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  1. Jalview
  2. JAL-3691

Conservation and Quality tracks are shown but not calculated and no protein or DNA score models are available for tree/PCA calculation when launched under certain locales (e.g. tr_TR)

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    Details

    • Type: Bug
    • Status: Being tested
    • Priority: Major
    • Resolution: Unresolved
    • Affects Version/s: 2.11.0, 2.11.1.0
    • Fix Version/s: 2.11.1.1, 2.11.2
    • Component/s: None
    • Labels:
    • Environment:
      Windows
      OSX
      Linux
      JVM options: -Duser.language=tr

      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.

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            Assignee:
            jprocter Jim Procter
            Reporter:
            jprocter Jim Procter
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              Dates

              Created:
              Updated: