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

rcholicrcholic DenverPosts: 68Member
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):
Post edited by rcholic on

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