To celebrate the release of GATK 4.0, we are giving away free credits for running the GATK4 Best Practices pipelines in FireCloud, our secure online analysis portal. It’s first come first serve, so sign up now to claim your free credits worth $250. Sponsored by Google Cloud. Learn more at https://software.broadinstitute.org/firecloud/documentation/freecredits

Exception in thread "main" java.awt.HeadlessException while running GenomeAnalysisTk-4_1.jar

saniyaalekar94saniyaalekar94 NYMember
edited June 2017 in Ask the GATK team

Running the following command using the latest GATK4 jar file (GenomeAnalysisTk-4_1.jar):
java -jar GenomeAnalysisTk-4_1.jar PrintReads -I /home/exampleBAM.bam -O outputBAM.bam

At first I had this error:
Exception in thread "main" java.awt.HeadlessException:
No X11 DISPLAY variable was set, but this program performed an operation which requires it.
at java.awt.GraphicsEnvironment.checkHeadless(GraphicsEnvironment.java:204)
at java.awt.Window.(Window.java:536)
at java.awt.Frame.(Frame.java:420)
at java.awt.Frame.(Frame.java:385)
at javax.swing.JFrame.(JFrame.java:189)
at org.broadinstitute.hellbender.Main.displaySnpy(Main.java:413)
at org.broadinstitute.hellbender.Main.mainEntry(Main.java:146)
at org.broadinstitute.hellbender.Main.main(Main.java:207)

After trying to set the DISPLAY variable to various values like:
MyIPAddress:0.0 OR
localhost:0.0 OR
:0 OR
:0.0
I get the following error for each value:

Exception in thread "main" java.awt.AWTError: Can't connect to X11 window server using ':0.0' as the value of the DISPLAY variable.
at sun.awt.X11GraphicsEnvironment.initDisplay(Native Method)
at sun.awt.X11GraphicsEnvironment.access$200(X11GraphicsEnvironment.java:65)
at sun.awt.X11GraphicsEnvironment$1.run(X11GraphicsEnvironment.java:115)
at java.security.AccessController.doPrivileged(Native Method)
at sun.awt.X11GraphicsEnvironment.(X11GraphicsEnvironment.java:74)
at java.lang.Class.forName0(Native Method)
at java.lang.Class.forName(Class.java:264)
at java.awt.GraphicsEnvironment.createGE(GraphicsEnvironment.java:103)
at java.awt.GraphicsEnvironment.getLocalGraphicsEnvironment(GraphicsEnvironment.java:82)
at sun.awt.X11.XToolkit.(XToolkit.java:126)
at java.lang.Class.forName0(Native Method)
at java.lang.Class.forName(Class.java:264)
at java.awt.Toolkit$2.run(Toolkit.java:860)
at java.awt.Toolkit$2.run(Toolkit.java:855)
at java.security.AccessController.doPrivileged(Native Method)
at java.awt.Toolkit.getDefaultToolkit(Toolkit.java:854)
at java.awt.Component.getToolkitImpl(Component.java:1226)
at java.awt.Component.getToolkit(Component.java:1214)
at java.awt.Component.checkImage(Component.java:3749)
at java.awt.ImageMediaEntry.getStatus(MediaTracker.java:951)
at java.awt.MediaTracker.statusID(MediaTracker.java:715)
at java.awt.MediaTracker.waitForID(MediaTracker.java:663)
at javax.swing.ImageIcon.loadImage(ImageIcon.java:314)
at javax.swing.ImageIcon.(ImageIcon.java:244)
at org.broadinstitute.hellbender.Main.displaySnpy(Main.java:412)
at org.broadinstitute.hellbender.Main.mainEntry(Main.java:146)
at org.broadinstitute.hellbender.Main.main(Main.java:207)

After including -Djava.awt.headless=true in the command, I get the following error:
Exception in thread "main" java.awt.HeadlessException
at java.awt.GraphicsEnvironment.checkHeadless(GraphicsEnvironment.java:204)
at java.awt.Window.(Window.java:536)
at java.awt.Frame.(Frame.java:420)
at java.awt.Frame.(Frame.java:385)
at javax.swing.JFrame.(JFrame.java:189)
at org.broadinstitute.hellbender.Main.displaySnpy(Main.java:413)
at org.broadinstitute.hellbender.Main.mainEntry(Main.java:146)
at org.broadinstitute.hellbender.Main.main(Main.java:207)

My java version is:
java version "1.8.0_111"
Java(TM) SE Runtime Environment (build 1.8.0_111-b14)
Java HotSpot(TM) 64-Bit Server VM (build 25.111-b14, mixed mode)

Tagged:

Best Answer

Answers

Sign In or Register to comment.