IGV crashing DefaultExceptionHandler.java:49 + Unhandled exception java.lang.NullPointerException

[Roberto Galindo]

Dear IGV team

I've been using IGV with no problems but since 3 weeks ago I got this message:

INFO [2016-04-15 11:58:51,513]  [DirectoryManager.java:163] [main]  IGV Directory: /root/igv
INFO [2016-04-15 11:58:51,513] [DirectoryManager.java:163]  IGV Directory: /root/igv
INFO [2016-04-15 11:58:51,533]  [Main.java:99] [main]  Startup  IGV Version 2.3.66 (95)11/19/2015 03:06 AM
INFO [2016-04-15 11:58:51,545]  [Main.java:100] [main]  Java 1.7.0_99
INFO [2016-04-15 11:58:51,546]  [DirectoryManager.java:72] [main]  Fetching user directory...
INFO [2016-04-15 11:58:51,643]  [Main.java:101] [main]  Default User Directory: /root
INFO [2016-04-15 11:58:51,643]  [Main.java:102] [main]  OS: Linux
ERROR [2016-04-15 11:58:52,479]  [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:173)
    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:1069)
    at org.broad.igv.ui.IGV.createHandCursor(IGV.java:1162)
    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)
INFO [2016-04-15 11:58:52,482]  [ShutdownThread.java:51] [Thread-2]  Shutting down
ERROR [2016-04-15 11:58:52,498]  [DefaultExceptionHandler.java:49] [Thread-2]  Unhandled exception
java.lang.NullPointerException
    at org.broad.igv.ui.IGV.getTrackPanels(IGV.java:1345)
    at org.broad.igv.ui.IGV.getAllTracks(IGV.java:2032)
    at org.broad.igv.ui.ShutdownThread.runS(ShutdownThread.java:56)
    at org.broad.igv.ui.ShutdownThread.run(ShutdownThread.java:64)

I also tried with the last bin version and a I compiled the last version but the same result

INFO [2016-04-15 12:03:58,579]  [DirectoryManager.java:163] [main]  IGV Directory: /root/igv
INFO [2016-04-15 12:03:58,579] [DirectoryManager.java:163]  IGV Directory: /root/igv
INFO [2016-04-15 12:03:58,582]  [Main.java:99] [main]  Startup  IGV Version 2.3.72 (105)04/01/2016 11:33 AM
INFO [2016-04-15 12:03:58,582]  [Main.java:100] [main]  Java 1.7.0_99
INFO [2016-04-15 12:03:58,583]  [DirectoryManager.java:72] [main]  Fetching user directory...
INFO [2016-04-15 12:03:58,666]  [Main.java:101] [main]  Default User Directory: /root
INFO [2016-04-15 12:03:58,667]  [Main.java:102] [main]  OS: Linux
ERROR [2016-04-15 12:04:03,245]  [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:173)
    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:1069)
    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)
INFO [2016-04-15 12:04:03,249]  [ShutdownThread.java:51] [Thread-2]  Shutting down
ERROR [2016-04-15 12:04:03,267]  [DefaultExceptionHandler.java:49] [Thread-2]  Unhandled exception
java.lang.NullPointerException
    at org.broad.igv.ui.IGV.getTrackPanels(IGV.java:1346)
    at org.broad.igv.ui.IGV.getAllTracks(IGV.java:2035)
    at org.broad.igv.ui.ShutdownThread.runS(ShutdownThread.java:56)
    at org.broad.igv.ui.ShutdownThread.run(ShutdownThread.java:64)

I tried to find a solution but none worked for me, my current server configuration is:

  Icon name: computer-server
  Chassis: server
  Operating System: CentOS Linux 7 (Core)
       CPE OS Name: cpe:/o:centos:centos:7
       Kernel: Linux 3.10.0-327.13.1.el7.x86_64
       Architecture: x86-64

My java version:

java version "1.7.0_99"
OpenJDK Runtime Environment (rhel-2.6.5.0.el7_2-x86_64 u99-b00)
OpenJDK 64-Bit Server VM (build 24.95-b01, mixed mode)

Another thing is when I connect remotely to my server using ssh -X, works fine from the client display...I tried installing several desktop manager (GNOME, KDE, XCFE) but the same error is shown.

Any help would be really appreciate.

[Jim Robinson]

Roberto,  could you possible try Oracle java, or update the OpenJDK java? 

--

---
You received this message because you are subscribed to the Google Groups "igv-help" group.
To unsubscribe from this group and stop receiving emails from it, send an email to igv-help+u...@googlegroups.com.
To view this discussion on the web visit https://groups.google.com/d/msgid/igv-help/e2023384-76b9-4429-b462-a99d51894bf7%40googlegroups.com.
For more options, visit https://groups.google.com/d/optout.

[Roberto Galindo]

Already done, with JDK and JRE (1.7 & 1.8), I tried this rpm from ORACLE http://www.oracle.com/technetwork/java/javase/downloads/index.html

jdk-8u77-linux-x64.rpm
jre-8u77-linux-x64.rpm

Using  the next command to choose between different versions installed in my server

update-alternatives --config java

But none worked for me

I am running out ideas.

[Jim Robinson]

Do you have any idea what changed 3 weeks ago, when the problem started?  Had you installed a new version of IGV?

Looking at the code,  I can hypothesize causes but have not been able to produce the problem myself.  I can add some diagnostic messages if you are able to download a test version and run it.    I could do this later today.  If you want to try that let me know and I will send instructions when it is ready.

Jim

To view this discussion on the web visit https://groups.google.com/d/msgid/igv-help/45793368-fa3c-453c-a1b9-849f253f7542%40googlegroups.com.

[Jim Robinson]

Hi,

Could you try the development snapshot build, available at the link below, and let us know if it solves the problem?

http://www.broadinstitute.org/software/igv/download_snapshot

Jim

[Roberto Galindo]

Hi Jim,

I tried IGV_Snapshot with different versions of Java:

  1           /usr/java/jdk1.8.0_77/jre/bin/java
  2           /usr/java/jre1.8.0_77/bin/java
  3           /usr/lib/jvm/java-1.7.0-openjdk-1.7.0.99-2.6.5.0.el7_2.x86_64/jre/bin/java
  4           /usr/lib/jvm/java-1.8.0-openjdk-1.8.0.77-0.b03.el7_2.x86_64/jre/bin/java

And the results are the same:

WARN [2016-04-15 14:28:05,121]  [Globals.java:150] [main]  Development mode is enabled
WARN [2016-04-15 14:28:05,121] [Globals.java:150]  Development mode is enabled
INFO [2016-04-15 14:28:05,122]  [DirectoryManager.java:163] [main]  IGV Directory: /home/admin/igv
INFO [2016-04-15 14:28:05,122] [DirectoryManager.java:163]  IGV Directory: /home/admin/igv
INFO [2016-04-15 14:28:05,124]  [Main.java:99] [main]  Startup  IGV Version Snapshot (500 (500))04/15/2016 02:23 PM
INFO [2016-04-15 14:28:05,124]  [Main.java:100] [main]  Java 1.7.0_99
INFO [2016-04-15 14:28:05,125]  [DirectoryManager.java:72] [main]  Fetching user directory...
INFO [2016-04-15 14:28:05,207]  [Main.java:101] [main]  Default User Directory: /home/admin
INFO [2016-04-15 14:28:05,208]  [Main.java:102] [main]  OS: Linux
ERROR [2016-04-15 14:28:05,519]  [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:173)
    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:1069)

    at org.broad.igv.ui.IGV.createHandCursor(IGV.java:1176)
    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)

INFO [2016-04-15 14:28:05,522]  [ShutdownThread.java:51] [Thread-2]  Shutting down
ERROR [2016-04-15 14:28:05,546]  [DefaultExceptionHandler.java:49] [Thread-2]  Unhandled exception
java.lang.NullPointerException
    at org.broad.igv.ui.IGV.getTrackPanels(IGV.java:1377)
    at org.broad.igv.ui.IGV.getAllTracks(IGV.java:2066)

    at org.broad.igv.ui.ShutdownThread.runS(ShutdownThread.java:56)
    at org.broad.igv.ui.ShutdownThread.run(ShutdownThread.java:64)

[admin@datarockstar IGV_Snapshot]$ /usr/java/jdk1.8.0_77/jre/bin/java -jar igv.jar
WARN [2016-04-15 14:34:43,931]  [Globals.java:150] [main]  Development mode is enabled
WARN [2016-04-15 14:34:43,931] [Globals.java:150]  Development mode is enabled
INFO [2016-04-15 14:34:43,932]  [DirectoryManager.java:163] [main]  IGV Directory: /home/admin/igv
INFO [2016-04-15 14:34:43,932] [DirectoryManager.java:163]  IGV Directory: /home/admin/igv
INFO [2016-04-15 14:34:43,934]  [Main.java:99] [main]  Startup  IGV Version Snapshot (500 (500))04/15/2016 02:23 PM
INFO [2016-04-15 14:34:43,934]  [Main.java:100] [main]  Java 1.8.0_77
INFO [2016-04-15 14:34:43,935]  [DirectoryManager.java:72] [main]  Fetching user directory...
INFO [2016-04-15 14:34:44,068]  [Main.java:101] [main]  Default User Directory: /home/admin
INFO [2016-04-15 14:34:44,068]  [Main.java:102] [main]  OS: Linux
ERROR [2016-04-15 14:34:44,357]  [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.createHandCursor(IGV.java:1176)
    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)

INFO [2016-04-15 14:34:44,361]  [ShutdownThread.java:51] [Thread-2]  Shutting down
ERROR [2016-04-15 14:34:44,372]  [DefaultExceptionHandler.java:49] [Thread-2]  Unhandled exception
java.lang.NullPointerException
    at org.broad.igv.ui.IGV.getTrackPanels(IGV.java:1377)
    at org.broad.igv.ui.IGV.getAllTracks(IGV.java:2066)

    at org.broad.igv.ui.ShutdownThread.runS(ShutdownThread.java:56)
    at org.broad.igv.ui.ShutdownThread.run(ShutdownThread.java:64)

[admin@datarockstar IGV_Snapshot]$ /usr/java/jre1.8.0_77/bin/java -jar igv.jar
WARN [2016-04-15 14:36:40,004]  [Globals.java:150] [main]  Development mode is enabled
WARN [2016-04-15 14:36:40,004] [Globals.java:150]  Development mode is enabled
INFO [2016-04-15 14:36:40,007]  [DirectoryManager.java:163] [main]  IGV Directory: /home/admin/igv
INFO [2016-04-15 14:36:40,007] [DirectoryManager.java:163]  IGV Directory: /home/admin/igv
INFO [2016-04-15 14:36:40,010]  [Main.java:99] [main]  Startup  IGV Version Snapshot (500 (500))04/15/2016 02:23 PM
INFO [2016-04-15 14:36:40,010]  [Main.java:100] [main]  Java 1.8.0_77
INFO [2016-04-15 14:36:40,011]  [DirectoryManager.java:72] [main]  Fetching user directory...
INFO [2016-04-15 14:36:40,265]  [Main.java:101] [main]  Default User Directory: /home/admin
INFO [2016-04-15 14:36:40,265]  [Main.java:102] [main]  OS: Linux
ERROR [2016-04-15 14:36:41,006]  [DefaultExceptionHandler.java:49] [main]  Unhandled exception

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

    at java.awt.image.ReplicateScaleFilter.<init>(Unknown Source)
    at java.awt.Image.getScaledInstance(Unknown Source)
    at sun.awt.CustomCursor.<init>(Unknown Source)
    at sun.awt.X11CustomCursor.<init>(Unknown Source)
    at sun.awt.X11.XCustomCursor.<init>(Unknown Source)
    at sun.awt.X11.XToolkit.createCustomCursor(Unknown Source)
    at org.broad.igv.ui.IGV.createHandCursor(IGV.java:1176)
    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)

INFO [2016-04-15 14:36:41,010]  [ShutdownThread.java:51] [Thread-2]  Shutting down
ERROR [2016-04-15 14:36:41,055]  [DefaultExceptionHandler.java:49] [Thread-2]  Unhandled exception
java.lang.NullPointerException
    at org.broad.igv.ui.IGV.getTrackPanels(IGV.java:1377)
    at org.broad.igv.ui.IGV.getAllTracks(IGV.java:2066)

    at org.broad.igv.ui.ShutdownThread.runS(ShutdownThread.java:56)
    at org.broad.igv.ui.ShutdownThread.run(ShutdownThread.java:64)

[admin@datarockstar IGV_Snapshot]$ /usr/lib/jvm/java-1.7.0-openjdk-1.7.0.99-2.6.5.0.el7_2.x86_64/jre/bin/java -jar igv.jar
WARN [2016-04-15 14:36:59,408]  [Globals.java:150] [main]  Development mode is enabled
WARN [2016-04-15 14:36:59,408] [Globals.java:150]  Development mode is enabled
INFO [2016-04-15 14:36:59,410]  [DirectoryManager.java:163] [main]  IGV Directory: /home/admin/igv
INFO [2016-04-15 14:36:59,410] [DirectoryManager.java:163]  IGV Directory: /home/admin/igv
INFO [2016-04-15 14:36:59,411]  [Main.java:99] [main]  Startup  IGV Version Snapshot (500 (500))04/15/2016 02:23 PM
INFO [2016-04-15 14:36:59,412]  [Main.java:100] [main]  Java 1.7.0_99
INFO [2016-04-15 14:36:59,412]  [DirectoryManager.java:72] [main]  Fetching user directory...
INFO [2016-04-15 14:36:59,486]  [Main.java:101] [main]  Default User Directory: /home/admin
INFO [2016-04-15 14:36:59,487]  [Main.java:102] [main]  OS: Linux
ERROR [2016-04-15 14:36:59,807]  [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:173)
    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:1069)

    at org.broad.igv.ui.IGV.createHandCursor(IGV.java:1176)
    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)

INFO [2016-04-15 14:36:59,810]  [ShutdownThread.java:51] [Thread-2]  Shutting down
ERROR [2016-04-15 14:36:59,838]  [DefaultExceptionHandler.java:49] [Thread-2]  Unhandled exception
java.lang.NullPointerException
    at org.broad.igv.ui.IGV.getTrackPanels(IGV.java:1377)
    at org.broad.igv.ui.IGV.getAllTracks(IGV.java:2066)

    at org.broad.igv.ui.ShutdownThread.runS(ShutdownThread.java:56)
    at org.broad.igv.ui.ShutdownThread.run(ShutdownThread.java:64)

[admin@datarockstar IGV_Snapshot]$ /usr/lib/jvm/java-1.8.0-openjdk-1.8.0.77-0.b03.el7_2.x86_64/jre/bin/java -jar igv.jar
WARN [2016-04-15 14:37:17,301]  [Globals.java:150] [main]  Development mode is enabled
WARN [2016-04-15 14:37:17,301] [Globals.java:150]  Development mode is enabled
INFO [2016-04-15 14:37:17,303]  [DirectoryManager.java:163] [main]  IGV Directory: /home/admin/igv
INFO [2016-04-15 14:37:17,303] [DirectoryManager.java:163]  IGV Directory: /home/admin/igv
INFO [2016-04-15 14:37:17,305]  [Main.java:99] [main]  Startup  IGV Version Snapshot (500 (500))04/15/2016 02:23 PM
INFO [2016-04-15 14:37:17,305]  [Main.java:100] [main]  Java 1.8.0_77
INFO [2016-04-15 14:37:17,305]  [DirectoryManager.java:72] [main]  Fetching user directory...
INFO [2016-04-15 14:37:17,406]  [Main.java:101] [main]  Default User Directory: /home/admin
INFO [2016-04-15 14:37:17,407]  [Main.java:102] [main]  OS: Linux
ERROR [2016-04-15 14:37:17,658]  [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.createHandCursor(IGV.java:1176)
    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)

INFO [2016-04-15 14:37:17,660]  [ShutdownThread.java:51] [Thread-2]  Shutting down
ERROR [2016-04-15 14:37:17,682]  [DefaultExceptionHandler.java:49] [Thread-2]  Unhandled exception
java.lang.NullPointerException
    at org.broad.igv.ui.IGV.getTrackPanels(IGV.java:1377)
    at org.broad.igv.ui.IGV.getAllTracks(IGV.java:2066)

    at org.broad.igv.ui.ShutdownThread.runS(ShutdownThread.java:56)
    at org.broad.igv.ui.ShutdownThread.run(ShutdownThread.java:64)

About what changed in the last 3 week, there were 2 major system updates with some new kernels and a few things non-related to java.

Any ideas or how can I run a diagnostics?

[Jim Robinson]

Are you running mir and/or xmir?

[Jim Robinson]

Here's a long thread on this bug, its a bit dated but might be relevant.


https://bugs.launchpad.net/ubuntu/+source/xorg-server/+bug/1232471

On 4/15/16 12:42 PM, Roberto Galindo wrote:

[Roberto Galindo]

I am not sure, I am using a lightweight desktop Xfce. But initially everything was running ok in GNOME

[Roberto Galindo]

I tried the workaround

ssh -X localhost

No success, It continues with the same error. No mir or xmir running on Centos

[admin@datarockstar IGV_Snapshot]$ java -jar igv.jar
WARN [2016-04-15 15:18:34,715]  [Globals.java:150] [main]  Development mode is enabled
WARN [2016-04-15 15:18:34,715] [Globals.java:150]  Development mode is enabled
INFO [2016-04-15 15:18:34,717]  [DirectoryManager.java:163] [main]  IGV Directory: /home/admin/igv
INFO [2016-04-15 15:18:34,717] [DirectoryManager.java:163]  IGV Directory: /home/admin/igv
INFO [2016-04-15 15:18:34,719]  [Main.java:99] [main]  Startup  IGV Version Snapshot (500 (500))04/15/2016 02:23 PM
INFO [2016-04-15 15:18:34,719]  [Main.java:100] [main]  Java 1.8.0_77
INFO [2016-04-15 15:18:34,719]  [DirectoryManager.java:72] [main]  Fetching user directory...
INFO [2016-04-15 15:18:34,852]  [Main.java:101] [main]  Default User Directory: /home/admin
INFO [2016-04-15 15:18:34,852]  [Main.java:102] [main]  OS: Linux
ERROR [2016-04-15 15:18:35,135]  [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.createHandCursor(IGV.java:1176)
    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)

INFO [2016-04-15 15:18:35,138]  [ShutdownThread.java:51] [Thread-2]  Shutting down
ERROR [2016-04-15 15:18:35,153]  [DefaultExceptionHandler.java:49] [Thread-2]  Unhandled exception

java.lang.NullPointerException
    at org.broad.igv.ui.IGV.getTrackPanels(IGV.java:1377)
    at org.broad.igv.ui.IGV.getAllTracks(IGV.java:2066)
    at org.broad.igv.ui.ShutdownThread.runS(ShutdownThread.java:56)
    at org.broad.igv.ui.ShutdownThread.run(ShutdownThread.java:64)

[admin@datarockstar IGV_Snapshot]$ ps afx | grep unity-system-compositor
 21214 pts/5    S+     0:00              \_ grep --color=auto unity-system-compositor
[admin@datarockstar IGV_Snapshot]$ unity-system-compositor
bash: unity-system-compositor: command not found...
[admin@datarockstar IGV_Snapshot]$ kill -9 unity-system-compositor
-bash: kill: unity-system-compositor: arguments must be process or job IDs
[admin@datarockstar IGV_Snapshot]$ kill -9 21214
-bash: kill: (21214) - No such process
[admin@datarockstar IGV_Snapshot]$ service mir status
Redirecting to /bin/systemctl status  mir.service
● mir.service
   Loaded: not-found (Reason: No such file or directory)
   Active: inactive (dead)
[admin@datarockstar IGV_Snapshot]$ service xmir status
Redirecting to /bin/systemctl status  xmir.service
● xmir.service
   Loaded: not-found (Reason: No such file or directory)
   Active: inactive (dead)
[admin@datarockstar IGV_Snapshot]$ exit
logout
Connection to localhost closed.

[Jim Robinson]

Well,  if it worked until 3 weeks ago what changed, if you know?  This type of error is not IGV specific,  it is a Java conflict with something in your system.

If you download and try the snapshot again it should get you past the initial problem, but other errors might occur later.   I am catching these errors and just continuing.   Let me know the results.

Jim

--

---
You received this message because you are subscribed to the Google Groups "igv-help" group.
To unsubscribe from this group and stop receiving emails from it, send an email to igv-help+u...@googlegroups.com.

To view this discussion on the web visit https://groups.google.com/d/msgid/igv-help/ca64c49e-c085-4ecd-9c79-b9e196bba202%40googlegroups.com.

[Roberto Galindo]

Hi Jim

Ok, I will keep looking at those errors and let you know.

It is very strange, like I said before there were 2 major system updates but that's all.

Regards.

[Jim Robinson]

Do try the latest snapshot,  its updated since your first try. 

To view this discussion on the web visit https://groups.google.com/d/msgid/igv-help/79977040-2b31-482e-b5a8-61d3acb24231%40googlegroups.com.

[Bochao Lin]

Hello, I am wondering if this issue has been solved. I got the same error message, when I run in the server. I am wondering is that something wrong in the script? Because if I do not include igvbatch script . Only run ./igv.sh donot have any error message.

Thanks for any suggestion.

在 2016年4月15日星期五 UTC+2下午7:17:18，Roberto Galindo写道：

[James Robinson]

What to you mean exactly that you got the same error message? Its a very generic message.   If you are having errors specific to your script I will need a script I can run to reproduce.   Please open a github issue with a script and instructions for me to reproduce.  

--

---
You received this message because you are subscribed to the Google Groups "igv-help" group.

To unsubscribe from this group and stop receiving emails from it, send an email to igv-help+unsubscribe@googlegroups.com.

To view this discussion on the web visit https://groups.google.com/d/msgid/igv-help/88eaf181-746a-4298-846a-eded4fa099c5%40googlegroups.com.

[zefeng wu]

i have met same problem when open igv on ubuntu. However, after i delete the igv configure file named "IGV" in the home direction, it will reload the genome and open successfully.

在 2016年4月16日星期六 UTC+8上午1:17:18，Roberto Galindo写道：