Test-drive the GATK tools and Best Practices pipelines on Terra


Check out this blog post to learn how you can get started with GATK and try out the pipelines in preconfigured workspaces (with a user-friendly interface!) without having to install anything.

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 ------------------------------------------------------------------------------------------

Answers

Sign In or Register to comment.