chapmanb/adam-clojure-deps.txt

## adam-clojure-deps.txt
 [clojure-complete "0.2.3" :exclusions [[org.clojure/clojure]]]
 [edu.berkeley.cs.amplab.adam/adam-cli "0.7.1"]
   [args4j "2.0.23"]
   [org.scala-lang/scala-library "2.10.3"]
   [org.slf4j/slf4j-log4j12 "1.7.5"]
     [log4j "1.2.17"]
     [org.slf4j/slf4j-api "1.7.5"]
 [edu.berkeley.cs.amplab.adam/adam-core "0.7.1"]
   [cofoja "1.0"]
   [com.twitter/parquet-avro "1.3.2"]
     [com.twitter/parquet-column "1.3.2"]
       [com.twitter/parquet-common "1.3.2"]
       [com.twitter/parquet-encoding "1.3.2"]
         [com.twitter/parquet-generator "1.3.2"]
     [com.twitter/parquet-format "2.0.0"]
     [com.twitter/parquet-hadoop "1.3.2"]
       [com.twitter/parquet-jackson "1.3.2"]
   [commons-io "1.3.2"]
   [fi.tkk.ics.hadoop.bam/hadoop-bam "6.1-SNAPSHOT"]
   [org.apache.avro/avro "1.7.4"]
     [com.thoughtworks.paranamer/paranamer "2.3"]
     [org.apache.commons/commons-compress "1.4.1"]
       [org.tukaani/xz "1.0"]
     [org.codehaus.jackson/jackson-core-asl "1.8.8"]
     [org.codehaus.jackson/jackson-mapper-asl "1.8.8"]
   [org.apache.hadoop/hadoop-client "2.2.0" :exclusions [[asm] [org.jboss.netty/netty] [org.codehaus.jackson/*] [org.sonatype.sisu.inject/*]]]
     [org.apache.hadoop/hadoop-annotations "2.2.0" :exclusions [[jdk.tools]]]
     [org.apache.hadoop/hadoop-common "2.2.0" :exclusions [[tomcat/jasper-compiler] [tomcat/jasper-runtime] [javax.servlet/servlet-api] [javax.servlet.jsp/jsp-api] [commons-logging/commons-logging-api] [jetty/org.mortbay.jetty] [org.mortbay.jetty/jetty] [org.mortbay.jetty/jetty-util] [org.mortbay.jetty/jsp-api-2.1] [org.mortbay.jetty/servlet-api-2.5] [com.sun.jersey/jersey-core] [com.sun.jersey/jersey-json] [com.sun.jersey/jersey-server] [org.eclipse.jdt/core] [org.apache.avro/avro-ipc] [net.sf.kosmosfs/kfs] [net.java.dev.jets3t/jets3t] [com.jcraft/jsch] [commons-el]]]
       [com.google.protobuf/protobuf-java "2.5.0"]
       [commons-cli "1.2"]
       [commons-codec "1.4"]
       [commons-configuration "1.6"]
         [commons-beanutils/commons-beanutils-core "1.8.0"]
         [commons-collections "3.2.1"]
         [commons-digester "1.8"]
           [commons-beanutils "1.7.0"]
       [commons-httpclient "3.1"]
       [commons-lang "2.5"]
       [commons-logging "1.1.1" :exclusions [[avalon-framework] [logkit] [javax.servlet/servlet-api]]]
       [commons-net "3.1"]
       [org.apache.commons/commons-math "2.1"]
       [org.apache.hadoop/hadoop-auth "2.2.0"]
       [xmlenc "0.52"]
     [org.apache.hadoop/hadoop-hdfs "2.2.0" :exclusions [[commons-daemon] [org.apache.avro/avro] [org.mortbay.jetty/jetty] [com.sun.jersey/jersey-core] [com.sun.jersey/jersey-server] [javax.servlet/servlet-api] [javax.servlet.jsp/jsp-api] [tomcat/jasper-runtime]]]
       [org.mortbay.jetty/jetty-util "6.1.26"]
     [org.apache.hadoop/hadoop-mapreduce-client-app "2.2.0" :exclusions [[javax.servlet/servlet-api] [org.apache.hadoop/hadoop-yarn-server-nodemanager] [org.apache.hadoop/hadoop-yarn-server-web-proxy] [org.apache.hadoop/hadoop-annotations] [com.google.inject.extensions/guice-servlet] [junit] [org.apache.avro/avro] [jline] [io.netty/netty]]]
       [org.apache.hadoop/hadoop-mapreduce-client-common "2.2.0"]
         [org.apache.hadoop/hadoop-yarn-client "2.2.0"]
           [com.google.inject/guice "3.0"]
             [aopalliance "1.0"]
             [javax.inject "1"]
           [com.sun.jersey.contribs/jersey-guice "1.9"]
           [com.sun.jersey.jersey-test-framework/jersey-test-framework-grizzly2 "1.9"]
             [com.sun.jersey.jersey-test-framework/jersey-test-framework-core "1.9"]
               [com.sun.jersey/jersey-client "1.9"]
               [javax.servlet/javax.servlet-api "3.0.1"]
             [com.sun.jersey/jersey-grizzly2 "1.9"]
               [org.glassfish.grizzly/grizzly-http-server "2.1.2"]
                 [org.glassfish.grizzly/grizzly-rcm "2.1.2"]
               [org.glassfish.grizzly/grizzly-http-servlet "2.1.2"]
               [org.glassfish.grizzly/grizzly-http "2.1.2"]
                 [org.glassfish.grizzly/grizzly-framework "2.1.2"]
                   [org.glassfish.gmbal/gmbal-api-only "3.0.0-b023"]
                     [org.glassfish.external/management-api "3.0.0-b012"]
               [org.glassfish/javax.servlet "3.1"]
           [com.sun.jersey/jersey-json "1.9" :exclusions [[javax.xml.stream/stax-api]]]
             [com.sun.xml.bind/jaxb-impl "2.2.3-1"]
               [javax.xml.bind/jaxb-api "2.2.2"]
                 [javax.activation/activation "1.1"]
             [org.codehaus.jettison/jettison "1.1"]
               [stax/stax-api "1.0.1"]
           [com.sun.jersey/jersey-server "1.9"]
             [com.sun.jersey/jersey-core "1.9"]
         [org.apache.hadoop/hadoop-yarn-server-common "2.2.0"]
       [org.apache.hadoop/hadoop-mapreduce-client-shuffle "2.2.0"]
     [org.apache.hadoop/hadoop-mapreduce-client-core "2.2.0" :exclusions [[junit] [com.google.inject/guice] [com.sun.jersey.jersey-test-framework/jersey-test-framework-grizzly2] [com.sun.jersey/jersey-server] [com.sun.jersey.contribs/jersey-guice] [org.apache.avro/avro] [org.apache.hadoop/hadoop-annotations] [com.google.inject.extensions/guice-servlet] [com.sun.jersey/jersey-json] [io.netty/netty]]]
       [org.apache.hadoop/hadoop-yarn-common "2.2.0"]
     [org.apache.hadoop/hadoop-mapreduce-client-jobclient "2.2.0" :exclusions [[junit] [org.apache.avro/avro] [org.apache.hadoop/hadoop-annotations] [com.google.inject.extensions/guice-servlet] [io.netty/netty]]]
     [org.apache.hadoop/hadoop-yarn-api "2.2.0" :exclusions [[org.apache.hadoop/hadoop-annotations] [com.google.inject/guice] [com.sun.jersey.jersey-test-framework/jersey-test-framework-grizzly2] [com.sun.jersey/jersey-server] [com.sun.jersey.contribs/jersey-guice] [com.google.inject.extensions/guice-servlet] [org.apache.avro/avro] [com.sun.jersey/jersey-core] [com.sun.jersey/jersey-json] [io.netty/netty]]]
   [org.apache.spark/spark-core_2.10 "0.9.0-incubating"]
     [colt "1.2.0"]
       [concurrent "1.3.4"]
     [com.clearspring.analytics/stream "2.4.0"]
     [com.codahale.metrics/metrics-core "3.0.0"]
     [com.codahale.metrics/metrics-ganglia "3.0.0"]
       [info.ganglia.gmetric4j/gmetric4j "1.0.3"]
         [org.acplt/oncrpc "1.0.7"]
     [com.codahale.metrics/metrics-graphite "3.0.0"]
     [com.codahale.metrics/metrics-json "3.0.0"]
       [com.fasterxml.jackson.core/jackson-databind "2.2.2"]
         [com.fasterxml.jackson.core/jackson-annotations "2.2.2"]
         [com.fasterxml.jackson.core/jackson-core "2.2.2"]
     [com.codahale.metrics/metrics-jvm "3.0.0"]
     [com.google.code.findbugs/jsr305 "1.3.9"]
     [com.google.guava/guava "14.0.1"]
     [com.ning/compress-lzf "1.0.0"]
     [com.twitter/chill-java "0.3.1"]
     [com.twitter/chill_2.10 "0.3.1"]
       [com.esotericsoftware.kryo/kryo "2.21"]
         [com.esotericsoftware.minlog/minlog "1.2"]
         [com.esotericsoftware.reflectasm/reflectasm "1.07" :classifier "shaded"]
         [org.objenesis/objenesis "1.2"]
       [org.ow2.asm/asm-commons "4.0"]
         [org.ow2.asm/asm-tree "4.0"]
     [io.netty/netty-all "4.0.13.Final"]
     [it.unimi.dsi/fastutil "6.4.4"]
     [net.java.dev.jets3t/jets3t "0.7.1"]
     [net.liftweb/lift-json_2.10 "2.5.1" :exclusions [[org.scala-lang/scalap]]]
     [org.apache.avro/avro-ipc "1.7.4" :exclusions [[org.jboss.netty/netty] [io.netty/netty]]]
       [org.apache.velocity/velocity "1.7"]
       [org.mortbay.jetty/jetty "6.1.26"]
       [org.mortbay.jetty/servlet-api "2.5-20081211"]
     [org.apache.mesos/mesos "0.13.0"]
     [org.apache.zookeeper/zookeeper "3.4.5" :exclusions [[org.jboss.netty/netty]]]
       [jline "0.9.94"]
         [junit "3.8.1"]
     [org.eclipse.jetty/jetty-server "7.6.8.v20121106"]
       [org.eclipse.jetty.orbit/javax.servlet "2.5.0.v201103041518"]
       [org.eclipse.jetty/jetty-continuation "7.6.8.v20121106"]
       [org.eclipse.jetty/jetty-http "7.6.8.v20121106"]
         [org.eclipse.jetty/jetty-io "7.6.8.v20121106"]
           [org.eclipse.jetty/jetty-util "7.6.8.v20121106"]
     [org.ow2.asm/asm "4.0"]
     [org.spark-project.akka/akka-remote_2.10 "2.2.3-shaded-protobuf" :exclusions [[org.jboss.netty/netty]]]
       [io.netty/netty "3.6.6.Final"]
       [org.spark-project.akka/akka-actor_2.10 "2.2.3-shaded-protobuf"]
         [com.typesafe/config "1.0.2"]
       [org.spark-project.protobuf/protobuf-java "2.4.1-shaded"]
       [org.uncommons.maths/uncommons-maths "1.2.2a" :exclusions [[jfree/jcommon] [jfree/jfreechart]]]
     [org.spark-project.akka/akka-slf4j_2.10 "2.2.3-shaded-protobuf" :exclusions [[org.jboss.netty/netty]]]
     [org.xerial.snappy/snappy-java "1.0.5"]
   [picard "1.93"]
   [samtools "1.93"]
   [tribble "1.93"]
   [variant "1.93"]
 [edu.berkeley.cs.amplab.adam/adam-format "0.7.1"]
 [midje "1.6.3" :exclusions [[commons-codec]]]
   [clj-time "0.6.0"]
   [colorize "0.1.1" :exclusions [[org.clojure/clojure]]]
   [dynapath "0.2.0"]
   [gui-diff "0.5.0"]
     [org.clojars.trptcolin/sjacket "0.1.3" :exclusions [[org.clojure/clojure]]]
       [net.cgrand/parsley "0.9.1"]
       [net.cgrand/regex "1.1.0"]
   [ordered "1.2.0" :exclusions [[org.clojure/clojure]]]
   [org.clojure/core.unify "0.5.2" :exclusions [[org.clojure/clojure]]]
   [org.clojure/math.combinatorics "0.0.7"]
   [org.clojure/tools.macro "0.1.5"]
   [org.clojure/tools.namespace "0.2.4"]
   [slingshot "0.10.3"]
   [swiss-arrows "1.0.0"]
   [utilize "0.2.3" :exclusions [[org.clojure/clojure]]]
     [joda-time "2.0"]
 [org.apache.spark/spark-streaming_2.10 "0.9.0-incubating" :exclusions [[org.apache.hadoop/hadoop-client] [org.apache.spark/spark-core_2.10] [org.codehaus.jackson/jackson-mapper-asl] [org.eclipse.jetty/jetty-server] [org.scala-lang/scala-library] [com.thoughtworks.paranamer/paranamer] [org.slf4j/slf4j-api] [com.google.protobuf/protobuf-java] [commons-codec] [commons-io] [commons-lang]]]
 [org.clojars.r0man/clj-spark "0.1.0-20140206.151117-4"]
   [org.clojars.mlimotte/serializable-fn "0.0.3"]
   [org.clojure/tools.cli "0.3.1"]
   [org.clojure/tools.logging "0.2.6"]
 [org.clojure/clojure "1.5.1"]
 [org.clojure/tools.nrepl "0.2.3" :exclusions [[org.clojure/clojure]]]

## traceback.txt
$ lein midje
2014-03-24 20:44:34 WARN  Utils:61 - Your hostname, kunkel resolves to a loopback address: 127.0.1.1; using 192.168.122.1 instead (on interface virbr0)
2014-03-24 20:44:34 WARN  Utils:61 - Set SPARK_LOCAL_IP if you need to bind to another address
2014-03-24 20:44:36 WARN  NativeCodeLoader:62 - Unable to load native-hadoop library for your platform... using builtin-java classes where applicable
Exception in thread "main" java.lang.IncompatibleClassChangeError: class org.apache.spark.util.InnerClosureFinder has interface org.objectweb.asm.ClassVisitor as super class
	at java.lang.ClassLoader.defineClass1(Native Method)
	at java.lang.ClassLoader.defineClass(ClassLoader.java:800)
	at java.security.SecureClassLoader.defineClass(SecureClassLoader.java:142)
	at java.net.URLClassLoader.defineClass(URLClassLoader.java:449)
	at java.net.URLClassLoader.access$100(URLClassLoader.java:71)
	at java.net.URLClassLoader$1.run(URLClassLoader.java:361)
	at java.net.URLClassLoader$1.run(URLClassLoader.java:355)
	at java.security.AccessController.doPrivileged(Native Method)
	at java.net.URLClassLoader.findClass(URLClassLoader.java:354)
	at java.lang.ClassLoader.loadClass(ClassLoader.java:425)
	at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:308)
	at java.lang.ClassLoader.loadClass(ClassLoader.java:358)
	at org.apache.spark.util.ClosureCleaner$.getInnerClasses(ClosureCleaner.scala:87)
	at org.apache.spark.util.ClosureCleaner$.clean(ClosureCleaner.scala:107)
	at org.apache.spark.SparkContext.clean(SparkContext.scala:982)
	at org.apache.spark.SparkContext.runJob(SparkContext.scala:849)
	at org.apache.spark.SparkContext.runJob(SparkContext.scala:870)
	at org.apache.spark.SparkContext.runJob(SparkContext.scala:884)
	at org.apache.spark.SparkContext.runJob(SparkContext.scala:898)
	at org.apache.spark.rdd.RDD.count(RDD.scala:720)
	at edu.berkeley.cs.amplab.adam.rdd.variation.ADAMVariationContext.adamVCFLoad(ADAMVariationContext.scala:82)
	at bcbio.adam$variant__GT_rdd_genotype_w_adam.invoke(adam.clj:17)
	at bcbio.test_adam$eval8088$fn__8089$fn__8090.invoke(test_adam.clj:7)
	at midje.util.thread_safe_var_nesting$with_altered_roots_STAR_.invoke(thread_safe_var_nesting.clj:32)
	at bcbio.test_adam$eval8088$fn__8089.invoke(test_adam.clj:7)
	at clojure.lang.AFn.applyToHelper(AFn.java:159)
	at clojure.lang.AFn.applyTo(AFn.java:151)
	at clojure.lang.AFunction$1.doInvoke(AFunction.java:29)
	at clojure.lang.RestFn.invoke(RestFn.java:397)
	at midje.checking.facts$check_one$fn__6175.invoke(facts.clj:31)
	at midje.checking.facts$check_one.invoke(facts.clj:30)
	at midje.checking.facts$creation_time_check.invoke(facts.clj:35)
	at bcbio.test_adam$eval8088.invoke(test_adam.clj:7)
	at clojure.lang.Compiler.eval(Compiler.java:6619)
	at clojure.lang.Compiler.load(Compiler.java:7064)
	at clojure.lang.RT.loadResourceScript(RT.java:370)
	at clojure.lang.RT.loadResourceScript(RT.java:361)
	at clojure.lang.RT.load(RT.java:440)
	at clojure.lang.RT.load(RT.java:411)
	at clojure.core$load$fn__5018.invoke(core.clj:5530)
	at clojure.core$load.doInvoke(core.clj:5529)
	at clojure.lang.RestFn.invoke(RestFn.java:408)
	at clojure.core$load_one.invoke(core.clj:5336)
	at clojure.core$load_lib$fn__4967.invoke(core.clj:5375)
	at clojure.core$load_lib.doInvoke(core.clj:5374)
	at clojure.lang.RestFn.applyTo(RestFn.java:142)
	at clojure.core$apply.invoke(core.clj:619)
	at clojure.core$load_libs.doInvoke(core.clj:5413)
	at clojure.lang.RestFn.applyTo(RestFn.java:137)
	at clojure.core$apply.invoke(core.clj:619)
	at clojure.core$require.doInvoke(core.clj:5496)
	at clojure.lang.RestFn.invoke(RestFn.java:421)
	at midje.repl$load_facts$fn__7979.invoke(repl.clj:206)
	at midje.repl$load_facts.doInvoke(repl.clj:192)
	at clojure.lang.RestFn.invoke(RestFn.java:397)
	at user$eval8042.invoke(form-init3909074720187961954.clj:1)
	at clojure.lang.Compiler.eval(Compiler.java:6619)
	at clojure.lang.Compiler.eval(Compiler.java:6609)
	at clojure.lang.Compiler.load(Compiler.java:7064)
	at clojure.lang.Compiler.loadFile(Compiler.java:7020)
	at clojure.main$load_script.invoke(main.clj:294)
	at clojure.main$init_opt.invoke(main.clj:299)
	at clojure.main$initialize.invoke(main.clj:327)
	at clojure.main$null_opt.invoke(main.clj:362)
	at clojure.main$main.doInvoke(main.clj:440)
	at clojure.lang.RestFn.invoke(RestFn.java:421)
	at clojure.lang.Var.invoke(Var.java:419)
	at clojure.lang.AFn.applyToHelper(AFn.java:163)
	at clojure.lang.Var.applyTo(Var.java:532)
	at clojure.main.main(main.java:37)
Subprocess failed
	[clojure-complete "0.2.3" :exclusions [[org.clojure/clojure]]]
	[edu.berkeley.cs.amplab.adam/adam-cli "0.7.1"]
	[args4j "2.0.23"]
	[org.scala-lang/scala-library "2.10.3"]
	[org.slf4j/slf4j-log4j12 "1.7.5"]
	[log4j "1.2.17"]
	[org.slf4j/slf4j-api "1.7.5"]
	[edu.berkeley.cs.amplab.adam/adam-core "0.7.1"]
	[cofoja "1.0"]
	[com.twitter/parquet-avro "1.3.2"]
	[com.twitter/parquet-column "1.3.2"]
	[com.twitter/parquet-common "1.3.2"]
	[com.twitter/parquet-encoding "1.3.2"]
	[com.twitter/parquet-generator "1.3.2"]
	[com.twitter/parquet-format "2.0.0"]
	[com.twitter/parquet-hadoop "1.3.2"]
	[com.twitter/parquet-jackson "1.3.2"]
	[commons-io "1.3.2"]
	[fi.tkk.ics.hadoop.bam/hadoop-bam "6.1-SNAPSHOT"]
	[org.apache.avro/avro "1.7.4"]
	[com.thoughtworks.paranamer/paranamer "2.3"]
	[org.apache.commons/commons-compress "1.4.1"]
	[org.tukaani/xz "1.0"]
	[org.codehaus.jackson/jackson-core-asl "1.8.8"]
	[org.codehaus.jackson/jackson-mapper-asl "1.8.8"]
	[org.apache.hadoop/hadoop-client "2.2.0" :exclusions [[asm] [org.jboss.netty/netty] [org.codehaus.jackson/] [org.sonatype.sisu.inject/]]]
	[org.apache.hadoop/hadoop-annotations "2.2.0" :exclusions [[jdk.tools]]]
	[org.apache.hadoop/hadoop-common "2.2.0" :exclusions [[tomcat/jasper-compiler] [tomcat/jasper-runtime] [javax.servlet/servlet-api] [javax.servlet.jsp/jsp-api] [commons-logging/commons-logging-api] [jetty/org.mortbay.jetty] [org.mortbay.jetty/jetty] [org.mortbay.jetty/jetty-util] [org.mortbay.jetty/jsp-api-2.1] [org.mortbay.jetty/servlet-api-2.5] [com.sun.jersey/jersey-core] [com.sun.jersey/jersey-json] [com.sun.jersey/jersey-server] [org.eclipse.jdt/core] [org.apache.avro/avro-ipc] [net.sf.kosmosfs/kfs] [net.java.dev.jets3t/jets3t] [com.jcraft/jsch] [commons-el]]]
	[com.google.protobuf/protobuf-java "2.5.0"]
	[commons-cli "1.2"]
	[commons-codec "1.4"]
	[commons-configuration "1.6"]
	[commons-beanutils/commons-beanutils-core "1.8.0"]
	[commons-collections "3.2.1"]
	[commons-digester "1.8"]
	[commons-beanutils "1.7.0"]
	[commons-httpclient "3.1"]
	[commons-lang "2.5"]
	[commons-logging "1.1.1" :exclusions [[avalon-framework] [logkit] [javax.servlet/servlet-api]]]
	[commons-net "3.1"]
	[org.apache.commons/commons-math "2.1"]
	[org.apache.hadoop/hadoop-auth "2.2.0"]
	[xmlenc "0.52"]
	[org.apache.hadoop/hadoop-hdfs "2.2.0" :exclusions [[commons-daemon] [org.apache.avro/avro] [org.mortbay.jetty/jetty] [com.sun.jersey/jersey-core] [com.sun.jersey/jersey-server] [javax.servlet/servlet-api] [javax.servlet.jsp/jsp-api] [tomcat/jasper-runtime]]]
	[org.mortbay.jetty/jetty-util "6.1.26"]
	[org.apache.hadoop/hadoop-mapreduce-client-app "2.2.0" :exclusions [[javax.servlet/servlet-api] [org.apache.hadoop/hadoop-yarn-server-nodemanager] [org.apache.hadoop/hadoop-yarn-server-web-proxy] [org.apache.hadoop/hadoop-annotations] [com.google.inject.extensions/guice-servlet] [junit] [org.apache.avro/avro] [jline] [io.netty/netty]]]
	[org.apache.hadoop/hadoop-mapreduce-client-common "2.2.0"]
	[org.apache.hadoop/hadoop-yarn-client "2.2.0"]
	[com.google.inject/guice "3.0"]
	[aopalliance "1.0"]
	[javax.inject "1"]
	[com.sun.jersey.contribs/jersey-guice "1.9"]
	[com.sun.jersey.jersey-test-framework/jersey-test-framework-grizzly2 "1.9"]
	[com.sun.jersey.jersey-test-framework/jersey-test-framework-core "1.9"]
	[com.sun.jersey/jersey-client "1.9"]
	[javax.servlet/javax.servlet-api "3.0.1"]
	[com.sun.jersey/jersey-grizzly2 "1.9"]
	[org.glassfish.grizzly/grizzly-http-server "2.1.2"]
	[org.glassfish.grizzly/grizzly-rcm "2.1.2"]
	[org.glassfish.grizzly/grizzly-http-servlet "2.1.2"]
	[org.glassfish.grizzly/grizzly-http "2.1.2"]
	[org.glassfish.grizzly/grizzly-framework "2.1.2"]
	[org.glassfish.gmbal/gmbal-api-only "3.0.0-b023"]
	[org.glassfish.external/management-api "3.0.0-b012"]
	[org.glassfish/javax.servlet "3.1"]
	[com.sun.jersey/jersey-json "1.9" :exclusions [[javax.xml.stream/stax-api]]]
	[com.sun.xml.bind/jaxb-impl "2.2.3-1"]
	[javax.xml.bind/jaxb-api "2.2.2"]
	[javax.activation/activation "1.1"]
	[org.codehaus.jettison/jettison "1.1"]
	[stax/stax-api "1.0.1"]
	[com.sun.jersey/jersey-server "1.9"]
	[com.sun.jersey/jersey-core "1.9"]
	[org.apache.hadoop/hadoop-yarn-server-common "2.2.0"]
	[org.apache.hadoop/hadoop-mapreduce-client-shuffle "2.2.0"]
	[org.apache.hadoop/hadoop-mapreduce-client-core "2.2.0" :exclusions [[junit] [com.google.inject/guice] [com.sun.jersey.jersey-test-framework/jersey-test-framework-grizzly2] [com.sun.jersey/jersey-server] [com.sun.jersey.contribs/jersey-guice] [org.apache.avro/avro] [org.apache.hadoop/hadoop-annotations] [com.google.inject.extensions/guice-servlet] [com.sun.jersey/jersey-json] [io.netty/netty]]]
	[org.apache.hadoop/hadoop-yarn-common "2.2.0"]
	[org.apache.hadoop/hadoop-mapreduce-client-jobclient "2.2.0" :exclusions [[junit] [org.apache.avro/avro] [org.apache.hadoop/hadoop-annotations] [com.google.inject.extensions/guice-servlet] [io.netty/netty]]]
	[org.apache.hadoop/hadoop-yarn-api "2.2.0" :exclusions [[org.apache.hadoop/hadoop-annotations] [com.google.inject/guice] [com.sun.jersey.jersey-test-framework/jersey-test-framework-grizzly2] [com.sun.jersey/jersey-server] [com.sun.jersey.contribs/jersey-guice] [com.google.inject.extensions/guice-servlet] [org.apache.avro/avro] [com.sun.jersey/jersey-core] [com.sun.jersey/jersey-json] [io.netty/netty]]]
	[org.apache.spark/spark-core_2.10 "0.9.0-incubating"]
	[colt "1.2.0"]
	[concurrent "1.3.4"]
	[com.clearspring.analytics/stream "2.4.0"]
	[com.codahale.metrics/metrics-core "3.0.0"]
	[com.codahale.metrics/metrics-ganglia "3.0.0"]
	[info.ganglia.gmetric4j/gmetric4j "1.0.3"]
	[org.acplt/oncrpc "1.0.7"]
	[com.codahale.metrics/metrics-graphite "3.0.0"]
	[com.codahale.metrics/metrics-json "3.0.0"]
	[com.fasterxml.jackson.core/jackson-databind "2.2.2"]
	[com.fasterxml.jackson.core/jackson-annotations "2.2.2"]
	[com.fasterxml.jackson.core/jackson-core "2.2.2"]
	[com.codahale.metrics/metrics-jvm "3.0.0"]
	[com.google.code.findbugs/jsr305 "1.3.9"]
	[com.google.guava/guava "14.0.1"]
	[com.ning/compress-lzf "1.0.0"]
	[com.twitter/chill-java "0.3.1"]
	[com.twitter/chill_2.10 "0.3.1"]
	[com.esotericsoftware.kryo/kryo "2.21"]
	[com.esotericsoftware.minlog/minlog "1.2"]
	[com.esotericsoftware.reflectasm/reflectasm "1.07" :classifier "shaded"]
	[org.objenesis/objenesis "1.2"]
	[org.ow2.asm/asm-commons "4.0"]
	[org.ow2.asm/asm-tree "4.0"]
	[io.netty/netty-all "4.0.13.Final"]
	[it.unimi.dsi/fastutil "6.4.4"]
	[net.java.dev.jets3t/jets3t "0.7.1"]
	[net.liftweb/lift-json_2.10 "2.5.1" :exclusions [[org.scala-lang/scalap]]]
	[org.apache.avro/avro-ipc "1.7.4" :exclusions [[org.jboss.netty/netty] [io.netty/netty]]]
	[org.apache.velocity/velocity "1.7"]
	[org.mortbay.jetty/jetty "6.1.26"]
	[org.mortbay.jetty/servlet-api "2.5-20081211"]
	[org.apache.mesos/mesos "0.13.0"]
	[org.apache.zookeeper/zookeeper "3.4.5" :exclusions [[org.jboss.netty/netty]]]
	[jline "0.9.94"]
	[junit "3.8.1"]
	[org.eclipse.jetty/jetty-server "7.6.8.v20121106"]
	[org.eclipse.jetty.orbit/javax.servlet "2.5.0.v201103041518"]
	[org.eclipse.jetty/jetty-continuation "7.6.8.v20121106"]
	[org.eclipse.jetty/jetty-http "7.6.8.v20121106"]
	[org.eclipse.jetty/jetty-io "7.6.8.v20121106"]
	[org.eclipse.jetty/jetty-util "7.6.8.v20121106"]
	[org.ow2.asm/asm "4.0"]
	[org.spark-project.akka/akka-remote_2.10 "2.2.3-shaded-protobuf" :exclusions [[org.jboss.netty/netty]]]
	[io.netty/netty "3.6.6.Final"]
	[org.spark-project.akka/akka-actor_2.10 "2.2.3-shaded-protobuf"]
	[com.typesafe/config "1.0.2"]
	[org.spark-project.protobuf/protobuf-java "2.4.1-shaded"]
	[org.uncommons.maths/uncommons-maths "1.2.2a" :exclusions [[jfree/jcommon] [jfree/jfreechart]]]
	[org.spark-project.akka/akka-slf4j_2.10 "2.2.3-shaded-protobuf" :exclusions [[org.jboss.netty/netty]]]
	[org.xerial.snappy/snappy-java "1.0.5"]
	[picard "1.93"]
	[samtools "1.93"]
	[tribble "1.93"]
	[variant "1.93"]
	[edu.berkeley.cs.amplab.adam/adam-format "0.7.1"]
	[midje "1.6.3" :exclusions [[commons-codec]]]
	[clj-time "0.6.0"]
	[colorize "0.1.1" :exclusions [[org.clojure/clojure]]]
	[dynapath "0.2.0"]
	[gui-diff "0.5.0"]
	[org.clojars.trptcolin/sjacket "0.1.3" :exclusions [[org.clojure/clojure]]]
	[net.cgrand/parsley "0.9.1"]
	[net.cgrand/regex "1.1.0"]
	[ordered "1.2.0" :exclusions [[org.clojure/clojure]]]
	[org.clojure/core.unify "0.5.2" :exclusions [[org.clojure/clojure]]]
	[org.clojure/math.combinatorics "0.0.7"]
	[org.clojure/tools.macro "0.1.5"]
	[org.clojure/tools.namespace "0.2.4"]
	[slingshot "0.10.3"]
	[swiss-arrows "1.0.0"]
	[utilize "0.2.3" :exclusions [[org.clojure/clojure]]]
	[joda-time "2.0"]
	[org.apache.spark/spark-streaming_2.10 "0.9.0-incubating" :exclusions [[org.apache.hadoop/hadoop-client] [org.apache.spark/spark-core_2.10] [org.codehaus.jackson/jackson-mapper-asl] [org.eclipse.jetty/jetty-server] [org.scala-lang/scala-library] [com.thoughtworks.paranamer/paranamer] [org.slf4j/slf4j-api] [com.google.protobuf/protobuf-java] [commons-codec] [commons-io] [commons-lang]]]
	[org.clojars.r0man/clj-spark "0.1.0-20140206.151117-4"]
	[org.clojars.mlimotte/serializable-fn "0.0.3"]
	[org.clojure/tools.cli "0.3.1"]
	[org.clojure/tools.logging "0.2.6"]
	[org.clojure/clojure "1.5.1"]
	[org.clojure/tools.nrepl "0.2.3" :exclusions [[org.clojure/clojure]]]
	$ lein midje
	2014-03-24 20:44:34 WARN Utils:61 - Your hostname, kunkel resolves to a loopback address: 127.0.1.1; using 192.168.122.1 instead (on interface virbr0)
	2014-03-24 20:44:34 WARN Utils:61 - Set SPARK_LOCAL_IP if you need to bind to another address
	2014-03-24 20:44:36 WARN NativeCodeLoader:62 - Unable to load native-hadoop library for your platform... using builtin-java classes where applicable
	Exception in thread "main" java.lang.IncompatibleClassChangeError: class org.apache.spark.util.InnerClosureFinder has interface org.objectweb.asm.ClassVisitor as super class
	at java.lang.ClassLoader.defineClass1(Native Method)
	at java.lang.ClassLoader.defineClass(ClassLoader.java:800)
	at java.security.SecureClassLoader.defineClass(SecureClassLoader.java:142)
	at java.net.URLClassLoader.defineClass(URLClassLoader.java:449)
	at java.net.URLClassLoader.access$100(URLClassLoader.java:71)
	at java.net.URLClassLoader$1.run(URLClassLoader.java:361)
	at java.net.URLClassLoader$1.run(URLClassLoader.java:355)
	at java.security.AccessController.doPrivileged(Native Method)
	at java.net.URLClassLoader.findClass(URLClassLoader.java:354)
	at java.lang.ClassLoader.loadClass(ClassLoader.java:425)
	at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:308)
	at java.lang.ClassLoader.loadClass(ClassLoader.java:358)
	at org.apache.spark.util.ClosureCleaner$.getInnerClasses(ClosureCleaner.scala:87)
	at org.apache.spark.util.ClosureCleaner$.clean(ClosureCleaner.scala:107)
	at org.apache.spark.SparkContext.clean(SparkContext.scala:982)
	at org.apache.spark.SparkContext.runJob(SparkContext.scala:849)
	at org.apache.spark.SparkContext.runJob(SparkContext.scala:870)
	at org.apache.spark.SparkContext.runJob(SparkContext.scala:884)
	at org.apache.spark.SparkContext.runJob(SparkContext.scala:898)
	at org.apache.spark.rdd.RDD.count(RDD.scala:720)
	at edu.berkeley.cs.amplab.adam.rdd.variation.ADAMVariationContext.adamVCFLoad(ADAMVariationContext.scala:82)
	at bcbio.adam$variant__GT_rdd_genotype_w_adam.invoke(adam.clj:17)
	at bcbio.test_adam$eval8088$fn__8089$fn__8090.invoke(test_adam.clj:7)
	at midje.util.thread_safe_var_nesting$with_altered_roots_STAR_.invoke(thread_safe_var_nesting.clj:32)
	at bcbio.test_adam$eval8088$fn__8089.invoke(test_adam.clj:7)
	at clojure.lang.AFn.applyToHelper(AFn.java:159)
	at clojure.lang.AFn.applyTo(AFn.java:151)
	at clojure.lang.AFunction$1.doInvoke(AFunction.java:29)
	at clojure.lang.RestFn.invoke(RestFn.java:397)
	at midje.checking.facts$check_one$fn__6175.invoke(facts.clj:31)
	at midje.checking.facts$check_one.invoke(facts.clj:30)
	at midje.checking.facts$creation_time_check.invoke(facts.clj:35)
	at bcbio.test_adam$eval8088.invoke(test_adam.clj:7)
	at clojure.lang.Compiler.eval(Compiler.java:6619)
	at clojure.lang.Compiler.load(Compiler.java:7064)
	at clojure.lang.RT.loadResourceScript(RT.java:370)
	at clojure.lang.RT.loadResourceScript(RT.java:361)
	at clojure.lang.RT.load(RT.java:440)
	at clojure.lang.RT.load(RT.java:411)
	at clojure.core$load$fn__5018.invoke(core.clj:5530)
	at clojure.core$load.doInvoke(core.clj:5529)
	at clojure.lang.RestFn.invoke(RestFn.java:408)
	at clojure.core$load_one.invoke(core.clj:5336)
	at clojure.core$load_lib$fn__4967.invoke(core.clj:5375)
	at clojure.core$load_lib.doInvoke(core.clj:5374)
	at clojure.lang.RestFn.applyTo(RestFn.java:142)
	at clojure.core$apply.invoke(core.clj:619)
	at clojure.core$load_libs.doInvoke(core.clj:5413)
	at clojure.lang.RestFn.applyTo(RestFn.java:137)
	at clojure.core$apply.invoke(core.clj:619)
	at clojure.core$require.doInvoke(core.clj:5496)
	at clojure.lang.RestFn.invoke(RestFn.java:421)
	at midje.repl$load_facts$fn__7979.invoke(repl.clj:206)
	at midje.repl$load_facts.doInvoke(repl.clj:192)
	at clojure.lang.RestFn.invoke(RestFn.java:397)
	at user$eval8042.invoke(form-init3909074720187961954.clj:1)
	at clojure.lang.Compiler.eval(Compiler.java:6619)
	at clojure.lang.Compiler.eval(Compiler.java:6609)
	at clojure.lang.Compiler.load(Compiler.java:7064)
	at clojure.lang.Compiler.loadFile(Compiler.java:7020)
	at clojure.main$load_script.invoke(main.clj:294)
	at clojure.main$init_opt.invoke(main.clj:299)
	at clojure.main$initialize.invoke(main.clj:327)
	at clojure.main$null_opt.invoke(main.clj:362)
	at clojure.main$main.doInvoke(main.clj:440)
	at clojure.lang.RestFn.invoke(RestFn.java:421)
	at clojure.lang.Var.invoke(Var.java:419)
	at clojure.lang.AFn.applyToHelper(AFn.java:163)
	at clojure.lang.Var.applyTo(Var.java:532)
	at clojure.main.main(main.java:37)
	Subprocess failed