Details
Description
Hi, where a common mistake like this (keeping a space in the sequence name) used to be automatically repaired with an underscore (_) now a unrecoverable error occurs and all ongoing stuff will be lost.
stack output:
Picked up _JAVA_OPTIONS: -Dawt.useSystemAAFontSettings=on -Dswing.aatext=true -Dswing.defaultlaf=com.sun.java.swing.plaf.gtk.GTKLookAndFeel
Running jalview.bin.Jalview with memory setting -Xmx15766658048
Picked up _JAVA_OPTIONS: -Dawt.useSystemAAFontSettings=on -Dswing.aatext=true -Dswing.defaultlaf=com.sun.java.swing.plaf.gtk.GTKLookAndFeel
Java version: 11.0.17
Java home: /usr/lib64/java
Java arch: amd64 Linux 6.1.28
Jalview Develop version: 2.11.3.0-d20230517 (Source git-commit:b3fb6325a8 [develop])
Setting initial log level to INFO
WARNING: sun.reflect.Reflection.getCallerClass is not supported. This will impact performance.
SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
SLF4J: Defaulting to no-operation (NOP) logger implementation
SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
INFO - Loaded Sequence Ontology from so-xp-simple.obo.zip (150ms)
INFO - Getting messages for lang: en_GB
Linux platform only! You may have the following warning next: "WARNING: An illegal reflective access operation has occurred"
This is expected and cannot be avoided, sorry about that.
WARNING: An illegal reflective access operation has occurred
WARNING: Illegal reflective access by jalview.gui.Desktop (file:/home/rob/WORK/BIOINFO/JALVIEW/jalview-all-2.11.3.0-d20230517-j11.jar) to field sun.awt.X11.XToolkit.awtAppClassName
WARNING: Please consider reporting this to the maintainers of jalview.gui.Desktop
WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations
WARNING: All illegal access operations will be denied in a future release
WARN - Error when running commands
May 19, 2023 1:39:14 PM javax.xml.soap.FactoryFinder find
WARNING: Using deprecated META-INF/services mechanism with non-standard property: javax.xml.soap.MetaFactory. Property javax.xml.soap.SAAJMetaFactory should be used instead.
May 19, 2023 1:39:14 PM javax.xml.soap.FactoryFinder find
WARNING: Using deprecated META-INF/services mechanism with non-standard property: javax.xml.soap.MetaFactory. Property javax.xml.soap.SAAJMetaFactory should be used instead.
May 19, 2023 1:39:14 PM javax.xml.soap.FactoryFinder find
WARNING: Using deprecated META-INF/services mechanism with non-standard property: javax.xml.soap.MetaFactory. Property javax.xml.soap.SAAJMetaFactory should be used instead.
May 19, 2023 1:39:14 PM javax.xml.soap.FactoryFinder find
WARNING: Using deprecated META-INF/services mechanism with non-standard property: javax.xml.soap.MetaFactory. Property javax.xml.soap.SAAJMetaFactory should be used instead.
May 19, 2023 1:39:14 PM compbio.ws.client.Jws2Client connectToRegistry
INFO: Connected to RegistryWS successfully!
registry.getSupportedServices: [AAConWS, DisemblWS, MSAprobsWS, GLprobsWS, ProbconsWS, GlobPlotWS, MafftWS, ClustalWS, RNAalifoldWS, TcoffeeWS, MuscleWS, JronnWS, IUPredWS, ClustalOWS]
Attempting to connect with MafftWS...
May 19, 2023 1:39:15 PM compbio.ws.client.Jws2Client connect
INFO: Connected successfully!
Discovered service: http://www.compbio.dundee.ac.uk/jabaws jalview.ws.jws2.jabaws2.Jws2Instance@2adf9390
Attempting to connect with MuscleWS...
May 19, 2023 1:39:16 PM compbio.ws.client.Jws2Client connect
INFO: Connected successfully!
Discovered service: http://www.compbio.dundee.ac.uk/jabaws jalview.ws.jws2.jabaws2.Jws2Instance@3f79e7cf
Attempting to connect with ClustalWS...
May 19, 2023 1:39:17 PM compbio.ws.client.Jws2Client connect
INFO: Connected successfully!
Discovered service: http://www.compbio.dundee.ac.uk/jabaws jalview.ws.jws2.jabaws2.Jws2Instance@58b3502d
Attempting to connect with ClustalOWS...
May 19, 2023 1:39:19 PM compbio.ws.client.Jws2Client connect
INFO: Connected successfully!
Discovered service: http://www.compbio.dundee.ac.uk/jabaws jalview.ws.jws2.jabaws2.Jws2Instance@b44920e
Attempting to connect with TcoffeeWS...
May 19, 2023 1:39:19 PM compbio.ws.client.Jws2Client connect
INFO: Connected successfully!
Discovered service: http://www.compbio.dundee.ac.uk/jabaws jalview.ws.jws2.jabaws2.Jws2Instance@645490cb
Attempting to connect with ProbconsWS...
May 19, 2023 1:39:20 PM compbio.ws.client.Jws2Client connect
INFO: Connected successfully!
Discovered service: http://www.compbio.dundee.ac.uk/jabaws jalview.ws.jws2.jabaws2.Jws2Instance@47778f15
Attempting to connect with MSAprobsWS...
May 19, 2023 1:39:21 PM compbio.ws.client.Jws2Client connect
INFO: Connected successfully!
Discovered service: http://www.compbio.dundee.ac.uk/jabaws jalview.ws.jws2.jabaws2.Jws2Instance@6d114f49
Attempting to connect with GLprobsWS...
May 19, 2023 1:39:22 PM compbio.ws.client.Jws2Client connect
INFO: Connected successfully!
Discovered service: http://www.compbio.dundee.ac.uk/jabaws jalview.ws.jws2.jabaws2.Jws2Instance@456acf0d
Attempting to connect with AAConWS...
May 19, 2023 1:39:23 PM compbio.ws.client.Jws2Client connect
INFO: Connected successfully!
Discovered service: http://www.compbio.dundee.ac.uk/jabaws jalview.ws.jws2.jabaws2.Jws2Instance@610580d2
Attempting to connect with RNAalifoldWS...
May 19, 2023 1:39:24 PM compbio.ws.client.Jws2Client connect
INFO: Connected successfully!
Discovered service: http://www.compbio.dundee.ac.uk/jabaws jalview.ws.jws2.jabaws2.Jws2Instance@ae5d1a9
Attempting to connect with JronnWS...
May 19, 2023 1:39:25 PM compbio.ws.client.Jws2Client connect
INFO: Connected successfully!
Discovered service: http://www.compbio.dundee.ac.uk/jabaws jalview.ws.jws2.jabaws2.Jws2Instance@68155115
Attempting to connect with DisemblWS...
May 19, 2023 1:39:26 PM compbio.ws.client.Jws2Client connect
INFO: Connected successfully!
Discovered service: http://www.compbio.dundee.ac.uk/jabaws jalview.ws.jws2.jabaws2.Jws2Instance@5e6ce4ac
Attempting to connect with GlobPlotWS...
May 19, 2023 1:39:27 PM compbio.ws.client.Jws2Client connect
INFO: Connected successfully!
Discovered service: http://www.compbio.dundee.ac.uk/jabaws jalview.ws.jws2.jabaws2.Jws2Instance@3baa15d0
Attempting to connect with IUPredWS...
May 19, 2023 1:39:28 PM compbio.ws.client.Jws2Client connect
INFO: Connected successfully!
Discovered service: http://www.compbio.dundee.ac.uk/jabaws jalview.ws.jws2.jabaws2.Jws2Instance@533a0d1
INFO - I18N missing key with root label.colourScheme_: en_GB label.colourScheme_rgg
Serious - RSBS descriptions in user preferences are corrupt!
java.lang.NullPointerException
at jalview.ws.rest.RestServiceDescription.parseServiceList(RestServiceDescription.java:566)
at jalview.ws.rest.RestServiceDescription.parseDescriptions(RestServiceDescription.java:892)
at jalview.ws.rest.RestClient.getRestClients(RestClient.java:414)
at jalview.gui.AlignFrame.build_urlServiceMenu(AlignFrame.java:4484)
at jalview.gui.AlignFrame$14$1.run(AlignFrame.java:4428)
at java.desktop/java.awt.event.InvocationEvent.dispatch(InvocationEvent.java:313)
at java.desktop/java.awt.EventQueue.dispatchEventImpl(EventQueue.java:770)
at java.desktop/java.awt.EventQueue$4.run(EventQueue.java:721)
at java.desktop/java.awt.EventQueue$4.run(EventQueue.java:715)
at java.base/java.security.AccessController.doPrivileged(Native Method)
at java.base/java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:85)
at java.desktop/java.awt.EventQueue.dispatchEvent(EventQueue.java:740)
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)
stack output:
Picked up _JAVA_OPTIONS: -Dawt.useSystemAAFontSettings=on -Dswing.aatext=true -Dswing.defaultlaf=com.sun.java.swing.plaf.gtk.GTKLookAndFeel
Running jalview.bin.Jalview with memory setting -Xmx15766658048
Picked up _JAVA_OPTIONS: -Dawt.useSystemAAFontSettings=on -Dswing.aatext=true -Dswing.defaultlaf=com.sun.java.swing.plaf.gtk.GTKLookAndFeel
Java version: 11.0.17
Java home: /usr/lib64/java
Java arch: amd64 Linux 6.1.28
Jalview Develop version: 2.11.3.0-d20230517 (Source git-commit:b3fb6325a8 [develop])
Setting initial log level to INFO
WARNING: sun.reflect.Reflection.getCallerClass is not supported. This will impact performance.
SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
SLF4J: Defaulting to no-operation (NOP) logger implementation
SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
INFO - Loaded Sequence Ontology from so-xp-simple.obo.zip (150ms)
INFO - Getting messages for lang: en_GB
Linux platform only! You may have the following warning next: "WARNING: An illegal reflective access operation has occurred"
This is expected and cannot be avoided, sorry about that.
WARNING: An illegal reflective access operation has occurred
WARNING: Illegal reflective access by jalview.gui.Desktop (file:/home/rob/WORK/BIOINFO/JALVIEW/jalview-all-2.11.3.0-d20230517-j11.jar) to field sun.awt.X11.XToolkit.awtAppClassName
WARNING: Please consider reporting this to the maintainers of jalview.gui.Desktop
WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations
WARNING: All illegal access operations will be denied in a future release
WARN - Error when running commands
May 19, 2023 1:39:14 PM javax.xml.soap.FactoryFinder find
WARNING: Using deprecated META-INF/services mechanism with non-standard property: javax.xml.soap.MetaFactory. Property javax.xml.soap.SAAJMetaFactory should be used instead.
May 19, 2023 1:39:14 PM javax.xml.soap.FactoryFinder find
WARNING: Using deprecated META-INF/services mechanism with non-standard property: javax.xml.soap.MetaFactory. Property javax.xml.soap.SAAJMetaFactory should be used instead.
May 19, 2023 1:39:14 PM javax.xml.soap.FactoryFinder find
WARNING: Using deprecated META-INF/services mechanism with non-standard property: javax.xml.soap.MetaFactory. Property javax.xml.soap.SAAJMetaFactory should be used instead.
May 19, 2023 1:39:14 PM javax.xml.soap.FactoryFinder find
WARNING: Using deprecated META-INF/services mechanism with non-standard property: javax.xml.soap.MetaFactory. Property javax.xml.soap.SAAJMetaFactory should be used instead.
May 19, 2023 1:39:14 PM compbio.ws.client.Jws2Client connectToRegistry
INFO: Connected to RegistryWS successfully!
registry.getSupportedServices: [AAConWS, DisemblWS, MSAprobsWS, GLprobsWS, ProbconsWS, GlobPlotWS, MafftWS, ClustalWS, RNAalifoldWS, TcoffeeWS, MuscleWS, JronnWS, IUPredWS, ClustalOWS]
Attempting to connect with MafftWS...
May 19, 2023 1:39:15 PM compbio.ws.client.Jws2Client connect
INFO: Connected successfully!
Discovered service: http://www.compbio.dundee.ac.uk/jabaws jalview.ws.jws2.jabaws2.Jws2Instance@2adf9390
Attempting to connect with MuscleWS...
May 19, 2023 1:39:16 PM compbio.ws.client.Jws2Client connect
INFO: Connected successfully!
Discovered service: http://www.compbio.dundee.ac.uk/jabaws jalview.ws.jws2.jabaws2.Jws2Instance@3f79e7cf
Attempting to connect with ClustalWS...
May 19, 2023 1:39:17 PM compbio.ws.client.Jws2Client connect
INFO: Connected successfully!
Discovered service: http://www.compbio.dundee.ac.uk/jabaws jalview.ws.jws2.jabaws2.Jws2Instance@58b3502d
Attempting to connect with ClustalOWS...
May 19, 2023 1:39:19 PM compbio.ws.client.Jws2Client connect
INFO: Connected successfully!
Discovered service: http://www.compbio.dundee.ac.uk/jabaws jalview.ws.jws2.jabaws2.Jws2Instance@b44920e
Attempting to connect with TcoffeeWS...
May 19, 2023 1:39:19 PM compbio.ws.client.Jws2Client connect
INFO: Connected successfully!
Discovered service: http://www.compbio.dundee.ac.uk/jabaws jalview.ws.jws2.jabaws2.Jws2Instance@645490cb
Attempting to connect with ProbconsWS...
May 19, 2023 1:39:20 PM compbio.ws.client.Jws2Client connect
INFO: Connected successfully!
Discovered service: http://www.compbio.dundee.ac.uk/jabaws jalview.ws.jws2.jabaws2.Jws2Instance@47778f15
Attempting to connect with MSAprobsWS...
May 19, 2023 1:39:21 PM compbio.ws.client.Jws2Client connect
INFO: Connected successfully!
Discovered service: http://www.compbio.dundee.ac.uk/jabaws jalview.ws.jws2.jabaws2.Jws2Instance@6d114f49
Attempting to connect with GLprobsWS...
May 19, 2023 1:39:22 PM compbio.ws.client.Jws2Client connect
INFO: Connected successfully!
Discovered service: http://www.compbio.dundee.ac.uk/jabaws jalview.ws.jws2.jabaws2.Jws2Instance@456acf0d
Attempting to connect with AAConWS...
May 19, 2023 1:39:23 PM compbio.ws.client.Jws2Client connect
INFO: Connected successfully!
Discovered service: http://www.compbio.dundee.ac.uk/jabaws jalview.ws.jws2.jabaws2.Jws2Instance@610580d2
Attempting to connect with RNAalifoldWS...
May 19, 2023 1:39:24 PM compbio.ws.client.Jws2Client connect
INFO: Connected successfully!
Discovered service: http://www.compbio.dundee.ac.uk/jabaws jalview.ws.jws2.jabaws2.Jws2Instance@ae5d1a9
Attempting to connect with JronnWS...
May 19, 2023 1:39:25 PM compbio.ws.client.Jws2Client connect
INFO: Connected successfully!
Discovered service: http://www.compbio.dundee.ac.uk/jabaws jalview.ws.jws2.jabaws2.Jws2Instance@68155115
Attempting to connect with DisemblWS...
May 19, 2023 1:39:26 PM compbio.ws.client.Jws2Client connect
INFO: Connected successfully!
Discovered service: http://www.compbio.dundee.ac.uk/jabaws jalview.ws.jws2.jabaws2.Jws2Instance@5e6ce4ac
Attempting to connect with GlobPlotWS...
May 19, 2023 1:39:27 PM compbio.ws.client.Jws2Client connect
INFO: Connected successfully!
Discovered service: http://www.compbio.dundee.ac.uk/jabaws jalview.ws.jws2.jabaws2.Jws2Instance@3baa15d0
Attempting to connect with IUPredWS...
May 19, 2023 1:39:28 PM compbio.ws.client.Jws2Client connect
INFO: Connected successfully!
Discovered service: http://www.compbio.dundee.ac.uk/jabaws jalview.ws.jws2.jabaws2.Jws2Instance@533a0d1
INFO - I18N missing key with root label.colourScheme_: en_GB label.colourScheme_rgg
Serious - RSBS descriptions in user preferences are corrupt!
java.lang.NullPointerException
at jalview.ws.rest.RestServiceDescription.parseServiceList(RestServiceDescription.java:566)
at jalview.ws.rest.RestServiceDescription.parseDescriptions(RestServiceDescription.java:892)
at jalview.ws.rest.RestClient.getRestClients(RestClient.java:414)
at jalview.gui.AlignFrame.build_urlServiceMenu(AlignFrame.java:4484)
at jalview.gui.AlignFrame$14$1.run(AlignFrame.java:4428)
at java.desktop/java.awt.event.InvocationEvent.dispatch(InvocationEvent.java:313)
at java.desktop/java.awt.EventQueue.dispatchEventImpl(EventQueue.java:770)
at java.desktop/java.awt.EventQueue$4.run(EventQueue.java:721)
at java.desktop/java.awt.EventQueue$4.run(EventQueue.java:715)
at java.base/java.security.AccessController.doPrivileged(Native Method)
at java.base/java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:85)
at java.desktop/java.awt.EventQueue.dispatchEvent(EventQueue.java:740)
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)