I got this error during local realignment
ERROR ------------------------------------------------------------------------------------------
ERROR stack trace
java.lang.InternalError
at sun.misc.URLClassPath$JarLoader.getResource(URLClassPath.java:838)
at sun.misc.URLClassPath.getResource(URLClassPath.java:199)
at sun.misc.URLClassPath.getResource(URLClassPath.java:251)
at java.lang.ClassLoader.getBootstrapResource(ClassLoader.java:1305)
at java.lang.ClassLoader.getResource(ClassLoader.java:1144)
at java.lang.ClassLoader.getResource(ClassLoader.java:1142)
at java.lang.ClassLoader.getSystemResource(ClassLoader.java:1267)
at java.lang.ClassLoader.getSystemResourceAsStream(ClassLoader.java:1370)
at java.lang.Class.getResourceAsStream(Class.java:2101)
at javax.xml.stream.SecuritySupport$4.run(SecuritySupport.java:92)
at java.security.AccessController.doPrivileged(Native Method)
at javax.xml.stream.SecuritySupport.getResourceAsStream(SecuritySupport.java:87)
at javax.xml.stream.FactoryFinder.findJarServiceProvider(FactoryFinder.java:335)
at javax.xml.stream.FactoryFinder.find(FactoryFinder.java:302)
at javax.xml.stream.FactoryFinder.find(FactoryFinder.java:215)
at javax.xml.stream.XMLInputFactory.newInstance(XMLInputFactory.java:154)
at org.simpleframework.xml.stream.NodeBuilder.(NodeBuilder.java:48)
at org.simpleframework.xml.core.Persister.write(Persister.java:1000)
at org.simpleframework.xml.core.Persister.write(Persister.java:982)
at org.simpleframework.xml.core.Persister.write(Persister.java:963)
at org.broadinstitute.sting.gatk.phonehome.GATKRunReport.postReportToStream(GATKRunReport.java:377)
at org.broadinstitute.sting.gatk.phonehome.GATKRunReport.postReportToAWSS3(GATKRunReport.java:569)
at org.broadinstitute.sting.gatk.phonehome.GATKRunReport.postReport(GATKRunReport.java:352)
at org.broadinstitute.sting.gatk.CommandLineExecutable.generateGATKRunReport(CommandLineExecutable.java:16
at org.broadinstitute.sting.gatk.CommandLineExecutable.generateGATKRunReport(CommandLineExecutable.java:17
at org.broadinstitute.sting.gatk.CommandLineExecutable.execute(CommandLineExecutable.java:122)
at org.broadinstitute.sting.commandline.CommandLineProgram.start(CommandLineProgram.java:248)
at org.broadinstitute.sting.commandline.CommandLineProgram.start(CommandLineProgram.java:155)
at org.broadinstitute.sting.gatk.CommandLineGATK.main(CommandLineGATK.java:107)
Caused by: java.io.FileNotFoundException: /usr/lib/jvm/java-1.7.0-openjdk-1.7.0.75.x86_64/jre/lib/resources.jar
at sun.misc.URLClassPath$JarLoader.getJarFile(URLClassPath.java:726)
at sun.misc.URLClassPath$JarLoader.access$600(URLClassPath.java:591)
at sun.misc.URLClassPath$JarLoader$1.run(URLClassPath.java:673)
at sun.misc.URLClassPath$JarLoader$1.run(URLClassPath.java:666)
at java.security.AccessController.doPrivileged(Native Method)
at sun.misc.URLClassPath$JarLoader.ensureOpen(URLClassPath.java:665)
at sun.misc.URLClassPath$JarLoader.getResource(URLClassPath.java:836)
... 28 more
ERROR ------------------------------------------------------------------------------------------
ERROR A GATK RUNTIME ERROR has occurred (version 3.1-1-g07a4bf8):
ERROR
ERROR This might be a bug. Please check the documentation guide to see if this is a known problem.
ERROR If not, please post the error message, with stack trace, to the GATK forum.
ERROR Visit our website and forum for extensive documentation and answers to
ERROR commonly asked questions http://www.broadinstitute.org/gatk
ERROR
ERROR MESSAGE: Code exception (see stack trace for error itself)
ERROR ------------------------------------------------------------------------------------------
Would you tell me how to correct this error Image may be NSFW.
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