Details
Description
Symptom is as shown in attached figure. When Jalview is started with the Java Console enabled, errors are shown when loading BLOSUM62, PAM250 and DNA score models. There are also exceptions from the Quality and Conservation calculation routines:
Jalview Version: 2.11.1.0
Jalview Installation: Source git-commit:30119dce1 [releases/Release_2_11_1_Branch]
Build Date: 00:13:39 22 April 2020
Java version: 1.8.0_202
x86_64 Mac OS X 10.13.6
Install4j version: null
Install4j template version: null
Launcher version: 1.8.3-1.2.4_JVL
Cannot set Taskbar
Warning: class ch.randelshofer.quaqua.osx.OSXFile couldn't load library "libquaqua64.dylib". java.lang.UnsatisfiedLinkError: no quaqua64 in java.library.path
File format identified as Fasta
Warning: SidebarTreeModel uses default user items.
Warning: class ch.randelshofer.quaqua.osx.OSXImageIO couldn't load library "libquaqua64.dylib". java.lang.UnsatisfiedLinkError: no quaqua64 in java.library.path
Error reading scoreModel/blosum62.scm: Format error: 'ScoreMatrix <name>' should be the first non-comment line
Error reading scoreModel/pam250.scm: Format error: 'ScoreMatrix <name>' should be the first non-comment line
Error reading scoreModel/dna.scm: Format error: 'ScoreMatrix <name>' should be the first non-comment line
Exception in thread "class jalview.workers.ConservationThread" java.lang.NullPointerException
at jalview.analysis.Conservation.findQuality(Conservation.java:628)
at jalview.analysis.Conservation.findQuality(Conservation.java:560)
at jalview.analysis.Conservation.calculateConservation(Conservation.java:847)
at jalview.workers.ConservationThread.run(ConservationThread.java:98)
at java.lang.Thread.run(Thread.java:748)
Workaround is to add -Duser.language=en to the JVM arguments by adding an 'extra.txt' file in the getdown/app directory of the Jalview installation.
Jalview Version: 2.11.1.0
Jalview Installation: Source git-commit:30119dce1 [releases/Release_2_11_1_Branch]
Build Date: 00:13:39 22 April 2020
Java version: 1.8.0_202
x86_64 Mac OS X 10.13.6
Install4j version: null
Install4j template version: null
Launcher version: 1.8.3-1.2.4_JVL
Cannot set Taskbar
Warning: class ch.randelshofer.quaqua.osx.OSXFile couldn't load library "libquaqua64.dylib". java.lang.UnsatisfiedLinkError: no quaqua64 in java.library.path
File format identified as Fasta
Warning: SidebarTreeModel uses default user items.
Warning: class ch.randelshofer.quaqua.osx.OSXImageIO couldn't load library "libquaqua64.dylib". java.lang.UnsatisfiedLinkError: no quaqua64 in java.library.path
Error reading scoreModel/blosum62.scm: Format error: 'ScoreMatrix <name>' should be the first non-comment line
Error reading scoreModel/pam250.scm: Format error: 'ScoreMatrix <name>' should be the first non-comment line
Error reading scoreModel/dna.scm: Format error: 'ScoreMatrix <name>' should be the first non-comment line
Exception in thread "class jalview.workers.ConservationThread" java.lang.NullPointerException
at jalview.analysis.Conservation.findQuality(Conservation.java:628)
at jalview.analysis.Conservation.findQuality(Conservation.java:560)
at jalview.analysis.Conservation.calculateConservation(Conservation.java:847)
at jalview.workers.ConservationThread.run(ConservationThread.java:98)
at java.lang.Thread.run(Thread.java:748)
Workaround is to add -Duser.language=en to the JVM arguments by adding an 'extra.txt' file in the getdown/app directory of the Jalview installation.