Encountered Fatal: Launch Error: while launching IGV 2.3/snapshot via direct JNLP or from binary

[Sharbadeb Kundu]

Hi All,

I tried to run IGV 2.3 / IGV (snapshot) from CentOS 7 but encountered the following error.

net.sourceforge.jnlp.LaunchException: Fatal: Launch Error: Could not launch JNLP file. The application has not been initialized, for more information execute javaws/browser from the command line and send a bug report.

at net.sourceforge.jnlp.Launcher.launchApplication(Launcher.java:580)

at net.sourceforge.jnlp.Launcher$TgThread.run(Launcher.java:936)

Caused by: java.lang.reflect.InvocationTargetException

at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)

at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)

at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)

at java.lang.reflect.Method.invoke(Method.java:498)

at net.sourceforge.jnlp.Launcher.launchApplication(Launcher.java:574)

... 1 more

Caused by: java.lang.IllegalArgumentException: Width (0) and height (0) must be non-zero

at java.awt.image.ReplicateScaleFilter.<init>(ReplicateScaleFilter.java:102)

at java.awt.Image.getScaledInstance(Image.java:174)

at sun.awt.CustomCursor.<init>(CustomCursor.java:69)

at sun.awt.X11CustomCursor.<init>(X11CustomCursor.java:43)

at sun.awt.X11.XCustomCursor.<init>(XCustomCursor.java:42)

at sun.awt.X11.XToolkit.createCustomCursor(XToolkit.java:1140)

at org.broad.igv.ui.IGV.createHandCursor(IGV.java:1163)

at org.broad.igv.ui.IGV.<init>(IGV.java:275)

at org.broad.igv.ui.IGV.createInstance(IGV.java:181)

at org.broad.igv.ui.Main.open(Main.java:238)

at org.broad.igv.ui.Main.main(Main.java:85)

... 6 more

Initially, I tried to run the JNLP file directly. But it didn't work. Then I downloaded the binary files for it. This time also, it did not work. So, please help me and suggest what I'm supposed to do to resolve this issue.

Thanks,

- Sharbadeb

[Jim Robinson]

Hi Sharbadeb,

Could you please try the development version of IGV located here: http://www.broadinstitute.org/software/igv/download_snapshot.   Let us know if that fixes the problem.  

Jim

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[Sharbadeb Kundu]

Hi Jim,

I tried this development version as you suggested. This time, the error came as -

WARN [2016-05-09 13:24:42,450]  [Globals.java:150] [main]  Development mode is enabled

WARN [2016-05-09 13:24:42,450] [Globals.java:150]  Development mode is enabled

INFO [2016-05-09 13:24:42,452]  [DirectoryManager.java:163] [main]  IGV Directory: /home/skg/igv

INFO [2016-05-09 13:24:42,452] [DirectoryManager.java:163]  IGV Directory: /home/skg/igv

INFO [2016-05-09 13:24:42,454]  [Main.java:99] [main]  Startup  IGV Version Snapshot (526 (526))05/05/2016 05:06 PM

INFO [2016-05-09 13:24:42,454]  [Main.java:100] [main]  Java 1.8.0_77

INFO [2016-05-09 13:24:42,455]  [DirectoryManager.java:72] [main]  Fetching user directory... 

INFO [2016-05-09 13:24:42,586]  [Main.java:101] [main]  Default User Directory: /home/skg:101] [main]  Default User Directory: /home/skg

INFO [2016-05-09 13:24:42,586]  [Main.java:102] [main]  OS: Linux:102] [main]  OS: Linux

ERROR [2016-05-09 13:24:42,989]  [IGV.java:1184] [main]  Could not create fistCursor:1184] [main]  Could not create fistCursor

java.lang.IllegalArgumentException: Width (0) and height (0) must be non-zero

at java.awt.image.ReplicateScaleFilter.<init>(ReplicateScaleFilter.java:102)

at java.awt.Image.getScaledInstance(Image.java:174)

at sun.awt.CustomCursor.<init>(CustomCursor.java:69)

at sun.awt.X11CustomCursor.<init>(X11CustomCursor.java:43)

at sun.awt.X11.XCustomCursor.<init>(XCustomCursor.java:42)

at sun.awt.X11.XToolkit.createCustomCursor(XToolkit.java:1140)

at org.broad.igv.ui.IGV.createHandCursor(IGV.java:1182)

at org.broad.igv.ui.IGV.<init>(IGV.java:276)

at org.broad.igv.ui.IGV.createInstance(IGV.java:182)

at org.broad.igv.ui.Main.open(Main.java:238)

at org.broad.igv.ui.Main.main(Main.java:85)

ERROR [2016-05-09 13:24:42,991]  [DefaultExceptionHandler.java:49] [main]  Unhandled exception

java.lang.IllegalArgumentException: Width (0) and height (0) must be non-zero

at java.awt.image.ReplicateScaleFilter.<init>(ReplicateScaleFilter.java:102)

at java.awt.Image.getScaledInstance(Image.java:174)

at sun.awt.CustomCursor.<init>(CustomCursor.java:69)

at sun.awt.X11CustomCursor.<init>(X11CustomCursor.java:43)

at sun.awt.X11.XCustomCursor.<init>(XCustomCursor.java:42)

at sun.awt.X11.XToolkit.createCustomCursor(XToolkit.java:1140)

at org.broad.igv.ui.IGV.createZoomCursors(IGV.java:1128)

at org.broad.igv.ui.IGV.<init>(IGV.java:277)

at org.broad.igv.ui.IGV.createInstance(IGV.java:182)

at org.broad.igv.ui.Main.open(Main.java:238)

at org.broad.igv.ui.Main.main(Main.java:85)

INFO [2016-05-09 13:24:42,992]  [ShutdownThread.java:51] [Thread-2]  Shutting down

ERROR [2016-05-09 13:24:42,996]  [DefaultExceptionHandler.java:49] [Thread-2]  Unhandled exception

java.lang.NullPointerException

at org.broad.igv.ui.IGV.getTrackPanels(IGV.java:1391)

at org.broad.igv.ui.IGV.getAllTracks(IGV.java:2080)

at org.broad.igv.ui.ShutdownThread.runS(ShutdownThread.java:56)

at org.broad.igv.ui.ShutdownThread.run(ShutdownThread.java:64)

Then I tried the JNLP file. It too showed the error message as -

net.sourceforge.jnlp.LaunchException: Fatal: Initialization Error: Could not initialize application. The application has not been initialized, for more information execute javaws from the command line.

at net.sourceforge.jnlp.Launcher.createApplication(Launcher.java:813)

at net.sourceforge.jnlp.Launcher.launchApplication(Launcher.java:532)

at net.sourceforge.jnlp.Launcher$TgThread.run(Launcher.java:936)

Caused by: net.sourceforge.jnlp.LaunchException: Fatal: Initialization Error: A fatal error occurred while trying to verify jars. An exception has been thrown in class JarCertVerifier. Being unable to read the cacerts or trusted.certs files could be a possible cause for this exception.: error in opening zip file

at net.sourceforge.jnlp.runtime.JNLPClassLoader.initializeResources(JNLPClassLoader.java:671)

at net.sourceforge.jnlp.runtime.JNLPClassLoader.<init>(JNLPClassLoader.java:285)

at net.sourceforge.jnlp.runtime.JNLPClassLoader.createInstance(JNLPClassLoader.java:357)

at net.sourceforge.jnlp.runtime.JNLPClassLoader.getInstance(JNLPClassLoader.java:429)

at net.sourceforge.jnlp.runtime.JNLPClassLoader.getInstance(JNLPClassLoader.java:403)

at net.sourceforge.jnlp.Launcher.createApplication(Launcher.java:805)

... 2 more

Please suggest what to do.

Thanking you,

With regards,

Sharbadeb Kundu, M. Tech

Research Scholar, DST-INSPIRE Fellow

Molecular Medicine Laboratory

Dept. Of Biotechnology

Assam (Central) University

Silchar - 788011, Assam, India

Mob: (+91)9401356054/(+91)8255007155

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[Jim Robinson]

Hi,

Sorry I don't have any further suggestions.  If you could be more detailed on what "didn't work" means that might be helpful.   The error you see in the log is informational, it shouldn't happen but if it does it should nor prevent IGV from launching.  

You might try a different Java.  If you are using OpenJDK try the Oracle distribution.

Jim