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

[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

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

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

Spectrum31110 scans: 16890 [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.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: 716852264java.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)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 Spectrum31110 scans: 16890 [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.insertObject(ObjectsDB.java:299)at com.compomics.util.experiment.identification.IdentificationDB.addAssumptions(IdentificationDB.java:453)at com.compomics.util.experiment.identification.Identification.addAssumptions(Identification.java:1302)at com.compomics.util.experiment.identification.Identification.addAssumptions(Identification.java:1347)at eu.isas.peptideshaker.fileimport.PsmImporter.importAssumptions(PsmImporter.java:700)at eu.isas.peptideshaker.fileimport.PsmImporter.importPsm(PsmImporter.java:422)at eu.isas.peptideshaker.fileimport.PsmImporter.access$000(PsmImporter.java:68)at eu.isas.peptideshaker.fileimport.PsmImporter$PsmImporterRunnable.run(PsmImporter.java:1473)at java.util.concurrent.Executors$RunnableAdapter.call(Unknown Source)at java.util.concurrent.FutureTask.run(Unknown Source)at java.util.concurrent.ThreadPoolExecutor.runWorker(Unknown Source)at java.util.concurrent.ThreadPoolExecutor$Worker.run(Unknown Source)at java.lang.Thread.run(Unknown Source)Fri Nov 11 10:21:27 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: 94711640.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: 48.1/163.1processors available: 12useCommandThread: falseFri Nov 11 15:40:22 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: 99351896.Java version: 1.8.0_102.java.lang.IllegalArgumentException: Object 20160704_19_D_04.mgf_cus_File230635 Spectrum47900 scans: 26339 [S:\p2069\Proteomics\FUSION_1\seeschwalbe_20160704_MS_brain_HILIC_D\20160704_19_D_04.raw] corresponding to entry Testtest_testtest_0_id_ccs_"20160704_19_D_04.mgf_assumptions"_ccs_20160704_19_D_04.mgf_cus_File230635 Spectrum47900 scans: 26339 [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.addAssumptions(IdentificationDB.java:453)at com.compomics.util.experiment.identification.Identification.addAssumptions(Identification.java:1302)at com.compomics.util.experiment.identification.Identification.addAssumptions(Identification.java:1347)at eu.isas.peptideshaker.fileimport.PsmImporter.importAssumptions(PsmImporter.java:700)at eu.isas.peptideshaker.fileimport.PsmImporter.importPsm(PsmImporter.java:422)at eu.isas.peptideshaker.fileimport.PsmImporter.access$000(PsmImporter.java:68)at eu.isas.peptideshaker.fileimport.PsmImporter$PsmImporterRunnable.run(PsmImporter.java:1473)at java.util.concurrent.Executors$RunnableAdapter.call(Unknown Source)at java.util.concurrent.FutureTask.run(Unknown Source)at java.util.concurrent.ThreadPoolExecutor.runWorker(Unknown Source)at java.util.concurrent.ThreadPoolExecutor$Worker.run(Unknown Source)at java.lang.Thread.run(Unknown Source)Mon Nov 14 09:50:06 CET 2016: PeptideShaker version 1.13.6.Memory given to the Java virtual machine: 3817865216.Total amount of memory in the Java virtual machine: 163053568.Free memory: 128945600.Java version: 1.8.0_102.1714 script command tokens(C) 2009 Jmol

Skip to content Navigation Menu GitHub Copilot Write better code with AI Security Find and fix vulnerabilities Actions Automate any workflow Codespaces Instant dev environments Issues Plan and track work Code Review Manage code changes Discussions Collaborate outside of code Code Search Find more, search less Explore Learning Pathways Events & Webinars Ebooks & Whitepapers Customer Stories Partners Executive Insights GitHub Sponsors Fund open source developers The ReadME Project GitHub community articles Enterprise platform AI-powered developer platform Pricing Provide feedback Saved searches Use saved searches to filter your results more quickly //voltron/issues_fragments/issue_layout;ref_cta:Sign up;ref_loc:header logged out"}"> Sign up Notifications You must be signed in to change notification settings Fork 18 Star 48 DescriptionHey Folks,i have problems with peptideshaker importing the data from the search gui.Thu Nov 10 13:21:02 CET 2016 Importing Data Canceled!Thu Nov 10 13:21:02 CET 2016 An error occurred while loading the identification files:Thu Nov 10 13:21:02 CET 2016 Object 2016_10_21_iG_C1.mgf_cus_2016_10_21_iG_C1.10942.10942.3 corresponding to entry CR_CR1_0_id_ccs_"2016_10_21_iG_C1.mgf_raw_assumptions"_ccs_2016_10_21_iG_C1.mgf_cus_2016_10_21_iG_C1.10942.10942.3 not found in cache when saving.here is the complete log:20161110 loading new project peptide shaker log.txt20161110 searchgui log.txtPeptideShaker 1.13.6 log.txti loaded 3 spectra files in the searchgui (CR1...CR3)Do you know what is the problem?