Jalview Version: 2.11.1.0
Jalview Installation: Source git-commit:3db6404 [bug/JAL-3628_Unable_to_save_update_to_existing_file_in_Windows]
Build Date: 02:00:31 07 July 2020
Java version: 1.8.0_242
amd64 Windows 10 10.0
Install4j version: 8.0.5
Install4j template version: 2.11.1.0_F10e9b8be_C3db6404
Launcher version: 1.8.3-1.2.4_JVL
DEBUG - ALIGNFRAME making backupfiles object for E:\PATH.fa
DEBUG - BACKUPFILES classInit
DEBUG - BACKUPFILES disabled
DEBUG - BACKUPFILESPRESETENTRY saved preset string is .bak%n 3 false false 3 false
DEBUG - BACKUPFILES preset scheme .bak%n 3 false false 3 false
DEBUG - BACKUPFILES confirm delete false
DEBUG - BACKUPFILESPRESETENTRY saved preset string is .bak%n 3 false false 3 false
DEBUG - BACKUPFILES [file!=null] attempting to create temp file for PATH.fa in dir E:\
DEBUG - BACKUPFILES using temp file E:\PATH.fa1540118307989593739.tmp_newfile
DEBUG - ALIGNFRAME setting PrintWriter to E:\PATH.fa1540118307989593739.tmp_newfile
DEBUG - ALIGNFRAME about to write to temp file E:\PATH.fa1540118307989593739.tmp_newfile
DEBUG - ALIGNFRAME about to close file
DEBUG - ALIGNFRAME closed file
DEBUG - ALIGNFRAME writing temp file was successful
DEBUG - ALIGNFRAME about to rollBackupsAndRenameTempFile
DEBUG - BACKUPFILES rollBackupFiles nothing to do., filename: PATH.fa, file exists: true, enabled: false, max: 3, suffix: '.bak%n'
DEBUG - BACKUPFILES deleting E:\PATH.fa
DEBUG - BACKUPFILES moving E:\PATH.fa1540118307989593739.tmp_newfile to E:\PATH.fa
WARN - Could not move file 'E:\PATH.fa1540118307989593739.tmp_newfile' to 'E:\PATH.fa'
ERROR - E:\PATH.fa: The process cannot access the file because it is being used by another process.

DEBUG - java.nio.file.FileSystemException: E:\PATH.fa: The process cannot access the file because it is being used by another process.

   at sun.nio.fs.WindowsException.translateToIOException(WindowsException.java:86)
   at sun.nio.fs.WindowsException.rethrowAsIOException(WindowsException.java:97)
   at sun.nio.fs.WindowsException.rethrowAsIOException(WindowsException.java:102)
   at sun.nio.fs.WindowsFileCopy.move(WindowsFileCopy.java:376)
   at sun.nio.fs.WindowsFileSystemProvider.move(WindowsFileSystemProvider.java:287)
   at java.nio.file.Files.move(Files.java:1395)
   at jalview.io.BackupFiles.moveFileToFile(BackupFiles.java:908)
   at jalview.io.BackupFiles.renameTempFile(BackupFiles.java:240)
   at jalview.io.BackupFiles.rollBackupsAndRenameTempFile(BackupFiles.java:767)
   at jalview.gui.AlignFrame.saveAlignment(AlignFrame.java:1245)
   at jalview.gui.AlignFrame.save_actionPerformed(AlignFrame.java:1102)
   at jalview.jbgui.GAlignFrame$106.actionPerformed(GAlignFrame.java:1603)
   at javax.swing.AbstractButton.fireActionPerformed(AbstractButton.java:2022)
   at javax.swing.AbstractButton$Handler.actionPerformed(AbstractButton.java:2348)
   at javax.swing.DefaultButtonModel.fireActionPerformed(DefaultButtonModel.java:402)
   at javax.swing.DefaultButtonModel.setPressed(DefaultButtonModel.java:259)
   at javax.swing.AbstractButton.doClick(AbstractButton.java:376)
   at javax.swing.plaf.basic.BasicMenuItemUI.doClick(BasicMenuItemUI.java:842)
   at javax.swing.plaf.basic.BasicMenuItemUI$Handler.mouseReleased(BasicMenuItemUI.java:886)
   at java.awt.Component.processMouseEvent(Component.java:6539)
   at javax.swing.JComponent.processMouseEvent(JComponent.java:3324)
   at java.awt.Component.processEvent(Component.java:6304)
   at java.awt.Container.processEvent(Container.java:2239)
   at java.awt.Component.dispatchEventImpl(Component.java:4889)
   at java.awt.Container.dispatchEventImpl(Container.java:2297)
   at java.awt.Component.dispatchEvent(Component.java:4711)
   at java.awt.LightweightDispatcher.retargetMouseEvent(Container.java:4904)
   at java.awt.LightweightDispatcher.processMouseEvent(Container.java:4535)
   at java.awt.LightweightDispatcher.dispatchEvent(Container.java:4476)
   at java.awt.Container.dispatchEventImpl(Container.java:2283)
   at java.awt.Window.dispatchEventImpl(Window.java:2746)
   at java.awt.Component.dispatchEvent(Component.java:4711)
   at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:760)
   at java.awt.EventQueue.access$500(EventQueue.java:97)
   at java.awt.EventQueue$3.run(EventQueue.java:709)
   at java.awt.EventQueue$3.run(EventQueue.java:703)
   at java.security.AccessController.doPrivileged(Native Method)
   at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:74)
   at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:84)
   at java.awt.EventQueue$4.run(EventQueue.java:733)
   at java.awt.EventQueue$4.run(EventQueue.java:731)
   at java.security.AccessController.doPrivileged(Native Method)
   at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:74)
   at java.awt.EventQueue.dispatchEvent(EventQueue.java:730)
   at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:205)
   at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:116)
   at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:105)
   at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:101)
   at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:93)
   at java.awt.EventDispatchThread.run(EventDispatchThread.java:82)

DEBUG - ALIGNFRAME performed rollBackupsAndRenameTempFile unsuccessfully

DEBUG - ALIGNFRAME making backupfiles object for E:\PATH.fa
DEBUG - BACKUPFILES classInit
DEBUG - BACKUPFILES disabled
DEBUG - BACKUPFILESPRESETENTRY saved preset string is .bak%n 3 false false 3 false
DEBUG - BACKUPFILES preset scheme .bak%n 3 false false 3 false
DEBUG - BACKUPFILES confirm delete false
DEBUG - BACKUPFILESPRESETENTRY saved preset string is .bak%n 3 false false 3 false
DEBUG - BACKUPFILES [file!=null] attempting to create temp file for PATH.fa in dir E:\
DEBUG - BACKUPFILES using temp file E:\PATH.fa6618576920405918060.tmp_newfile
DEBUG - ALIGNFRAME setting PrintWriter to E:\PATH.fa6618576920405918060.tmp_newfile
DEBUG - ALIGNFRAME about to write to temp file E:\PATH.fa6618576920405918060.tmp_newfile
DEBUG - ALIGNFRAME about to close file
DEBUG - ALIGNFRAME closed file
DEBUG - ALIGNFRAME writing temp file was successful
DEBUG - ALIGNFRAME about to rollBackupsAndRenameTempFile
DEBUG - BACKUPFILES rollBackupFiles nothing to do., filename: PATH.fa, file exists: true, enabled: false, max: 3, suffix: '.bak%n'
DEBUG - BACKUPFILES deleting E:\PATH.fa
DEBUG - BACKUPFILES moving E:\PATH.fa6618576920405918060.tmp_newfile to E:\PATH.fa
DEBUG - BACKUPFILES move seems to have succeeded
DEBUG - ALIGNFRAME performed rollBackupsAndRenameTempFile successfully