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Error: Can't connect to window server - not enough permissions, when running "RealignerTargetCreator

rcholicrcholic DenverMember
edited July 2013 in Ask the GATK team

I started with BWA-MEM to do alignment, used Picard to process the .SAM files (converted to bam, reorder, addorreplacegroup, etc). The GATK version I'm using is version 2.5-2-gf57256b, I cannot run 2.6 because the server only has Java 6 and I cannot upgrade it to Java 7.

I got a huge stack of error message when I run this command line (RealignerTargetCrator):

java -Xmx2g -jar $CLASSPATH/GenomeAnalysisTK.jar \

-T RealignerTargetCreator \
-R /Volumes/files/Users/user1/GATK_ref/hg19.fasta \
-I sorted_Deduped_reorder_grp.bam \
-o ./GATK/forIndelRealigner.intervals>

The error messages are these (sorry, a lot): I don't know why GATK needs to connect to window server? what permission problem? I am using a Mac OS X built server (remote). Thank you

ERROR ------------------------------------------------------------------------------------------
ERROR stack trace

java.lang.InternalError: Can't connect to window server - not enough permissions.
at java.lang.ClassLoader$NativeLibrary.load(Native Method)
at java.lang.ClassLoader.loadLibrary0(ClassLoader.java:1827)
at java.lang.ClassLoader.loadLibrary(ClassLoader.java:1724)
at java.lang.Runtime.loadLibrary0(Runtime.java:823)
at java.lang.System.loadLibrary(System.java:1045)
at sun.security.action.LoadLibraryAction.run(LoadLibraryAction.java:50)
at java.security.AccessController.doPrivileged(Native Method)
at java.awt.Toolkit.loadLibraries(Toolkit.java:1605)
at java.awt.Toolkit.(Toolkit.java:1627)
at sun.awt.AppContext$2.run(AppContext.java:240)
at sun.awt.AppContext$2.run(AppContext.java:226)
at java.security.AccessController.doPrivileged(Native Method)
at sun.awt.AppContext.initMainAppContext(AppContext.java:226)
at sun.awt.AppContext.access$200(AppContext.java:112)
at sun.awt.AppContext$3.run(AppContext.java:306)
at java.security.AccessController.doPrivileged(Native Method)
at sun.awt.AppContext.getAppContext(AppContext.java:287)
at com.sun.jmx.trace.Trace.out(Trace.java:180)
at com.sun.jmx.trace.Trace.isSelected(Trace.java:88)
at com.sun.jmx.interceptor.DefaultMBeanServerInterceptor.isTraceOn(DefaultMBeanServerInterceptor.java:1830)
at com.sun.jmx.interceptor.DefaultMBeanServerInterceptor.registerDynamicMBean(DefaultMBeanServerInterceptor.java:929)
at com.sun.jmx.interceptor.DefaultMBeanServerInterceptor.registerObject(DefaultMBeanServerInterceptor.java:916)
at com.sun.jmx.interceptor.DefaultMBeanServerInterceptor.registerMBean(DefaultMBeanServerInterceptor.java:312)
at com.sun.jmx.mbeanserver.JmxMBeanServer$2.run(JmxMBeanServer.java:1195)
at java.security.AccessController.doPrivileged(Native Method)
at com.sun.jmx.mbeanserver.JmxMBeanServer.initialize(JmxMBeanServer.java:1193)
at com.sun.jmx.mbeanserver.JmxMBeanServer.(JmxMBeanServer.java:225)
at com.sun.jmx.mbeanserver.JmxMBeanServer.(JmxMBeanServer.java:170)
at com.sun.jmx.mbeanserver.JmxMBeanServer.newMBeanServer(JmxMBeanServer.java:1401)
at javax.management.MBeanServerBuilder.newMBeanServer(MBeanServerBuilder.java:93)
at javax.management.MBeanServerFactory.newMBeanServer(MBeanServerFactory.java:311)
at javax.management.MBeanServerFactory.createMBeanServer(MBeanServerFactory.java:214)
at javax.management.MBeanServerFactory.createMBeanServer(MBeanServerFactory.java:175)
at sun.management.ManagementFactory.createPlatformMBeanServer(ManagementFactory.java:302)
at java.lang.management.ManagementFactory.getPlatformMBeanServer(ManagementFactory.java:504)
at org.broadinstitute.sting.gatk.executive.MicroScheduler.(MicroScheduler.java:222)
at org.broadinstitute.sting.gatk.executive.LinearMicroScheduler.(LinearMicroScheduler.java:70)
at org.broadinstitute.sting.gatk.executive.MicroScheduler.create(MicroScheduler.java:169)
at org.broadinstitute.sting.gatk.GenomeAnalysisEngine.createMicroscheduler(GenomeAnalysisEngine.java:443)
at org.broadinstitute.sting.gatk.GenomeAnalysisEngine.execute(GenomeAnalysisEngine.java:272)
at org.broadinstitute.sting.gatk.CommandLineExecutable.execute(CommandLineExecutable.java:113)
at org.broadinstitute.sting.commandline.CommandLineProgram.start(CommandLineProgram.java:245)
at org.broadinstitute.sting.commandline.CommandLineProgram.start(CommandLineProgram.java:152)
at org.broadinstitute.sting.gatk.CommandLineGATK.main(CommandLineGATK.java:91)

ERROR ------------------------------------------------------------------------------------------
ERROR A GATK RUNTIME ERROR has occurred (version 2.5-2-gf57256b):

Issue · Github
by Geraldine_VdAuwera

Issue Number
Last Updated
Closed By


  • rcholicrcholic DenverMember

    I think I found the answer to my question. After I include the "-Djava.awt.headless=true" option before "-jar" in my above command, GATK runs perfectly fine on my remote Mac server. I post this in case other people may find it helpful in future. - cheers.

  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie admin

    Thanks for posting the solution to your issue, @rcholic -- and sorry for not responding earlier. Glad your issue is resolved.

  • rcholicrcholic DenverMember

    @Geraldine_VdAuwera said:
    Thanks for posting the solution to your issue, rcholic -- and sorry for not responding earlier. Glad your issue is resolved.

    sure, you are welcome. Thank YOU GUYS for offering GATK. I think the code in GATK package may somehow triggers awt (accidentally?, might be a bug) during running, which is not possible to execute in SSH. I guess this is the main cause for my error messages posted in the original post. -cheers

  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie admin

    Yep, sounds like a bug -- we'll try to fix this issue in an upcoming version. But in the meantime it's good to have a workaround.

  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie admin
    edited April 2015

    @rcholic Just an update -- this has been lingering in the queue forever because versions that run on java 6 are deprecated, and it seems it doesn't happen with java 7, so we're now accepting that we just can't devote any effort to this at all, especially since you have a workaround and no work is blocked afaik. We're happy to take a patch from someone of course.

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