)at eu.isas.peptideshaker.fileimport.FileImporter$IdProcessorFromFile.importFiles(FileImporter.java:488)at eu.isas.peptideshaker.fileimport.FileImporter$IdProcessorFromFile.doInBackground(FileImporter.java:442)at javax.swing.SwingWorker$1.call(Unknown Source)at java.util.concurrent.FutureTask.run(Unknown Source)at javax.swing.SwingWorker.run(Unknown Source)at java.util.concurrent.ThreadPoolExecutor.runWorker(Unknown Source)at java.util.concurrent.ThreadPoolExecutor$Worker.run(Unknown Source)at java.lang.Thread.run(Unknown Source)Fri Nov 11 08:41:18 CET 2016: PeptideShaker version 1.13.6.Memory given to the Java virtual machine: 3817865216.Total amount of memory in the Java virtual machine: 128974848.Free memory: 95386640.Java version: 1.8.0_102.1714 script command tokens(C) 2009 Jmol DevelopmentJmol Version: 12.0.43 2011-05-03 14:21java.vendor: Oracle Corporationjava.version: 1.8.0_102os.name: Windows 8.1memory: 47.4/163.1processors available: 12useCommandThread: falsejava.io.EOFException: no more data available - expected end tags to close start tag from line 3375096 and start tag from line 3374999 and start tag from line 3374998 and start tag from line 3 and start tag from line 2, parser stopped on TEXT seen ...at org.xmlpull.mxp1.MXParser.fillBuf(MXParser.java:2919)at org.xmlpull.mxp1.MXParser.more(MXParser.java:2928)at org.xmlpull.mxp1.MXParser.parseAttribute(MXParser.java:1967)at org.xmlpull.mxp1.MXParser.parseStartTag(MXParser.java:1740)at org.xmlpull.mxp1.MXParser.nextImpl(MXParser.java:1095)at org.xmlpull.mxp1.MXParser.next(MXParser.java:1061)at com.compomics.util.experiment.io.identifications.idfilereaders.PepxmlIdfileReader.parseFile(PepxmlIdfileReader.java:142)at com.compomics.util.experiment.io.identifications.idfilereaders.PepxmlIdfileReader.getAllSpectrumMatches(PepxmlIdfileReader.java:691)at eu.isas.peptideshaker.fileimport.FileImporter$IdProcessorFromFile.importPsms(FileImporter.java:692)at eu.isas.peptideshaker.fileimport.FileImporter$IdProcessorFromFile.importFiles(FileImporter.java:488)at eu.isas.peptideshaker.fileimport.FileImporter$IdProcessorFromFile.doInBackground(FileImporter.java:442)at javax.swing.SwingWorker$1.call(Unknown Source)at java.util.concurrent.FutureTask.run(Unknown Source)at javax.swing.SwingWorker.run(Unknown Source)at java.util.concurrent.ThreadPoolExecutor.runWorker(Unknown Source)at java.util.concurrent.ThreadPoolExecutor$Worker.run(Unknown Source)at java.lang.Thread.run(Unknown Source)PeptideShaker processing failed. See the PeptideShaker log for details.java.lang.IllegalArgumentException: Object 20160704_12_C_04.mgf_cus_File230304 Spectrum29926 scans: 16690

Download PeptideShaker for Mac - MacUpdate

Corporationjava.version: 1.8.0_102os.name: Windows 8.1memory: 48.5/163.1processors available: 12useCommandThread: falseWed Nov 16 08:50:29 CET 2016: PeptideShaker version 1.13.6.Memory given to the Java virtual machine: 3817865216.Total amount of memory in the Java virtual machine: 128974848.Free memory: 95341936.Java version: 1.8.0_102.1714 script command tokens(C) 2009 Jmol DevelopmentJmol Version: 12.0.43 2011-05-03 14:21java.vendor: Oracle Corporationjava.version: 1.8.0_102os.name: Windows 8.1memory: 48.3/163.1processors available: 12useCommandThread: falsejava.io.EOFException: no more data available - expected end tags to close start tag from line 3342785 and start tag from line 3342780 and start tag from line 3342712 and start tag from line 3342711 and start tag from line 3 and start tag from line 2, parser stopped on TEXT seen ...\r\n at org.xmlpull.mxp1.MXParser.fillBuf(MXParser.java:2919)at org.xmlpull.mxp1.MXParser.more(MXParser.java:2928)at org.xmlpull.mxp1.MXParser.parseAttribute(MXParser.java:1862)at org.xmlpull.mxp1.MXParser.parseStartTag(MXParser.java:1740)at org.xmlpull.mxp1.MXParser.nextImpl(MXParser.java:1095)at org.xmlpull.mxp1.MXParser.next(MXParser.java:1061)at com.compomics.util.experiment.io.identifications.idfilereaders.PepxmlIdfileReader.parseSearchHit(PepxmlIdfileReader.java:414)at com.compomics.util.experiment.io.identifications.idfilereaders.PepxmlIdfileReader.parseFile(PepxmlIdfileReader.java:179)at com.compomics.util.experiment.io.identifications.idfilereaders.PepxmlIdfileReader.getAllSpectrumMatches(PepxmlIdfileReader.java:691)at eu.isas.peptideshaker.fileimport.FileImporter$IdProcessorFromFile.importPsms(FileImporter.java:692)at eu.isas.peptideshaker.fileimport.FileImporter$IdProcessorFromFile.importFiles(FileImporter.java:488)at eu.isas.peptideshaker.fileimport.FileImporter$IdProcessorFromFile.doInBackground(FileImporter.java:442)at javax.swing.SwingWorker$1.call(Unknown Source)at java.util.concurrent.FutureTask.run(Unknown Source)at javax.swing.SwingWorker.run(Unknown Source)at java.util.concurrent.ThreadPoolExecutor.runWorker(Unknown Source)at java.util.concurrent.ThreadPoolExecutor$Worker.run(Unknown Source)at java.lang.Thread.run(Unknown Source)java.io.EOFException: no more data available - expected end tags to close start tag from line 3825474 and start tag from line 3825473 and start tag from line 3825380 and start tag from line 3825379 and start tag from line 3 and start tag from line 2, parser stopped on END_TAG seen ...\r\n at org.xmlpull.mxp1.MXParser.fillBuf(MXParser.java:2919)at org.xmlpull.mxp1.MXParser.more(MXParser.java:2928)at org.xmlpull.mxp1.MXParser.nextImpl(MXParser.java:1133)at org.xmlpull.mxp1.MXParser.next(MXParser.java:1061)at com.compomics.util.experiment.io.identifications.idfilereaders.PepxmlIdfileReader.parseSearchHit(PepxmlIdfileReader.java:347)at com.compomics.util.experiment.io.identifications.idfilereaders.PepxmlIdfileReader.parseFile(PepxmlIdfileReader.java:179)at com.compomics.util.experiment.io.identifications.idfilereaders.PepxmlIdfileReader.getAllSpectrumMatches(PepxmlIdfileReader.java:691)at eu.isas.peptideshaker.fileimport.FileImporter$IdProcessorFromFile.importPsms(FileImporter.java:692)at eu.isas.peptideshaker.fileimport.FileImporter$IdProcessorFromFile.importFiles(FileImporter.java:488)at eu.isas.peptideshaker.fileimport.FileImporter$IdProcessorFromFile.doInBackground(FileImporter.java:442)at javax.swing.SwingWorker$1.call(Unknown Source)at java.util.concurrent.FutureTask.run(Unknown Source)at javax.swing.SwingWorker.run(Unknown Source)at java.util.concurrent.ThreadPoolExecutor.runWorker(Unknown Source)at java.util.concurrent.ThreadPoolExecutor$Worker.run(Unknown Source)at java.lang.Thread.run(Unknown Source)PeptideShaker processing failed. See the PeptideShaker log for details.java.lang.NullPointerExceptionat eu.isas.peptideshaker.parameters.PSPtmScores.changeRepresentativeSite(PSPtmScores.java:227)at eu.isas.peptideshaker.ptm.PtmScorer.peptideInference(PtmScorer.java:1876)at eu.isas.peptideshaker.PeptideShaker.processIdentifications(PeptideShaker.java:393)at eu.isas.peptideshaker.fileimport.FileImporter$IdProcessorFromFile.importFiles(FileImporter.java:559)at eu.isas.peptideshaker.fileimport.FileImporter$IdProcessorFromFile.doInBackground(FileImporter.java:442)at javax.swing.SwingWorker$1.call(Unknown Source)at java.util.concurrent.FutureTask.run(Unknown Source)at javax.swing.SwingWorker.run(Unknown Source)at java.util.concurrent.ThreadPoolExecutor.runWorker(Unknown Source)at java.util.concurrent.ThreadPoolExecutor$Worker.run(Unknown Source)at java.lang.Thread.run(Unknown Source)Free memory: 463007480

PeptideShaker and SearchGUI in Galaxy

We cannot recommend some algorithms over others ;-)Some tips when it comes to the combination though:- I prefer to have odd numbers of search engines: while we try to avoid such situations, it can help to have a majority in case of conflicts. So I generally run 1, 3, 5, or 7 search engines.- More is not always better, some algorithms might include high scoring false positives. These will impair the overall performance.- Depending on how much you want to squeeze out of your data, you might not want to include that many search engines, and keep the search time reasonable. Generally we work with 1 algorithm for testing and optimization, 3 for normal searches, 5 or 7 for the most important projects.- We try to use a combination of the most heterogeneous algorithms. For example, Tide and Comet are both built around Crux on the rationale of Sequest. So they will find more or less the same peptides, make the same mistakes. Using them together will give twice the weight to those peptides and hence bias the combination. Similarly, MS Amanda and Andromeda are built on the principle of Mascot, but there the link is not that strong. I don't know the details of the different implementations and we did not investigate the effect of algorithm similarities on PeptideShaker results, where each algorithm gets the same weight, so I might be wrong.Hope this helps,MarcMoritz Lasséunread,Mar 14, 2016, 1:54:43 PM3/14/16to peptide...@googlegroups.comthis is great info and just what I was looking for, much appreciated!Good paper by Sheynberg and I now use X!tandem, Comet, and MSGF. I like your approach of uneven numbers, Marc. Love the feature of exporting PTMs with localisation and confidence by the way!CheersMoe. Download MtL PeptideShaker ver. French version Keygen PeptideShaker vers. D57 Best on 10.13.5 Crack ke9x PeptideShaker Best! version App PeptideShaker 8YLJJq New Mojave Crack BQD62G PEPTIDESHAKER VERSION Updated 10.14.2 Software 0wT v. PeptideShaker