IGV do not launch

[Omeli WhiteDemon]

Hello.

We have troubles with launching IGV on one of our machines.

We've tried trought javaws and trought igv.sh

The same mistake: Width (0) and height (0) must be non-zero.

IGV version 2.3.90(also tried 2.3.89), java version - 1.8.0.111 and the latest - 1.8.0.121

igv.sh show output:

INFO [2017-01-19 12:35:00,504]  [DirectoryManager.java:169] [main]  IGV Directory: /home/moon/igv

INFO [2017-01-19 12:35:00,504] [DirectoryManager.java:169]  IGV Directory: /home/moon/igv

INFO [2017-01-19 12:35:00,510]  [Main.java:134] [main]  Startup  IGV Version 2.3.90 (143)01/08/2017 11:43 PM

INFO [2017-01-19 12:35:00,510]  [Main.java:135] [main]  Java 1.8.0_121

INFO [2017-01-19 12:35:00,510]  [DirectoryManager.java:72] [main]  Fetching user directory... 

INFO [2017-01-19 12:35:00,724]  [Main.java:136] [main]  Default User Directory: /home/moon

INFO [2017-01-19 12:35:00,725]  [Main.java:137] [main]  OS: Linux

INFO [2017-01-19 12:35:08,532]  [IGV.java:1188] [main]  Warning: could not create fistCursor

ERROR [2017-01-19 12:35:08,534]  [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.createZoomCursors(IGV.java:1132)

    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:274)

    at org.broad.igv.ui.Main.main(Main.java:94)

INFO [2017-01-19 12:35:10,134]  [ShutdownThread.java:51] [Thread-2]  Shutting down

ERROR [2017-01-19 12:35:10,145]  [DefaultExceptionHandler.java:49] [Thread-2]  Unhandled exception

java.lang.NullPointerException

    at org.broad.igv.ui.IGV.getTrackPanels(IGV.java:1395)

    at org.broad.igv.ui.IGV.getAllTracks(IGV.java:2082)

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

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

Thank you for your help.

[James Robinson]

Could you attach your "prefs.properties" file here.   Its located in an "igv" folder in the users home directory.

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[Omeli WhiteDemon]

четверг, 19 января 2017 г., 20:19:13 UTC+3 пользователь Jim Robinson написал:

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[James Robinson]

OK, thanks, if you delete that file it should work.  Here are the contents, notice the first line.    I'm not sure how it got in that state, that line saves the position and size of the window the last time it was closed.    I will add some protection in IGV so that it corrects for this in the future.

So delete "prefs.properties",  IGV will generate a new one upon start.

IGV.Bounds=0,0,0,0

IGV.Frame.ExtendedState=0

SKIP_VERSION=,2.3.84

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[Omeli WhiteDemon]

Didn't help.

The same mistake appears with igv.sh and igv.jnlp.

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[James Robinson]

As an experiment could you try this development build?  https://data.broadinstitute.org/igv/projects/3.0_alpha/igv_mm.jnlp

If that doesn't work I'm not sure what else to try.   You are having this problem on 1 particular machine?  Its possible its opening IGV iconified,  check the system tray or similar area if your UI manager provides one.

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