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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 issue - failed to load SearchGUI results #527

Closed mryanshi closed 11 months ago

mryanshi commented 11 months ago

Hi, I am a new user of SearchGUI and PeptideShaker. I ran into issues with loading data to PeptideShaker lately. Here is what the log says:

------------------------------------------------------------------

PeptideShaker 3.0.1 Report File

#

Originally saved by: i116gast @ I116LAB07

on: 03 Nov 2023, 11:17

as: Importing data canceled

------------------------------------------------------------------

Fri Nov 03 11:14:58 CET 2023 Import process for T parva

Fri Nov 03 11:14:59 CET 2023 Importing sequences from NCBI_Theileria_parva_tx333668_8112_231103_concatenated_target_decoy.fasta. Fri Nov 03 11:15:05 CET 2023 Importing gene mappings. Fri Nov 03 11:15:06 CET 2023 Establishing local database connection. Fri Nov 03 11:15:06 CET 2023 Reading identification files. Fri Nov 03 11:15:06 CET 2023 Parsing 2303047_Tparva_AP.comet.pep.xml.gz. Fri Nov 03 11:15:12 CET 2023 Checking spectra for 2303047_Tparva_AP.comet.pep.xml.gz. Fri Nov 03 11:15:12 CET 2023 Spectrum with title 'controllerType=0 controllerNumber=1 scan=2422' in file named '2303047_Tparva_AP' required to parse '2303047_Tparva_AP.comet.pep.xml.gz' not found.

Fri Nov 03 11:15:12 CET 2023 Importing Data Canceled!

This happened on results generated by different search engines of SearchGUI. Any solutions to fix it?

mryanshi commented 11 months ago

More detrails about this issue:

Thu Nov 02 19:08:29 CET 2023: PeptideShaker version 3.0.1. Memory given to the Java virtual machine: 3817865216. Total amount of memory in the Java virtual machine: 128974848. Free memory: 86467352. Java version: 1.8.0_391. jshortcut.dll loaded via tmp generated pathname: C:\Users\i116gast\AppData\Local\Temp\jshortcut-2898279363260973678.dll 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_391 os.name: Windows 10 memory: 67.8/163.1 processors available: 4 useCommandThread: false Exception in thread "AWT-EventQueue-0" java.lang.NullPointerException at eu.isas.peptideshaker.gui.pride.ProjectsFilterDialog.(ProjectsFilterDialog.java:72) at eu.isas.peptideshaker.gui.pride.PrideReshakeGUI.findMenuItemActionPerformed(PrideReshakeGUI.java:1583) at eu.isas.peptideshaker.gui.pride.PrideReshakeGUI.projectSearchLabelMouseReleased(PrideReshakeGUI.java:1753) at eu.isas.peptideshaker.gui.pride.PrideReshakeGUI.access$1800(PrideReshakeGUI.java:102) at eu.isas.peptideshaker.gui.pride.PrideReshakeGUI$11.mouseReleased(PrideReshakeGUI.java:896) at java.awt.AWTEventMulticaster.mouseReleased(Unknown Source) at java.awt.Component.processMouseEvent(Unknown Source) at javax.swing.JComponent.processMouseEvent(Unknown Source) at java.awt.Component.processEvent(Unknown Source) at java.awt.Container.processEvent(Unknown Source) at java.awt.Component.dispatchEventImpl(Unknown Source) at java.awt.Container.dispatchEventImpl(Unknown Source) at java.awt.Component.dispatchEvent(Unknown Source) at java.awt.LightweightDispatcher.retargetMouseEvent(Unknown Source) at java.awt.LightweightDispatcher.processMouseEvent(Unknown Source) at java.awt.LightweightDispatcher.dispatchEvent(Unknown Source) at java.awt.Container.dispatchEventImpl(Unknown Source) at java.awt.Window.dispatchEventImpl(Unknown Source) at java.awt.Component.dispatchEvent(Unknown Source) at java.awt.EventQueue.dispatchEventImpl(Unknown Source) at java.awt.EventQueue.access$500(Unknown Source) at java.awt.EventQueue$3.run(Unknown Source) at java.awt.EventQueue$3.run(Unknown Source) at java.security.AccessController.doPrivileged(Native Method) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(Unknown Source) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(Unknown Source) at java.awt.EventQueue$4.run(Unknown Source) at java.awt.EventQueue$4.run(Unknown Source) at java.security.AccessController.doPrivileged(Native Method) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(Unknown Source) at java.awt.EventQueue.dispatchEvent(Unknown Source) at java.awt.EventDispatchThread.pumpOneEventForFilters(Unknown Source) at java.awt.EventDispatchThread.pumpEventsForFilter(Unknown Source) at java.awt.EventDispatchThread.pumpEventsForHierarchy(Unknown Source) at java.awt.EventDispatchThread.pumpEvents(Unknown Source) at java.awt.EventDispatchThread.pumpEvents(Unknown Source) at java.awt.EventDispatchThread.run(Unknown Source) https://www.ebi.ac.uk/pride/ws/archive/project/count org.springframework.web.client.HttpClientErrorException$NotFound: 404 : "{ "timestamp" : 1698948857867, "status" : 404, "error" : "Not Found", "message" : "No message available", "path" : "/pride/ws/archive/v2/project/count"}" at org.springframework.web.client.HttpClientErrorException.create(HttpClientErrorException.java:113) at org.springframework.web.client.DefaultResponseErrorHandler.handleError(DefaultResponseErrorHandler.java:168) at org.springframework.web.client.DefaultResponseErrorHandler.handleError(DefaultResponseErrorHandler.java:122) at org.springframework.web.client.ResponseErrorHandler.handleError(ResponseErrorHandler.java:63) at org.springframework.web.client.RestTemplate.handleResponse(RestTemplate.java:819) at org.springframework.web.client.RestTemplate.doExecute(RestTemplate.java:777) at org.springframework.web.client.RestTemplate.execute(RestTemplate.java:711) at org.springframework.web.client.RestTemplate.getForEntity(RestTemplate.java:361) at eu.isas.peptideshaker.gui.pride.PrideReshakeGUI$33.run(PrideReshakeGUI.java:2523) Exception in thread "AWT-EventQueue-0" java.lang.NullPointerException at eu.isas.peptideshaker.gui.pride.ProjectsFilterDialog.(ProjectsFilterDialog.java:72) at eu.isas.peptideshaker.gui.pride.PrideReshakeGUI.findMenuItemActionPerformed(PrideReshakeGUI.java:1583) at eu.isas.peptideshaker.gui.pride.PrideReshakeGUI.projectSearchLabelMouseReleased(PrideReshakeGUI.java:1753) at eu.isas.peptideshaker.gui.pride.PrideReshakeGUI.access$1800(PrideReshakeGUI.java:102) at eu.isas.peptideshaker.gui.pride.PrideReshakeGUI$11.mouseReleased(PrideReshakeGUI.java:896) at java.awt.AWTEventMulticaster.mouseReleased(Unknown Source) at java.awt.Component.processMouseEvent(Unknown Source) at javax.swing.JComponent.processMouseEvent(Unknown Source) at java.awt.Component.processEvent(Unknown Source) at java.awt.Container.processEvent(Unknown Source) at java.awt.Component.dispatchEventImpl(Unknown Source) at java.awt.Container.dispatchEventImpl(Unknown Source) at java.awt.Component.dispatchEvent(Unknown Source) at java.awt.LightweightDispatcher.retargetMouseEvent(Unknown Source) at java.awt.LightweightDispatcher.processMouseEvent(Unknown Source) at java.awt.LightweightDispatcher.dispatchEvent(Unknown Source) at java.awt.Container.dispatchEventImpl(Unknown Source) at java.awt.Window.dispatchEventImpl(Unknown Source) at java.awt.Component.dispatchEvent(Unknown Source) at java.awt.EventQueue.dispatchEventImpl(Unknown Source) at java.awt.EventQueue.access$500(Unknown Source) at java.awt.EventQueue$3.run(Unknown Source) at java.awt.EventQueue$3.run(Unknown Source) at java.security.AccessController.doPrivileged(Native Method) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(Unknown Source) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(Unknown Source) at java.awt.EventQueue$4.run(Unknown Source) at java.awt.EventQueue$4.run(Unknown Source) at java.security.AccessController.doPrivileged(Native Method) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(Unknown Source) at java.awt.EventQueue.dispatchEvent(Unknown Source) at java.awt.EventDispatchThread.pumpOneEventForFilters(Unknown Source) at java.awt.EventDispatchThread.pumpEventsForFilter(Unknown Source) at java.awt.EventDispatchThread.pumpEventsForHierarchy(Unknown Source) at java.awt.EventDispatchThread.pumpEvents(Unknown Source) at java.awt.EventDispatchThread.pumpEvents(Unknown Source) at java.awt.EventDispatchThread.run(Unknown Source) https://www.ebi.ac.uk/pride/ws/archive/project/count org.springframework.web.client.HttpClientErrorException$NotFound: 404 : "{ "timestamp" : 1698948884364, "status" : 404, "error" : "Not Found", "message" : "No message available", "path" : "/pride/ws/archive/v2/project/count"}" at org.springframework.web.client.HttpClientErrorException.create(HttpClientErrorException.java:113) at org.springframework.web.client.DefaultResponseErrorHandler.handleError(DefaultResponseErrorHandler.java:168) at org.springframework.web.client.DefaultResponseErrorHandler.handleError(DefaultResponseErrorHandler.java:122) at org.springframework.web.client.ResponseErrorHandler.handleError(ResponseErrorHandler.java:63) at org.springframework.web.client.RestTemplate.handleResponse(RestTemplate.java:819) at org.springframework.web.client.RestTemplate.doExecute(RestTemplate.java:777) at org.springframework.web.client.RestTemplate.execute(RestTemplate.java:711) at org.springframework.web.client.RestTemplate.getForEntity(RestTemplate.java:361) at eu.isas.peptideshaker.gui.pride.PrideReshakeGUI$33.run(PrideReshakeGUI.java:2523)

Thu Nov 02 19:15:17 CET 2023: PeptideShaker version 3.0.1. Memory given to the Java virtual machine: 3817865216. Total amount of memory in the Java virtual machine: 128974848. Free memory: 87067272. Java version: 1.8.0_391. 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_391 os.name: Windows 10 memory: 66.9/163.1 processors available: 4 useCommandThread: false Exception in thread "AWT-EventQueue-0" java.lang.ArrayIndexOutOfBoundsException: 11 >= 3 at java.util.Vector.elementAt(Unknown Source) at javax.swing.table.DefaultTableColumnModel.getColumn(Unknown Source) at javax.swing.plaf.basic.BasicTableHeaderUI.paint(Unknown Source) at javax.swing.plaf.synth.SynthTableHeaderUI.paint(Unknown Source) at javax.swing.plaf.synth.SynthTableHeaderUI.update(Unknown Source) at javax.swing.JComponent.paintComponent(Unknown Source) at javax.swing.JComponent.paint(Unknown Source) at javax.swing.JComponent.paintToOffscreen(Unknown Source) at javax.swing.RepaintManager$PaintManager.paintDoubleBuffered(Unknown Source) at javax.swing.RepaintManager$PaintManager.paint(Unknown Source) at javax.swing.RepaintManager.paint(Unknown Source) at javax.swing.JComponent._paintImmediately(Unknown Source) at javax.swing.JComponent.paintImmediately(Unknown Source) at javax.swing.RepaintManager$4.run(Unknown Source) at javax.swing.RepaintManager$4.run(Unknown Source) at java.security.AccessController.doPrivileged(Native Method) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(Unknown Source) at javax.swing.RepaintManager.paintDirtyRegions(Unknown Source) at javax.swing.RepaintManager.paintDirtyRegions(Unknown Source) at javax.swing.RepaintManager.prePaintDirtyRegions(Unknown Source) at javax.swing.RepaintManager.access$1200(Unknown Source) at javax.swing.RepaintManager$ProcessingRunnable.run(Unknown Source) at java.awt.event.InvocationEvent.dispatch(Unknown Source) at java.awt.EventQueue.dispatchEventImpl(Unknown Source) at java.awt.EventQueue.access$500(Unknown Source) at java.awt.EventQueue$3.run(Unknown Source) at java.awt.EventQueue$3.run(Unknown Source) at java.security.AccessController.doPrivileged(Native Method) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(Unknown Source) at java.awt.EventQueue.dispatchEvent(Unknown Source) at java.awt.EventDispatchThread.pumpOneEventForFilters(Unknown Source) at java.awt.EventDispatchThread.pumpEventsForFilter(Unknown Source) at java.awt.EventDispatchThread.pumpEventsForFilter(Unknown Source) at java.awt.WaitDispatchSupport$2.run(Unknown Source) at java.awt.event.InvocationEvent.dispatch(Unknown Source) at java.awt.EventQueue.dispatchEventImpl(Unknown Source) at java.awt.EventQueue.access$500(Unknown Source) at java.awt.EventQueue$3.run(Unknown Source) at java.awt.EventQueue$3.run(Unknown Source) at java.security.AccessController.doPrivileged(Native Method) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(Unknown Source) at java.awt.EventQueue.dispatchEvent(Unknown Source) at java.awt.EventDispatchThread.pumpOneEventForFilters(Unknown Source) at java.awt.EventDispatchThread.pumpEventsForFilter(Unknown Source) at java.awt.EventDispatchThread.pumpEventsForHierarchy(Unknown Source) at java.awt.EventDispatchThread.pumpEvents(Unknown Source) at java.awt.EventDispatchThread.pumpEvents(Unknown Source) at java.awt.EventDispatchThread.run(Unknown Source)

Thu Nov 02 19:20:09 CET 2023: PeptideShaker version 3.0.1. Memory given to the Java virtual machine: 3817865216. Total amount of memory in the Java virtual machine: 128974848. Free memory: 86449528. Java version: 1.8.0_391. 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_391 os.name: Windows 10 memory: 67.8/163.1 processors available: 4 useCommandThread: false

Thu Nov 02 19:42:51 CET 2023: PeptideShaker version 3.0.1. Memory given to the Java virtual machine: 3817865216. Total amount of memory in the Java virtual machine: 128974848. Free memory: 86455104. Java version: 1.8.0_391. 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_391 os.name: Windows 10 memory: 66.1/163.1 processors available: 4 useCommandThread: false

Thu Nov 02 19:47:38 CET 2023: PeptideShaker version 3.0.1. Memory given to the Java virtual machine: 3817865216. Total amount of memory in the Java virtual machine: 128974848. Free memory: 86505464. Java version: 1.8.0_391. 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_391 os.name: Windows 10 memory: 67.4/163.1 processors available: 4 useCommandThread: false

Thu Nov 02 19:57:33 CET 2023: PeptideShaker version 3.0.1. Memory given to the Java virtual machine: 3817865216. Total amount of memory in the Java virtual machine: 128974848. Free memory: 113723896. Java version: 1.8.0_391.

Thu Nov 02 20:01:11 CET 2023: PeptideShaker version 3.0.1. Memory given to the Java virtual machine: 3817865216. Total amount of memory in the Java virtual machine: 128974848. Free memory: 86417880. Java version: 1.8.0_391. 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_391 os.name: Windows 10 memory: 66.9/163.1 processors available: 4 useCommandThread: false

Fri Nov 03 11:14:26 CET 2023: PeptideShaker version 3.0.1. Memory given to the Java virtual machine: 3817865216. Total amount of memory in the Java virtual machine: 128974848. Free memory: 86457096. Java version: 1.8.0_391. 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_391 os.name: Windows 10 memory: 66.7/163.1 processors available: 4 useCommandThread: false

Fri Nov 03 11:24:09 CET 2023: PeptideShaker version 3.0.1. Memory given to the Java virtual machine: 3817865216. Total amount of memory in the Java virtual machine: 128974848. Free memory: 86462168. Java version: 1.8.0_391. 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_391 os.name: Windows 10 memory: 66.7/163.1 processors available: 4 useCommandThread: false

Fri Nov 03 11:25:46 CET 2023: PeptideShaker version 3.0.1. Memory given to the Java virtual machine: 11185160192. Total amount of memory in the Java virtual machine: 128974848. Free memory: 86264400. Java version: 1.8.0_391. 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_391 os.name: Windows 10 memory: 66.4/163.1 processors available: 4 useCommandThread: false

Command line: "C:\Program Files\Java\jre-1.8\bin\java" -splash:resources\conf\peptide-shaker-splash.png -Xms128M -Xmx12000M -cp "C:\TEMP\PeptideShaker-3.0.1\PeptideShaker-3.0.1.jar" eu.isas.peptideshaker.gui.PeptideShakerGUI

Fri Nov 03 11:26:44 CET 2023: PeptideShaker version 3.0.1. Memory given to the Java virtual machine: 11185160192. Total amount of memory in the Java virtual machine: 128974848. Free memory: 86918768. Java version: 1.8.0_391. 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_391 os.name: Windows 10 memory: 67.5/163.1 processors available: 4 useCommandThread: false Process exitValue: 0

Fri Nov 03 11:34:06 CET 2023: PeptideShaker version 3.0.1. Memory given to the Java virtual machine: 11185160192. Total amount of memory in the Java virtual machine: 128974848. Free memory: 86502848. Java version: 1.8.0_391. 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_391 os.name: Windows 10 memory: 67.5/163.1 processors available: 4 useCommandThread: false

Fri Nov 03 11:52:20 CET 2023: PeptideShaker version 3.0.1. Memory given to the Java virtual machine: 11185160192. Total amount of memory in the Java virtual machine: 128974848. Free memory: 86487128. Java version: 1.8.0_391. 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_391 os.name: Windows 10 memory: 67.3/163.1 processors available: 4 useCommandThread: false

Fri Nov 03 11:56:04 CET 2023: PeptideShaker version 3.0.1. Memory given to the Java virtual machine: 11185160192. Total amount of memory in the Java virtual machine: 128974848. Free memory: 86442328. Java version: 1.8.0_391. 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_391 os.name: Windows 10 memory: 66.3/163.1 processors available: 4 useCommandThread: false

Fri Nov 03 12:00:08 CET 2023: PeptideShaker version 3.0.1. Memory given to the Java virtual machine: 11185160192. Total amount of memory in the Java virtual machine: 128974848. Free memory: 86477440. Java version: 1.8.0_391. 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_391 os.name: Windows 10 memory: 65.9/163.1 processors available: 4 useCommandThread: false Exception in thread "AWT-EventQueue-0" java.lang.NoSuchMethodError: java.nio.MappedByteBuffer.position(I)Ljava/nio/MappedByteBuffer; at com.compomics.util.experiment.io.mass_spectrometry.cms.CmsFileReader.getSpectrum(CmsFileReader.java:189) at com.compomics.util.experiment.io.mass_spectrometry.cms.CmsFileReader.getSpectrum(CmsFileReader.java:253) at com.compomics.util.experiment.io.mass_spectrometry.MsFileHandler.getSpectrum(MsFileHandler.java:253) at eu.isas.peptideshaker.gui.tabpanels.OverviewPanel.updateSpectrum(OverviewPanel.java:4802) at eu.isas.peptideshaker.gui.tabpanels.OverviewPanel.psmTableMouseReleased(OverviewPanel.java:2069) at eu.isas.peptideshaker.gui.tabpanels.OverviewPanel.updateSelection(OverviewPanel.java:6701) at eu.isas.peptideshaker.gui.tabpanels.OverviewPanel.updatePsmSelection(OverviewPanel.java:5151) at eu.isas.peptideshaker.gui.tabpanels.OverviewPanel.access$9200(OverviewPanel.java:102) at eu.isas.peptideshaker.gui.tabpanels.OverviewPanel$72.run(OverviewPanel.java:2235) at java.awt.event.InvocationEvent.dispatch(Unknown Source) at java.awt.EventQueue.dispatchEventImpl(Unknown Source) at java.awt.EventQueue.access$500(Unknown Source) at java.awt.EventQueue$3.run(Unknown Source) at java.awt.EventQueue$3.run(Unknown Source) at java.security.AccessController.doPrivileged(Native Method) at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(Unknown Source) at java.awt.EventQueue.dispatchEvent(Unknown Source) at java.awt.EventDispatchThread.pumpOneEventForFilters(Unknown Source) at java.awt.EventDispatchThread.pumpEventsForFilter(Unknown Source) at java.awt.EventDispatchThread.pumpEventsForHierarchy(Unknown Source) at java.awt.EventDispatchThread.pumpEvents(Unknown Source) at java.awt.EventDispatchThread.pumpEvents(Unknown Source) at java.awt.EventDispatchThread.run(Unknown Source)

Fri Nov 03 13:28:49 CET 2023: PeptideShaker version 3.0.1. Memory given to the Java virtual machine: 11185160192. Total amount of memory in the Java virtual machine: 128974848. Free memory: 86955896. Java version: 1.8.0_391. 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_391 os.name: Windows 10 memory: 66.1/163.1 processors available: 4 useCommandThread: false

hbarsnes commented 11 months ago

The problem seems to be that you are using a rather old Java version. So if you update your Java version the problem should hopefully be fixed. You can update your Java version here: https://adoptium.net/temurin/releases

mryanshi commented 11 months ago

Thanks for the quick reply! Yes, after updating Java I am able to open the results with PeptideShaker.