IndelRealigner runtime error with GATK version 3.5-0-g36282e4

luna5124luna5124 San DiegoMember

Hi, I was trying to map a WGS sequence following the GATK best practice. I used bwa -mem to map. Then I used picard to sort, mark duplicates before passing into the IndelRealigner. When running the IndelRealigner, a runtime error occurred. I'm wondering what might be the cause of this runtime error and what should I do?

Thank you!

My command line is:

java -Xmx10G -jar GenomeAnalysisTK.jar \
-T IndelRealigner \
-R hg38.fa \
-I input.bam \
-targetInterval indel_target_intervals.list \
-known 1000G_omni2.5.hg38.vcf.gz \
-known Mills_and_1000G_gold_standard.indels.hg38.vcf.gz \
-o realigned.bam

The error stack trace is:

##### 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$4.run(SecuritySupport.java:92)
        at java.security.AccessController.doPrivileged(Native Method)
        at javax.xml.stream.SecuritySupport.getResourceAsStream(SecuritySupport.java:87)
        at javax.xml.stream.FactoryFinder.findJarServiceProvider(FactoryFinder.java:335)
        at javax.xml.stream.FactoryFinder.find(FactoryFinder.java:302)
        at javax.xml.stream.FactoryFinder.find(FactoryFinder.java:215)
        at javax.xml.stream.XMLInputFactory.newInstance(XMLInputFactory.java:154)
        at org.simpleframework.xml.stream.NodeBuilder.<clinit>(NodeBuilder.java:48)
        at org.simpleframework.xml.core.Persister.write(Persister.java:1000)
        at org.simpleframework.xml.core.Persister.write(Persister.java:982)
        at org.simpleframework.xml.core.Persister.write(Persister.java:963)
        at org.broadinstitute.gatk.engine.phonehome.GATKRunReport.postReportToStream(GATKRunReport.java:377)
        at org.broadinstitute.gatk.engine.phonehome.GATKRunReport.postReportToAWSS3(GATKRunReport.java:569)
        at org.broadinstitute.gatk.engine.phonehome.GATKRunReport.postReport(GATKRunReport.java:352)
        at org.broadinstitute.gatk.engine.CommandLineExecutable.generateGATKRunReport(CommandLineExecutable.java:165)
        at org.broadinstitute.gatk.engine.CommandLineExecutable.generateGATKRunReport(CommandLineExecutable.java:176)
        at org.broadinstitute.gatk.engine.CommandLineExecutable.execute(CommandLineExecutable.java:122)
        at org.broadinstitute.gatk.utils.commandline.CommandLineProgram.start(CommandLineProgram.java:248)
        at org.broadinstitute.gatk.utils.commandline.CommandLineProgram.start(CommandLineProgram.java:155)
        at org.broadinstitute.gatk.engine.CommandLineGATK.main(CommandLineGATK.java:106)
Caused by: java.io.FileNotFoundException: /usr/lib/jvm/java-1.7.0-openjdk-1.7.0.75.x86_64/jre/lib/resources.jar
        at sun.misc.URLClassPath$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 3.5-0-g36282e4):
##### 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 ------------------------------------------------------------------------------------------

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