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compomics / peptide-shaker

Interpretation of proteomics identification results
http://compomics.github.io/projects/peptide-shaker.html
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PeptideShaker fails to import #227

Closed wolski closed 7 years ago

wolski commented 8 years ago

I did removed all the comet output from the search results. I still have 3 search engines MSGF, Myrimatch and Xtandem. I am still getting an peptide-shaker import error. I did checked the input files and they all have an ending tag.

Thanks in advance for valueable hints.

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_idccs"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.

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 Development Jmol Version: 12.0.43 2011-05-03 14:21 java.vendor: Oracle Corporation java.version: 1.8.0_102 os.name: Windows 8.1 memory: 49.8/163.1 processors available: 12 useCommandThread: false java.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 <s... @95380:7 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 Development Jmol Version: 12.0.43 2011-05-03 14:21 java.vendor: Oracle Corporation java.version: 1.8.0_102 os.name: Windows 8.1 memory: 47.4/163.1 processors available: 12 useCommandThread: false java.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 ...<search_hit hit_rank="10" peptide="QLPR... @3375096:43 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 [S:\p2069\Proteomics\FUSION_1\seeschwalbe_20160704_MS_brain_HILIC_C\20160704_12_C_04.raw] corresponding to entry GRAY_HD_GRAY_HD_0_idccs"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: 531727768 java.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 ...<search_hit hit_rank="10" peptide="QLPR... @3375096:43 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_idccs"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: 675726576

Fri 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 Development Jmol Version: 12.0.43 2011-05-03 14:21 java.vendor: Oracle Corporation java.version: 1.8.0_102 os.name: Windows 8.1 memory: 47.2/163.1 processors available: 12 useCommandThread: false java.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 ...<search_hit hit_rank="10" peptide="QLPR... @3375096:43 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_idccs"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.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: 716852264 java.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 ...<search_hit hit_rank="10" peptide="QLPR... @3375096:43 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_idccs"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 Development Jmol Version: 12.0.43 2011-05-03 14:21 java.vendor: Oracle Corporation java.version: 1.8.0_102 os.name: Windows 8.1 memory: 48.1/163.1 processors available: 12 useCommandThread: false

Fri 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_idccs"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 Development Jmol Version: 12.0.43 2011-05-03 14:21 java.vendor: Oracle Corporation java.version: 1.8.0_102 os.name: Windows 8.1 memory: 51.1/163.1 processors available: 12 useCommandThread: false

PeptideShaker 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_idccs"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: 1121204296

Mon 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_idccs"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: 840606056

Mon 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 Development Jmol Version: 12.0.43 2011-05-03 14:21 java.vendor: Oracle Corporation java.version: 1.8.0_102 os.name: Windows 8.1 memory: 48.3/163.1 processors available: 12 useCommandThread: false java.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_idccs"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 Development Jmol Version: 12.0.43 2011-05-03 14:21 java.vendor: Oracle Corporation java.version: 1.8.0_102 os.name: Windows 8.1 memory: 48.5/163.1 processors available: 12 useCommandThread: false

Wed 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 Development Jmol Version: 12.0.43 2011-05-03 14:21 java.vendor: Oracle Corporation java.version: 1.8.0_102 os.name: Windows 8.1 memory: 48.3/163.1 processors available: 12 useCommandThread: false java.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 <search_score name="xcorr" v... @3342785:33 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 <... @3825476:6 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.NullPointerException at 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

Wed Nov 16 14:46:22 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: 95203288. Java version: 1.8.0_102. 1714 script command tokens (C) 2009 Jmol Development Jmol Version: 12.0.43 2011-05-03 14:21 java.vendor: Oracle Corporation java.version: 1.8.0_102 os.name: Windows 8.1 memory: 48.5/163.1 processors available: 12 useCommandThread: false

PeptideShaker processing failed. See the PeptideShaker log for details.

java.lang.NullPointerException at 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: 886719600

hbarsnes commented 8 years ago

Hi,

Thanks for reporting this issue. Seems to be a problem with the PTM localization code. This is more Marc's domain so I'm assigning the issue to him. But would it be possible for you to share the data you are trying to load so that we can try to reproduce the error on our side?

Best regards, Harald

mvaudel commented 8 years ago

Hi again,

Looks like a threading problem with the cache (same as issue 220). I will look into it. In the meantime the only temporary fix I can think of is to increase the memory given to the tool or reduce the number of threads - hopefully that will help!

Sorry for the inconvenience,

Marc

wolski commented 8 years ago

Hi Marc,

What settings to start the petpide-shaker jar would you recommend please? Could you post a command line. Thank you a lot in advance.

regards

mvaudel commented 8 years ago

Hi again,

The settings in terms of memory and CPU are dependent on the dataset, and it seems that things are not really going as they should so it is hard to provide you with a good answer here.

I generally work on my laptop with 16 GB of ram and 8 CPUs when having less than 10 raw files. We use more RAM (32 GB) for larger datasets. That said, PeptideShaker is not able to compare projects so we usually don't run many raw files at a time and use MaxQuant when we need quantitative values.

Maybe you can try to reduce the number of threads if you encounter the issue - or even try with a single thread?

A simple way to get your command line premade is to select PeptideShaker from SearchGUI. Then the command line used will be printed in the log. Then you just need to remove the gui and add a temp_folder and log to redirect temporary files and logs.

On my side it gives something like this: Command line to create the project:

"C:\Program Files\Java\jre1.8.0_25\bin\java" -Xms128M -Xmx14096M -cp PeptideShaker-1.13.6.jar eu.isas.peptideshaker.cmd.PeptideShakerCLI -experiment testProject -sample testProject -replicate 0 -identification_files "C:\test\X!Tandem_searchgui_out.zip" -spectrum_files "C:\test\qExactive01819.mgf" -id_params "C:\test\tutorials new params.par" -out "C:\test\PeptideShaker_output.cpsx" -temp_folder "C:\test\temp" -log "C:\test\log"

Command line to open the project:

"C:\Program Files\Java\jre1.8.0_25\bin\java" -Xms128M -Xmx14096M -jar PeptideShaker-1.13.6.jar -cps "C:\test\PeptideShaker_output.cpsx"

You can change the number of threads using -threads n. More details can be found on the CLI wiki.

Hope this helps!

Marc

wolski commented 7 years ago

Just updated to peptide shaker 1.14.4 and increased memory to 40 GB. Still peptide shaker fails to import: This is the error message:

Mon Dec 12 16:30:58 CET 2016 Scoring PTMs in peptides.

Mon Dec 12 17:14:38 CET 2016 Importing Data Canceled! Mon Dec 12 17:14:38 CET 2016 An error occurred while loading the identification files: Mon Dec 12 17:14:38 CET 2016 Object MYYKEIKAIIHKGYTYKRITAIHPRIK_0.9840155826899988_15.99491461956 corresponding to entry GRAY_HD_GRAY_HD_0_id_ccs_peptides_ccs_MYYKEIKAIIHKGYTYKRITAIHPRIK_0.9840155826899988_15.99491461956 not found in cache when saving.

Any chance you can have a look into the problem please? I could provide the data.

hbarsnes commented 7 years ago

Hi,

Thanks for the update. Marc is already working on this one, which is a high priority issue as it has been reported be several users, the latest being https://github.com/compomics/peptide-shaker/issues/235. We'll hopefully have a fix and a new version available soon. We'll keep you posted.

Best regards, Harald

hbarsnes commented 7 years ago

Issue assumed resolved in later versions of PeptideShaker as the interaction with the cache has been cleaned up. If this is not the case, please let us know and we'll reopen the issue.