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chapmanb / bcbio.variation

Toolkit to analyze genomic variation data, built on the GATK with Clojure
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could not find the main class bcbio.variation.core #14

Closed acquarius1990 closed 10 years ago

acquarius1990 commented 10 years ago

Hello Dr. Chapman,

I tried to run bcbio.variation but got the following error. Could you help me? Thanks!

java -Xmx1g -jar bcbio.variation-0.1.2-standalone.jar variant-ensemble combine-callers.yaml ~/database/human_g1k_v37.fasta out.vcf gatk.vcf samtools.vcf Exception in thread "main" java.lang.UnsupportedClassVersionError: org/broadinstitute/sting/gatk/CommandLineGATK : Unsupported major.minor version 51.0 at java.lang.ClassLoader.defineClass1(Native Method) at java.lang.ClassLoader.defineClass(ClassLoader.java:621) at java.security.SecureClassLoader.defineClass(SecureClassLoader.java:124) at java.net.URLClassLoader.defineClass(URLClassLoader.java:260) at java.net.URLClassLoader.access$000(URLClassLoader.java:56) at java.net.URLClassLoader$1.run(URLClassLoader.java:195) at java.security.AccessController.doPrivileged(Native Method) at java.net.URLClassLoader.findClass(URLClassLoader.java:188) at java.lang.ClassLoader.loadClass(ClassLoader.java:307) at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:301) at java.lang.ClassLoader.loadClass(ClassLoader.java:252) at java.lang.ClassLoader.loadClassInternal(ClassLoader.java:320) at java.lang.Class.forName0(Native Method) at java.lang.Class.forName(Class.java:169) at bcbio.variation.core$loading4910auto.invoke(core.clj:1) at bcbio.variation.coreinit.load(Unknown Source) at bcbio.variation.coreinit.(Unknown Source) at java.lang.Class.forName0(Native Method) at java.lang.Class.forName(Class.java:247) at clojure.lang.RT.loadClassForName(RT.java:2098) at clojure.lang.RT.load(RT.java:430) at clojure.lang.RT.load(RT.java:411) at clojure.core$load$fn5018.invoke(core.clj:5530) at clojure.core$load.doInvoke(core.clj:5529) at clojure.lang.RestFn.invoke(RestFn.java:408) at clojure.lang.Var.invoke(Var.java:415) at bcbio.variation.core.(Unknown Source) Could not find the main class: bcbio.variation.core. Program will exit.

chapmanb commented 10 years ago

Thanks for trying out bcbio.variation. It currently requires java 1.7 due to the underlying GATK library dependencies and it appears you're running java 1.6. The cryptic Unsupported major.minor version 51.0 error is the giveaway. Apologies, this was not properly documented in the README. Hope this gets you up and running.

acquarius1990 commented 10 years ago

It works great. Thank you!