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A java question!

niuguohaoniuguohao Member
edited August 2018 in Ask the GATK team

Hello!
I'm using GATK4.0.4.0 but I got a problem on Java. That is everytime I run GATK it gives me a error file back.

Using GATK jar /home/gaotiangang/niuguohao/biosoft/GATK4/gatk-4.0.4.0/gatk-package-4.0.4.0-local.jar
Running:
java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribble=false -Dsamjdk.compression_level=2 -Xmx10240m -Djava.io.tmpdir=./ -jar /home/gaotiangang/niuguohao/biosoft/GATK4/gatk-4.0.4.0/gatk-package-4.0.4.0-local.jar AnalyzeCovariates -before seq103.4.table -after seq103.5.table -plots seq103.5.pdf --ignore-last-modification-times
Picked up _JAVA_OPTIONS: -Xmx20480m -Xms20480m
Exception in thread "main" java.lang.UnsatisfiedLinkError: no net in java.library.path
at java.lang.ClassLoader.loadLibrary(ClassLoader.java:1864)
at java.lang.Runtime.loadLibrary0(Runtime.java:870)
at java.lang.System.loadLibrary(System.java:1122)
at java.net.InetAddress$1.run(InetAddress.java:294)
at java.net.InetAddress$1.run(InetAddress.java:292)
at java.security.AccessController.doPrivileged(Native Method)
at java.net.InetAddress.(InetAddress.java:291)
at org.apache.logging.log4j.core.util.NetUtils.getLocalHostname(NetUtils.java:53)
at org.apache.logging.log4j.core.LoggerContext.setConfiguration(LoggerContext.java:486)
at org.apache.logging.log4j.core.LoggerContext.reconfigure(LoggerContext.java:562)
at org.apache.logging.log4j.core.LoggerContext.reconfigure(LoggerContext.java:578)
at org.apache.logging.log4j.core.LoggerContext.start(LoggerContext.java:214)
at org.apache.logging.log4j.core.impl.Log4jContextFactory.getContext(Log4jContextFactory.java:145)
at org.apache.logging.log4j.core.impl.Log4jContextFactory.getContext(Log4jContextFactory.java:41)
at org.apache.logging.log4j.LogManager.getContext(LogManager.java:182)
at org.apache.logging.log4j.LogManager.getLogger(LogManager.java:455)
at org.broadinstitute.hellbender.utils.Utils.(Utils.java:75)
at org.broadinstitute.hellbender.Main.(Main.java:45)

I really don't understand what it mean because it worked well yesterday !
Thanks!

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