Annotation for variant calling
REQUIRED for all errors and issues:
a) GATK version used: 4.4.0.0
b) Exact command used: gatk-4.4.0.0/gatk VariantAnnotator -R /home/databench/GRCz11_RefData/GRCz11.fa -A SnpEff --variant Affoutputf_raw_variants.vcf --snpEffFile Aff.ann.gatk.vcf -L Affoutput_raw_variants.vcf -o Aff.gatk.vcf
c) Entire program log: Using GATK jar /home/databench/gatk-4.4.0.0/gatk-package-4.4.0.0-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 -jar /home/databench/gatk-4.4.0.0/gatk-package-4.4.0.0-local.jar VariantAnnotator -R /home/databench/GRCz11_RefData/GRCz11.fa -A SnpEff --variant Affoutputf_raw_variants.vcf --snpEffFile Aff.ann.gatk.vcf -L Affoutput_raw_variants.vcf -o Aff.gatk.vcfc
Error: A JNI error has occurred, please check your installation and try again
Exception in thread "main" java.lang.UnsupportedClassVersionError: org/broadinstitute/hellbender/Main has been compiled by a more recent version of the Java Runtime (class file version 61.0), this version of the Java Runtime only recognizes class file versions up to 52.0
at java.lang.ClassLoader.defineClass1(Native Method)
at java.lang.ClassLoader.defineClass(ClassLoader.java:757)
at java.security.SecureClassLoader.defineClass(SecureClassLoader.java:142)
at java.net.URLClassLoader.defineClass(URLClassLoader.java:473)
at java.net.URLClassLoader.access$100(URLClassLoader.java:74)
at java.net.URLClassLoader$1.run(URLClassLoader.java:369)
at java.net.URLClassLoader$1.run(URLClassLoader.java:363)
at java.security.AccessController.doPrivileged(Native Method)
at java.net.URLClassLoader.findClass(URLClassLoader.java:362)
at java.lang.ClassLoader.loadClass(ClassLoader.java:419)
at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:352)
at java.lang.ClassLoader.loadClass(ClassLoader.java:352)
at sun.launcher.LauncherHelper.checkAndLoadMain(LauncherHelper.java:601)
It seems that it is a java error. But I am unable to fix it. Can you please help ?
-
Looks like you are using java 1.8 releases. GATK 4.4.0.0 release requires java 17 therefore you may need to upgrade your java runtime installation to 17.
Regards.
Please sign in to leave a comment.
1 comment