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GATK 3.3 Genotype GVCF Caused by: java.io.FileNotFoundException: (Too many open files)

ravichavravichav United StatesMember
edited November 2015 in Ask the GATK team

I am trying to run GenotypeGVCF using the following command on a cluster and am getting the following exception. How can I fix this? -- Thanks in advance!

java -Xmx30G -jar /opt/ngstools/variantcallers/gatk/GATK-3.3-0/GenomeAnalysisTK.jar -T GenotypeGVCFs -R /opt/ngstools/Human_Decoy_REF/hs37d5.fa -V /home/user/gvcfs.list -L /home/user/chr_1.bed -D /opt/ngstools/dbsnp_138.b37.vcf --out /home/user/chr_1.vcf

INFO 11:23:53,718 ProgressMeter - | processed | time | per 1M | | total | remaining
INFO 11:23:53,718 ProgressMeter - Location | sites | elapsed | sites | completed | runtime | runtime
INFO 11:23:56,923 GenotypeGVCFs - Notice that the -ploidy parameter is ignored in GenotypeGVCFs tool as this is automatically determined by the input variant files

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:2109)
at javax.xml.stream.SecuritySupport$4.run(SecuritySupport.java:92)
at java.security.AccessController.doPrivileged(Native Method)
at javax.xml.stream.SecuritySupport.getResourceAsStream(SecuritySupport.java:87)
at javax.xml.stream.FactoryFinder.findJarServiceProvider(FactoryFinder.java:335)
at javax.xml.stream.FactoryFinder.find(FactoryFinder.java:302)
at javax.xml.stream.FactoryFinder.find(FactoryFinder.java:215)
at javax.xml.stream.XMLInputFactory.newInstance(XMLInputFactory.java:154)
at org.simpleframework.xml.stream.NodeBuilder.(NodeBuilder.java:48)
at org.simpleframework.xml.core.Persister.write(Persister.java:1000)
at org.simpleframework.xml.core.Persister.write(Persister.java:982)
at org.simpleframework.xml.core.Persister.write(Persister.java:963)
at org.broadinstitute.gatk.engine.phonehome.GATKRunReport.postReportToStream(GATKRunReport.java:377)
at org.broadinstitute.gatk.engine.phonehome.GATKRunReport.postReportToAWSS3(GATKRunReport.java:569)
at org.broadinstitute.gatk.engine.phonehome.GATKRunReport.postReport(GATKRunReport.java:352)
at org.broadinstitute.gatk.engine.CommandLineExecutable.generateGATKRunReport(CommandLineExecutable.java:165)
at org.broadinstitute.gatk.engine.CommandLineExecutable.execute(CommandLineExecutable.java:124)
at org.broadinstitute.gatk.utils.commandline.CommandLineProgram.start(CommandLineProgram.java:248)
at org.broadinstitute.gatk.utils.commandline.CommandLineProgram.start(CommandLineProgram.java:155)
at org.broadinstitute.gatk.engine.CommandLineGATK.main(CommandLineGATK.java:107)
Caused by: java.io.FileNotFoundException: /usr/lib/jvm/java-1.7.0-openjdk-1.7.0.91.x86_64/jre/lib/resources.jar (Too many open files)
at java.util.zip.ZipFile.open(Native Method)
at java.util.zip.ZipFile.(ZipFile.java:215)
at java.util.zip.ZipFile.(ZipFile.java:145)
at java.util.jar.JarFile.(JarFile.java:154)
at java.util.jar.JarFile.(JarFile.java:91)
at sun.misc.URLClassPath$JarLoader.getJarFile(URLClassPath.java:728)
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)
... 27 more

ERROR ------------------------------------------------------------------------------------------
ERROR A GATK RUNTIME ERROR has occurred (version 3.3-0-g37228af):
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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