search

compomics / searchgui

Highly adaptable common interface for proteomics search and de novo engines
http://compomics.github.io/projects/searchgui.html
42 stars 15 forks source link

Error #320

Closed lpaul-BioAnalysis closed 2 years ago

lpaul-BioAnalysis commented 2 years ago

All,

I have been getting this error. Any help will be appreciated. Search GUI 4.1.12

"An Error occurred while loading the gene mappings" error

Thanks,

Lake

hbarsnes commented 2 years ago

Hi Lake,

Can you please share the PeptideShaker error log? You can find it via the PeptideShaker Welcome Dialog > Settings & Help > Help > Bug Report. This log will hopefully enable us to figure out what is going wrong.

Best regards, Harald

lpaul-BioAnalysis commented 2 years ago

Fri Feb 25 18:30:15 EST 2022: PeptideShaker version 2.2.5. Memory given to the Java virtual machine: 4294967296. Total amount of memory in the Java virtual machine: 134217728. Free memory: 72870968. Java version: 17.0.1. 1714 script command tokens (C) 2009 Jmol Development Jmol Version: 12.0.43 2011-05-03 14:21 java.vendor: Oracle Corporation java.version: 17.0.1 os.name: Windows 10 memory: 45.6/134.2 processors available: 16 useCommandThread: false

Sat Jun 11 15:21:17 EDT 2022: PeptideShaker version 2.2.5. Memory given to the Java virtual machine: 4294967296. Total amount of memory in the Java virtual machine: 134217728. Free memory: 109393920. Java version: 17.0.1. javax.xml.stream.XMLStreamException: ParseError at [row,col]:[1,50] Message: White spaces are required between publicId and systemId. at java.xml/com.sun.org.apache.xerces.internal.impl.XMLStreamReaderImpl.next(XMLStreamReaderImpl.java:652) at java.xml/com.sun.xml.internal.stream.XMLEventReaderImpl.nextEvent(XMLEventReaderImpl.java:83) at com.compomics.software.autoupdater.MetaDataXMLParser.(MetaDataXMLParser.java:31) at com.compomics.software.autoupdater.WebDAO.getLatestVersionNumberFromRemoteRepo(WebDAO.java:37) at com.compomics.software.autoupdater.WebDAO.newVersionReleased(WebDAO.java:105) at com.compomics.software.CompomicsWrapper.checkForNewDeployedVersion(CompomicsWrapper.java:522) at eu.isas.peptideshaker.gui.PeptideShakerGUI.checkForNewVersion(PeptideShakerGUI.java:8479) at eu.isas.peptideshaker.gui.PeptideShakerGUI.(PeptideShakerGUI.java:627) at eu.isas.peptideshaker.gui.PeptideShakerGUI.main(PeptideShakerGUI.java:538) An error occurred while saving C:\Users\lpaul/.compomics/userparameters.cup. java.io.FileNotFoundException: C:\Users\lpaul.compomics\userparameters.cup (Access is denied) at java.base/java.io.FileOutputStream.open0(Native Method) at java.base/java.io.FileOutputStream.open(FileOutputStream.java:293) at java.base/java.io.FileOutputStream.(FileOutputStream.java:235) at java.base/java.io.FileOutputStream.(FileOutputStream.java:184) at java.base/java.io.FileWriter.(FileWriter.java:96) at com.compomics.util.io.json.JsonMarshaller.saveObjectToJson(JsonMarshaller.java:105) at com.compomics.util.parameters.UtilitiesUserParameters.saveUserParameters(UtilitiesUserParameters.java:598) at eu.isas.peptideshaker.gui.PeptideShakerGUI.(PeptideShakerGUI.java:638) at eu.isas.peptideshaker.gui.PeptideShakerGUI.main(PeptideShakerGUI.java:538) 1714 script command tokens (C) 2009 Jmol Development Jmol Version: 12.0.43 2011-05-03 14:21 java.vendor: Oracle Corporation java.version: 17.0.1 os.name: Windows 10 memory: 49.1/134.2 processors available: 16 useCommandThread: false java.io.FileNotFoundException: C:\Users\lpaul.peptideshaker\userpreferences_2.0.cpf (Access is denied) at java.base/java.io.FileOutputStream.open0(Native Method) at java.base/java.io.FileOutputStream.open(FileOutputStream.java:293) at java.base/java.io.FileOutputStream.(FileOutputStream.java:235) at java.base/java.io.FileOutputStream.(FileOutputStream.java:184) at com.compomics.util.io.file.SerializationUtils.writeObject(SerializationUtils.java:29) at eu.isas.peptideshaker.preferences.UserPreferencesParent.saveUserParameters(UserPreferencesParent.java:53) at eu.isas.peptideshaker.gui.PeptideShakerGUI$92.run(PeptideShakerGUI.java:5677) at java.desktop/java.awt.event.InvocationEvent.dispatch(InvocationEvent.java:318) at java.desktop/java.awt.EventQueue.dispatchEventImpl(EventQueue.java:771) at java.desktop/java.awt.EventQueue$4.run(EventQueue.java:722) at java.desktop/java.awt.EventQueue$4.run(EventQueue.java:716) at java.base/java.security.AccessController.doPrivileged(AccessController.java:399) at java.base/java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:86) at java.desktop/java.awt.EventQueue.dispatchEvent(EventQueue.java:741) at java.desktop/java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:203) at java.desktop/java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:124) at java.desktop/java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:117) at java.desktop/java.awt.WaitDispatchSupport$2.run(WaitDispatchSupport.java:191) at java.desktop/java.awt.event.InvocationEvent.dispatch(InvocationEvent.java:318) at java.desktop/java.awt.EventQueue.dispatchEventImpl(EventQueue.java:771) at java.desktop/java.awt.EventQueue$4.run(EventQueue.java:722) at java.desktop/java.awt.EventQueue$4.run(EventQueue.java:716) at java.base/java.security.AccessController.doPrivileged(AccessController.java:399) at java.base/java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:86) at java.desktop/java.awt.EventQueue.dispatchEvent(EventQueue.java:741) at java.desktop/java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:203) at java.desktop/java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:124) at java.desktop/java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:113) at java.desktop/java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:109) at java.desktop/java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:101) at java.desktop/java.awt.EventDispatchThread.run(EventDispatchThread.java:90)

Sat Jun 11 15:22:12 EDT 2022: PeptideShaker version 2.2.5. Memory given to the Java virtual machine: 4294967296. Total amount of memory in the Java virtual machine: 134217728. Free memory: 109493760. Java version: 17.0.1. javax.xml.stream.XMLStreamException: ParseError at [row,col]:[1,50] Message: White spaces are required between publicId and systemId. at java.xml/com.sun.org.apache.xerces.internal.impl.XMLStreamReaderImpl.next(XMLStreamReaderImpl.java:652) at java.xml/com.sun.xml.internal.stream.XMLEventReaderImpl.nextEvent(XMLEventReaderImpl.java:83) at com.compomics.software.autoupdater.MetaDataXMLParser.(MetaDataXMLParser.java:31) at com.compomics.software.autoupdater.WebDAO.getLatestVersionNumberFromRemoteRepo(WebDAO.java:37) at com.compomics.software.autoupdater.WebDAO.newVersionReleased(WebDAO.java:105) at com.compomics.software.CompomicsWrapper.checkForNewDeployedVersion(CompomicsWrapper.java:522) at eu.isas.peptideshaker.gui.PeptideShakerGUI.checkForNewVersion(PeptideShakerGUI.java:8479) at eu.isas.peptideshaker.gui.PeptideShakerGUI.(PeptideShakerGUI.java:627) at eu.isas.peptideshaker.gui.PeptideShakerGUI.main(PeptideShakerGUI.java:538) An error occurred while saving C:\Users\lpaul/.compomics/userparameters.cup. java.io.FileNotFoundException: C:\Users\lpaul.compomics\userparameters.cup (Access is denied) at java.base/java.io.FileOutputStream.open0(Native Method) at java.base/java.io.FileOutputStream.open(FileOutputStream.java:293) at java.base/java.io.FileOutputStream.(FileOutputStream.java:235) at java.base/java.io.FileOutputStream.(FileOutputStream.java:184) at java.base/java.io.FileWriter.(FileWriter.java:96) at com.compomics.util.io.json.JsonMarshaller.saveObjectToJson(JsonMarshaller.java:105) at com.compomics.util.parameters.UtilitiesUserParameters.saveUserParameters(UtilitiesUserParameters.java:598) at eu.isas.peptideshaker.gui.PeptideShakerGUI.(PeptideShakerGUI.java:638) at eu.isas.peptideshaker.gui.PeptideShakerGUI.main(PeptideShakerGUI.java:538) 1714 script command tokens (C) 2009 Jmol Development Jmol Version: 12.0.43 2011-05-03 14:21 java.vendor: Oracle Corporation java.version: 17.0.1 os.name: Windows 10 memory: 48.8/134.2 processors available: 16 useCommandThread: false

hbarsnes commented 2 years ago

Thanks for the error log. However, I see now that I asked for the wrong log file. Can you send me the same file but for SearchGUI? You'll find it via Help > Bug Report in the main SearchGUI dialog.

lpaul-BioAnalysis commented 2 years ago

java.io.FileNotFoundException: C:\Users\lpaul.compomics\gene_mappings\ensembl_versions (Access is denied) at java.base/java.io.FileOutputStream.open0(Native Method) at java.base/java.io.FileOutputStream.open(FileOutputStream.java:293) at java.base/java.io.FileOutputStream.(FileOutputStream.java:235) at java.base/java.io.FileOutputStream.(FileOutputStream.java:184) at java.base/java.io.FileWriter.(FileWriter.java:96) at com.compomics.util.experiment.biology.genes.ProteinGeneDetailsProvider.updateEnsemblVersion(ProteinGeneDetailsProvider.java:857) at com.compomics.util.experiment.biology.genes.ProteinGeneDetailsProvider.createDefaultGeneMappingFilesGeneric(ProteinGeneDetailsProvider.java:768) at com.compomics.util.experiment.biology.genes.ProteinGeneDetailsProvider.initialize(ProteinGeneDetailsProvider.java:103) at eu.isas.searchgui.gui.SearchGUI.(SearchGUI.java:312) at eu.isas.searchgui.gui.SearchGUI.main(SearchGUI.java:7238) java.lang.IllegalArgumentException: Could not create or update the Ensembl versions file. at com.compomics.util.experiment.biology.genes.ProteinGeneDetailsProvider.createDefaultGeneMappingFilesGeneric(ProteinGeneDetailsProvider.java:779) at com.compomics.util.experiment.biology.genes.ProteinGeneDetailsProvider.initialize(ProteinGeneDetailsProvider.java:103) at eu.isas.searchgui.gui.SearchGUI.(SearchGUI.java:312) at eu.isas.searchgui.gui.SearchGUI.main(SearchGUI.java:7238) An error occurred while saving C:\Users\lpaul/.compomics/userparameters.cup. java.io.FileNotFoundException: C:\Users\lpaul.compomics\userparameters.cup (Access is denied) at java.base/java.io.FileOutputStream.open0(Native Method) at java.base/java.io.FileOutputStream.open(FileOutputStream.java:293) at java.base/java.io.FileOutputStream.(FileOutputStream.java:235) at java.base/java.io.FileOutputStream.(FileOutputStream.java:184) at java.base/java.io.FileWriter.(FileWriter.java:96) at com.compomics.util.io.json.JsonMarshaller.saveObjectToJson(JsonMarshaller.java:105) at com.compomics.util.parameters.UtilitiesUserParameters.saveUserParameters(UtilitiesUserParameters.java:598) at eu.isas.searchgui.gui.SearchGUI.(SearchGUI.java:331) at eu.isas.searchgui.gui.SearchGUI.main(SearchGUI.java:7238) jshortcut.dll loaded via tmp generated pathname: C:\Users\lpaul\AppData\Local\Temp\jshortcut-18252110924300497726.dll java.io.FileNotFoundException: C:\Users\lpaul.compomics\gene_mappings\ensembl_versions (Access is denied) at java.base/java.io.FileOutputStream.open0(Native Method) at java.base/java.io.FileOutputStream.open(FileOutputStream.java:293) at java.base/java.io.FileOutputStream.(FileOutputStream.java:235) at java.base/java.io.FileOutputStream.(FileOutputStream.java:184) at java.base/java.io.FileWriter.(FileWriter.java:96) at com.compomics.util.experiment.biology.genes.ProteinGeneDetailsProvider.updateEnsemblVersion(ProteinGeneDetailsProvider.java:857) at com.compomics.util.experiment.biology.genes.ProteinGeneDetailsProvider.createDefaultGeneMappingFilesGeneric(ProteinGeneDetailsProvider.java:768) at com.compomics.util.experiment.biology.genes.ProteinGeneDetailsProvider.initialize(ProteinGeneDetailsProvider.java:103) at eu.isas.searchgui.gui.SearchGUI.(SearchGUI.java:312) at eu.isas.searchgui.gui.SearchGUI.main(SearchGUI.java:7238) java.lang.IllegalArgumentException: Could not create or update the Ensembl versions file. at com.compomics.util.experiment.biology.genes.ProteinGeneDetailsProvider.createDefaultGeneMappingFilesGeneric(ProteinGeneDetailsProvider.java:779) at com.compomics.util.experiment.biology.genes.ProteinGeneDetailsProvider.initialize(ProteinGeneDetailsProvider.java:103) at eu.isas.searchgui.gui.SearchGUI.(SearchGUI.java:312) at eu.isas.searchgui.gui.SearchGUI.main(SearchGUI.java:7238) An error occurred while saving C:\Users\lpaul/.compomics/userparameters.cup. java.io.FileNotFoundException: C:\Users\lpaul.compomics\userparameters.cup (Access is denied) at java.base/java.io.FileOutputStream.open0(Native Method) at java.base/java.io.FileOutputStream.open(FileOutputStream.java:293) at java.base/java.io.FileOutputStream.(FileOutputStream.java:235) at java.base/java.io.FileOutputStream.(FileOutputStream.java:184) at java.base/java.io.FileWriter.(FileWriter.java:96) at com.compomics.util.io.json.JsonMarshaller.saveObjectToJson(JsonMarshaller.java:105) at com.compomics.util.parameters.UtilitiesUserParameters.saveUserParameters(UtilitiesUserParameters.java:598) at eu.isas.searchgui.gui.SearchGUI.(SearchGUI.java:331) at eu.isas.searchgui.gui.SearchGUI.main(SearchGUI.java:7238) An error occurred while saving C:\Users\lpaul/.compomics/userparameters.cup. java.io.FileNotFoundException: C:\Users\lpaul.compomics\userparameters.cup (Access is denied) at java.base/java.io.FileOutputStream.open0(Native Method) at java.base/java.io.FileOutputStream.open(FileOutputStream.java:293) at java.base/java.io.FileOutputStream.(FileOutputStream.java:235) at java.base/java.io.FileOutputStream.(FileOutputStream.java:184) at java.base/java.io.FileWriter.(FileWriter.java:96) at com.compomics.util.io.json.JsonMarshaller.saveObjectToJson(JsonMarshaller.java:105) at com.compomics.util.parameters.UtilitiesUserParameters.saveUserParameters(UtilitiesUserParameters.java:598) at eu.isas.searchgui.gui.SearchGUI$114.run(SearchGUI.java:2759) An error occurred while saving C:\Users\lpaul/.compomics/userparameters.cup. java.io.FileNotFoundException: C:\Users\lpaul.compomics\userparameters.cup (Access is denied) at java.base/java.io.FileOutputStream.open0(Native Method) at java.base/java.io.FileOutputStream.open(FileOutputStream.java:293) at java.base/java.io.FileOutputStream.(FileOutputStream.java:235) at java.base/java.io.FileOutputStream.(FileOutputStream.java:184) at java.base/java.io.FileWriter.(FileWriter.java:96) at com.compomics.util.io.json.JsonMarshaller.saveObjectToJson(JsonMarshaller.java:105) at com.compomics.util.parameters.UtilitiesUserParameters.saveUserParameters(UtilitiesUserParameters.java:598) at com.compomics.util.gui.parameters.identification.search.SequenceDbDetailsDialog.okButtonActionPerformed(SequenceDbDetailsDialog.java:1021) at com.compomics.util.gui.parameters.identification.search.SequenceDbDetailsDialog.access$900(SequenceDbDetailsDialog.java:43) at com.compomics.util.gui.parameters.identification.search.SequenceDbDetailsDialog$6.actionPerformed(SequenceDbDetailsDialog.java:740) at java.desktop/javax.swing.AbstractButton.fireActionPerformed(AbstractButton.java:1972) at java.desktop/javax.swing.AbstractButton$Handler.actionPerformed(AbstractButton.java:2313) at java.desktop/javax.swing.DefaultButtonModel.fireActionPerformed(DefaultButtonModel.java:405) at java.desktop/javax.swing.DefaultButtonModel.setPressed(DefaultButtonModel.java:262) at java.desktop/javax.swing.plaf.basic.BasicButtonListener.mouseReleased(BasicButtonListener.java:279) at java.desktop/java.awt.Component.processMouseEvent(Component.java:6626) at java.desktop/javax.swing.JComponent.processMouseEvent(JComponent.java:3389) at java.desktop/java.awt.Component.processEvent(Component.java:6391) at java.desktop/java.awt.Container.processEvent(Container.java:2266) at java.desktop/java.awt.Component.dispatchEventImpl(Component.java:5001) at java.desktop/java.awt.Container.dispatchEventImpl(Container.java:2324) at java.desktop/java.awt.Component.dispatchEvent(Component.java:4833) at java.desktop/java.awt.LightweightDispatcher.retargetMouseEvent(Container.java:4948) at java.desktop/java.awt.LightweightDispatcher.processMouseEvent(Container.java:4575) at java.desktop/java.awt.LightweightDispatcher.dispatchEvent(Container.java:4516) at java.desktop/java.awt.Container.dispatchEventImpl(Container.java:2310) at java.desktop/java.awt.Window.dispatchEventImpl(Window.java:2780) at java.desktop/java.awt.Component.dispatchEvent(Component.java:4833) at java.desktop/java.awt.EventQueue.dispatchEventImpl(EventQueue.java:773) at java.desktop/java.awt.EventQueue$4.run(EventQueue.java:722) at java.desktop/java.awt.EventQueue$4.run(EventQueue.java:716) at java.base/java.security.AccessController.doPrivileged(AccessController.java:399) at java.base/java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:86) at java.base/java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:97) at java.desktop/java.awt.EventQueue$5.run(EventQueue.java:746) at java.desktop/java.awt.EventQueue$5.run(EventQueue.java:744) at java.base/java.security.AccessController.doPrivileged(AccessController.java:399) at java.base/java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:86) at java.desktop/java.awt.EventQueue.dispatchEvent(EventQueue.java:743) at java.desktop/java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:203) at java.desktop/java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:124) at java.desktop/java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:117) at java.desktop/java.awt.WaitDispatchSupport$2.run(WaitDispatchSupport.java:191) at java.desktop/java.awt.WaitDispatchSupport$4.run(WaitDispatchSupport.java:236) at java.desktop/java.awt.WaitDispatchSupport$4.run(WaitDispatchSupport.java:234) at java.base/java.security.AccessController.doPrivileged(AccessController.java:318) at java.desktop/java.awt.WaitDispatchSupport.enter(WaitDispatchSupport.java:234) at java.desktop/java.awt.Dialog.show(Dialog.java:1080) at java.desktop/java.awt.Component.show(Component.java:1728) at java.desktop/java.awt.Component.setVisible(Component.java:1675) at java.desktop/java.awt.Window.setVisible(Window.java:1036) at java.desktop/java.awt.Dialog.setVisible(Dialog.java:1016) at eu.isas.searchgui.gui.SearchGUI.editDatabaseDetailsButtonActionPerformed(SearchGUI.java:5977) at eu.isas.searchgui.gui.SearchGUI.access$12800(SearchGUI.java:115) at eu.isas.searchgui.gui.SearchGUI$80.actionPerformed(SearchGUI.java:1912) at java.desktop/javax.swing.AbstractButton.fireActionPerformed(AbstractButton.java:1972) at java.desktop/javax.swing.AbstractButton$Handler.actionPerformed(AbstractButton.java:2313) at java.desktop/javax.swing.DefaultButtonModel.fireActionPerformed(DefaultButtonModel.java:405) at java.desktop/javax.swing.DefaultButtonModel.setPressed(DefaultButtonModel.java:262) at java.desktop/javax.swing.plaf.basic.BasicButtonListener.mouseReleased(BasicButtonListener.java:279) at java.desktop/java.awt.Component.processMouseEvent(Component.java:6626) at java.desktop/javax.swing.JComponent.processMouseEvent(JComponent.java:3389) at java.desktop/java.awt.Component.processEvent(Component.java:6391) at java.desktop/java.awt.Container.processEvent(Container.java:2266) at java.desktop/java.awt.Component.dispatchEventImpl(Component.java:5001) at java.desktop/java.awt.Container.dispatchEventImpl(Container.java:2324) at java.desktop/java.awt.Component.dispatchEvent(Component.java:4833) at java.desktop/java.awt.LightweightDispatcher.retargetMouseEvent(Container.java:4948) at java.desktop/java.awt.LightweightDispatcher.processMouseEvent(Container.java:4575) at java.desktop/java.awt.LightweightDispatcher.dispatchEvent(Container.java:4516) at java.desktop/java.awt.Container.dispatchEventImpl(Container.java:2310) at java.desktop/java.awt.Window.dispatchEventImpl(Window.java:2780) at java.desktop/java.awt.Component.dispatchEvent(Component.java:4833) at java.desktop/java.awt.EventQueue.dispatchEventImpl(EventQueue.java:773) at java.desktop/java.awt.EventQueue$4.run(EventQueue.java:722) at java.desktop/java.awt.EventQueue$4.run(EventQueue.java:716) at java.base/java.security.AccessController.doPrivileged(AccessController.java:399) at java.base/java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:86) at java.base/java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:97) at java.desktop/java.awt.EventQueue$5.run(EventQueue.java:746) at java.desktop/java.awt.EventQueue$5.run(EventQueue.java:744) at java.base/java.security.AccessController.doPrivileged(AccessController.java:399) at java.base/java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:86) at java.desktop/java.awt.EventQueue.dispatchEvent(EventQueue.java:743) at java.desktop/java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:203) at java.desktop/java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:124) at java.desktop/java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:113) at java.desktop/java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:109) at java.desktop/java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:101) at java.desktop/java.awt.EventDispatchThread.run(EventDispatchThread.java:90) An error occurred while saving C:\Users\lpaul/.compomics/userparameters.cup. java.io.FileNotFoundException: C:\Users\lpaul.compomics\userparameters.cup (Access is denied) at java.base/java.io.FileOutputStream.open0(Native Method) at java.base/java.io.FileOutputStream.open(FileOutputStream.java:293) at java.base/java.io.FileOutputStream.(FileOutputStream.java:235) at java.base/java.io.FileOutputStream.(FileOutputStream.java:184) at java.base/java.io.FileWriter.(FileWriter.java:96) at com.compomics.util.io.json.JsonMarshaller.saveObjectToJson(JsonMarshaller.java:105) at com.compomics.util.parameters.UtilitiesUserParameters.saveUserParameters(UtilitiesUserParameters.java:598) at eu.isas.searchgui.gui.SearchGUI.editResultFolderButtonActionPerformed(SearchGUI.java:2851) at eu.isas.searchgui.gui.SearchGUI.access$12600(SearchGUI.java:115) at eu.isas.searchgui.gui.SearchGUI$78.actionPerformed(SearchGUI.java:1888) at java.desktop/javax.swing.AbstractButton.fireActionPerformed(AbstractButton.java:1972) at java.desktop/javax.swing.AbstractButton$Handler.actionPerformed(AbstractButton.java:2313) at java.desktop/javax.swing.DefaultButtonModel.fireActionPerformed(DefaultButtonModel.java:405) at java.desktop/javax.swing.DefaultButtonModel.setPressed(DefaultButtonModel.java:262) at java.desktop/javax.swing.plaf.basic.BasicButtonListener.mouseReleased(BasicButtonListener.java:279) at java.desktop/java.awt.Component.processMouseEvent(Component.java:6626) at java.desktop/javax.swing.JComponent.processMouseEvent(JComponent.java:3389) at java.desktop/java.awt.Component.processEvent(Component.java:6391) at java.desktop/java.awt.Container.processEvent(Container.java:2266) at java.desktop/java.awt.Component.dispatchEventImpl(Component.java:5001) at java.desktop/java.awt.Container.dispatchEventImpl(Container.java:2324) at java.desktop/java.awt.Component.dispatchEvent(Component.java:4833) at java.desktop/java.awt.LightweightDispatcher.retargetMouseEvent(Container.java:4948) at java.desktop/java.awt.LightweightDispatcher.processMouseEvent(Container.java:4575) at java.desktop/java.awt.LightweightDispatcher.dispatchEvent(Container.java:4516) at java.desktop/java.awt.Container.dispatchEventImpl(Container.java:2310) at java.desktop/java.awt.Window.dispatchEventImpl(Window.java:2780) at java.desktop/java.awt.Component.dispatchEvent(Component.java:4833) at java.desktop/java.awt.EventQueue.dispatchEventImpl(EventQueue.java:773) at java.desktop/java.awt.EventQueue$4.run(EventQueue.java:722) at java.desktop/java.awt.EventQueue$4.run(EventQueue.java:716) at java.base/java.security.AccessController.doPrivileged(AccessController.java:399) at java.base/java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:86) at java.base/java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:97) at java.desktop/java.awt.EventQueue$5.run(EventQueue.java:746) at java.desktop/java.awt.EventQueue$5.run(EventQueue.java:744) at java.base/java.security.AccessController.doPrivileged(AccessController.java:399) at java.base/java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:86) at java.desktop/java.awt.EventQueue.dispatchEvent(EventQueue.java:743) at java.desktop/java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:203) at java.desktop/java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:124) at java.desktop/java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:113) at java.desktop/java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:109) at java.desktop/java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:101) at java.desktop/java.awt.EventDispatchThread.run(EventDispatchThread.java:90)

MetaMorpheus command: C:\SearchGUI-4.1.12\resources\MetaMorpheus\CMD.exe --mmsettings C:\SearchGUI-4.1.12\resources\temp\search_engines\metamorpheus -d C:\MS Data\Aruvant\P2021134\Fasta\Fasta\HCP\uniprot-proteome_UP000005640_concatenated_target_decoy.fasta -s C:\MS Data\Aruvant\P2021134\Data\BIA-1144-1_LysC-Tryp_1_A.mzML -t C:\SearchGUI-4.1.12\resources\temp\search_engines\metamorpheus\Search.toml -o C:\SearchGUI-4.1.12\resources\temp\search_engines\metamorpheus

java.io.FileNotFoundException: C:\Users\lpaul.compomics\identification_parameters_4\Trypsin.par (Access is denied) at java.base/java.io.FileOutputStream.open0(Native Method) at java.base/java.io.FileOutputStream.open(FileOutputStream.java:293) at java.base/java.io.FileOutputStream.(FileOutputStream.java:235) at java.base/java.io.FileOutputStream.(FileOutputStream.java:184) at java.base/java.io.FileWriter.(FileWriter.java:96) at com.compomics.util.io.json.JsonMarshaller.saveObjectToJson(JsonMarshaller.java:105) at com.compomics.util.parameters.identification.IdentificationParameters.saveIdentificationParameters(IdentificationParameters.java:614) at com.compomics.util.experiment.identification.identification_parameters.IdentificationParametersFactory.addIdentificationParameters(IdentificationParametersFactory.java:128) at eu.isas.searchgui.SearchHandler$SearchWorker.doInBackground(SearchHandler.java:3401) at java.desktop/javax.swing.SwingWorker$1.call(SwingWorker.java:304) at java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264) at java.desktop/javax.swing.SwingWorker.run(SwingWorker.java:343) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1136) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:635) at java.base/java.lang.Thread.run(Thread.java:833) java.io.FileNotFoundException: C:\Users\lpaul.compomics\gene_mappings\ensembl_versions (Access is denied) at java.base/java.io.FileOutputStream.open0(Native Method) at java.base/java.io.FileOutputStream.open(FileOutputStream.java:293) at java.base/java.io.FileOutputStream.(FileOutputStream.java:235) at java.base/java.io.FileOutputStream.(FileOutputStream.java:184) at java.base/java.io.FileWriter.(FileWriter.java:96) at com.compomics.util.experiment.biology.genes.ProteinGeneDetailsProvider.updateEnsemblVersion(ProteinGeneDetailsProvider.java:857) at com.compomics.util.experiment.biology.genes.ProteinGeneDetailsProvider.createDefaultGeneMappingFilesGeneric(ProteinGeneDetailsProvider.java:768) at com.compomics.util.experiment.biology.genes.ProteinGeneDetailsProvider.initialize(ProteinGeneDetailsProvider.java:103) at eu.isas.searchgui.gui.SearchGUI.(SearchGUI.java:312) at eu.isas.searchgui.gui.SearchGUI.main(SearchGUI.java:7238) java.lang.IllegalArgumentException: Could not create or update the Ensembl versions file. at com.compomics.util.experiment.biology.genes.ProteinGeneDetailsProvider.createDefaultGeneMappingFilesGeneric(ProteinGeneDetailsProvider.java:779) at com.compomics.util.experiment.biology.genes.ProteinGeneDetailsProvider.initialize(ProteinGeneDetailsProvider.java:103) at eu.isas.searchgui.gui.SearchGUI.(SearchGUI.java:312) at eu.isas.searchgui.gui.SearchGUI.main(SearchGUI.java:7238) An error occurred while saving C:\Users\lpaul/.compomics/userparameters.cup. java.io.FileNotFoundException: C:\Users\lpaul.compomics\userparameters.cup (Access is denied) at java.base/java.io.FileOutputStream.open0(Native Method) at java.base/java.io.FileOutputStream.open(FileOutputStream.java:293) at java.base/java.io.FileOutputStream.(FileOutputStream.java:235) at java.base/java.io.FileOutputStream.(FileOutputStream.java:184) at java.base/java.io.FileWriter.(FileWriter.java:96) at com.compomics.util.io.json.JsonMarshaller.saveObjectToJson(JsonMarshaller.java:105) at com.compomics.util.parameters.UtilitiesUserParameters.saveUserParameters(UtilitiesUserParameters.java:598) at eu.isas.searchgui.gui.SearchGUI.(SearchGUI.java:331) at eu.isas.searchgui.gui.SearchGUI.main(SearchGUI.java:7238) java.io.FileNotFoundException: C:\Users\lpaul.compomics\gene_mappings\ensembl_versions (Access is denied) at java.base/java.io.FileOutputStream.open0(Native Method) at java.base/java.io.FileOutputStream.open(FileOutputStream.java:293) at java.base/java.io.FileOutputStream.(FileOutputStream.java:235) at java.base/java.io.FileOutputStream.(FileOutputStream.java:184) at java.base/java.io.FileWriter.(FileWriter.java:96) at com.compomics.util.experiment.biology.genes.ProteinGeneDetailsProvider.updateEnsemblVersion(ProteinGeneDetailsProvider.java:857) at com.compomics.util.experiment.biology.genes.ProteinGeneDetailsProvider.createDefaultGeneMappingFilesGeneric(ProteinGeneDetailsProvider.java:768) at com.compomics.util.experiment.biology.genes.ProteinGeneDetailsProvider.initialize(ProteinGeneDetailsProvider.java:103) at eu.isas.searchgui.gui.SearchGUI.(SearchGUI.java:312) at eu.isas.searchgui.gui.SearchGUI.main(SearchGUI.java:7238) java.lang.IllegalArgumentException: Could not create or update the Ensembl versions file. at com.compomics.util.experiment.biology.genes.ProteinGeneDetailsProvider.createDefaultGeneMappingFilesGeneric(ProteinGeneDetailsProvider.java:779) at com.compomics.util.experiment.biology.genes.ProteinGeneDetailsProvider.initialize(ProteinGeneDetailsProvider.java:103) at eu.isas.searchgui.gui.SearchGUI.(SearchGUI.java:312) at eu.isas.searchgui.gui.SearchGUI.main(SearchGUI.java:7238) An error occurred while saving C:\Users\lpaul/.compomics/userparameters.cup. java.io.FileNotFoundException: C:\Users\lpaul.compomics\userparameters.cup (Access is denied) at java.base/java.io.FileOutputStream.open0(Native Method) at java.base/java.io.FileOutputStream.open(FileOutputStream.java:293) at java.base/java.io.FileOutputStream.(FileOutputStream.java:235) at java.base/java.io.FileOutputStream.(FileOutputStream.java:184) at java.base/java.io.FileWriter.(FileWriter.java:96) at com.compomics.util.io.json.JsonMarshaller.saveObjectToJson(JsonMarshaller.java:105) at com.compomics.util.parameters.UtilitiesUserParameters.saveUserParameters(UtilitiesUserParameters.java:598) at eu.isas.searchgui.gui.SearchGUI.(SearchGUI.java:331) at eu.isas.searchgui.gui.SearchGUI.main(SearchGUI.java:7238) java.io.FileNotFoundException: C:\Users\lpaul.compomics\gene_mappings\ensembl_versions (Access is denied) at java.base/java.io.FileOutputStream.open0(Native Method) at java.base/java.io.FileOutputStream.open(FileOutputStream.java:293) at java.base/java.io.FileOutputStream.(FileOutputStream.java:235) at java.base/java.io.FileOutputStream.(FileOutputStream.java:184) at java.base/java.io.FileWriter.(FileWriter.java:96) at com.compomics.util.experiment.biology.genes.ProteinGeneDetailsProvider.updateEnsemblVersion(ProteinGeneDetailsProvider.java:857) at com.compomics.util.experiment.biology.genes.ProteinGeneDetailsProvider.createDefaultGeneMappingFilesGeneric(ProteinGeneDetailsProvider.java:768) at com.compomics.util.experiment.biology.genes.ProteinGeneDetailsProvider.initialize(ProteinGeneDetailsProvider.java:103) at eu.isas.searchgui.gui.SearchGUI.(SearchGUI.java:312) at eu.isas.searchgui.gui.SearchGUI.main(SearchGUI.java:7238) java.lang.IllegalArgumentException: Could not create or update the Ensembl versions file. at com.compomics.util.experiment.biology.genes.ProteinGeneDetailsProvider.createDefaultGeneMappingFilesGeneric(ProteinGeneDetailsProvider.java:779) at com.compomics.util.experiment.biology.genes.ProteinGeneDetailsProvider.initialize(ProteinGeneDetailsProvider.java:103) at eu.isas.searchgui.gui.SearchGUI.(SearchGUI.java:312) at eu.isas.searchgui.gui.SearchGUI.main(SearchGUI.java:7238) An error occurred while saving C:\Users\lpaul/.compomics/userparameters.cup. java.io.FileNotFoundException: C:\Users\lpaul.compomics\userparameters.cup (Access is denied) at java.base/java.io.FileOutputStream.open0(Native Method) at java.base/java.io.FileOutputStream.open(FileOutputStream.java:293) at java.base/java.io.FileOutputStream.(FileOutputStream.java:235) at java.base/java.io.FileOutputStream.(FileOutputStream.java:184) at java.base/java.io.FileWriter.(FileWriter.java:96) at com.compomics.util.io.json.JsonMarshaller.saveObjectToJson(JsonMarshaller.java:105) at com.compomics.util.parameters.UtilitiesUserParameters.saveUserParameters(UtilitiesUserParameters.java:598) at eu.isas.searchgui.gui.SearchGUI.(SearchGUI.java:331) at eu.isas.searchgui.gui.SearchGUI.main(SearchGUI.java:7238) java.io.FileNotFoundException: C:\Users\lpaul.compomics\gene_mappings\ensembl_versions (Access is denied) at java.base/java.io.FileOutputStream.open0(Native Method) at java.base/java.io.FileOutputStream.open(FileOutputStream.java:293) at java.base/java.io.FileOutputStream.(FileOutputStream.java:235) at java.base/java.io.FileOutputStream.(FileOutputStream.java:184) at java.base/java.io.FileWriter.(FileWriter.java:96) at com.compomics.util.experiment.biology.genes.ProteinGeneDetailsProvider.updateEnsemblVersion(ProteinGeneDetailsProvider.java:857) at com.compomics.util.experiment.biology.genes.ProteinGeneDetailsProvider.createDefaultGeneMappingFilesGeneric(ProteinGeneDetailsProvider.java:768) at com.compomics.util.experiment.biology.genes.ProteinGeneDetailsProvider.initialize(ProteinGeneDetailsProvider.java:103) at eu.isas.searchgui.gui.SearchGUI.(SearchGUI.java:312) at eu.isas.searchgui.gui.SearchGUI.main(SearchGUI.java:7238) java.lang.IllegalArgumentException: Could not create or update the Ensembl versions file. at com.compomics.util.experiment.biology.genes.ProteinGeneDetailsProvider.createDefaultGeneMappingFilesGeneric(ProteinGeneDetailsProvider.java:779) at com.compomics.util.experiment.biology.genes.ProteinGeneDetailsProvider.initialize(ProteinGeneDetailsProvider.java:103) at eu.isas.searchgui.gui.SearchGUI.(SearchGUI.java:312) at eu.isas.searchgui.gui.SearchGUI.main(SearchGUI.java:7238) An error occurred while saving C:\Users\lpaul/.compomics/userparameters.cup. java.io.FileNotFoundException: C:\Users\lpaul.compomics\userparameters.cup (Access is denied) at java.base/java.io.FileOutputStream.open0(Native Method) at java.base/java.io.FileOutputStream.open(FileOutputStream.java:293) at java.base/java.io.FileOutputStream.(FileOutputStream.java:235) at java.base/java.io.FileOutputStream.(FileOutputStream.java:184) at java.base/java.io.FileWriter.(FileWriter.java:96) at com.compomics.util.io.json.JsonMarshaller.saveObjectToJson(JsonMarshaller.java:105) at com.compomics.util.parameters.UtilitiesUserParameters.saveUserParameters(UtilitiesUserParameters.java:598) at eu.isas.searchgui.gui.SearchGUI.(SearchGUI.java:331) at eu.isas.searchgui.gui.SearchGUI.main(SearchGUI.java:7238)

hbarsnes commented 2 years ago

It seems like you do not have writing access to the folder where the SearchGUI (and PeptideShaker) setting files are stored. The default location is your user home folder, which in your case seems to be "C:\Users\lpaul".

You can change the location via Edit > Resource Settings in SearchGUI. It is probably recommended to right-click in the table and use the "Set Default Path" option. This will allow you change all the paths in one operation. After this change you have to restart the tool.

If this works, I recommend doing the same for PeptideShaker as well. There you can do it via the Welcome Dialog > Settings & Help > Settings > Resource Settings.

hbarsnes commented 2 years ago

Issue assumed resolved. If this is not the case, please let us know and we'll reopen the issue.