{"action":"opened","issue":{"url":"https://api.github.com/repos/hammerlab/guacamole/issues/509","repository_url":"https://api.github.com/repos/hammerlab/guacamole","labels_url":"https://api.github.com/repos/hammerlab/guacamole/issues/509/labels{/name}","comments_url":"https://api.github.com/repos/hammerlab/guacamole/issues/509/comments","events_url":"https://api.github.com/repos/hammerlab/guacamole/issues/509/events","html_url":"https://github.com/hammerlab/guacamole/issues/509","id":167674752,"number":509,"title":"local invocation in README is broken","user":{"login":"timodonnell","id":467896,"avatar_url":"https://avatars.githubusercontent.com/u/467896?v=3","gravatar_id":"","url":"https://api.github.com/users/timodonnell","html_url":"https://github.com/timodonnell","followers_url":"https://api.github.com/users/timodonnell/followers","following_url":"https://api.github.com/users/timodonnell/following{/other_user}","gists_url":"https://api.github.com/users/timodonnell/gists{/gist_id}","starred_url":"https://api.github.com/users/timodonnell/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/timodonnell/subscriptions","organizations_url":"https://api.github.com/users/timodonnell/orgs","repos_url":"https://api.github.com/users/timodonnell/repos","events_url":"https://api.github.com/users/timodonnell/events{/privacy}","received_events_url":"https://api.github.com/users/timodonnell/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":0,"created_at":"2016-07-26T18:14:44Z","updated_at":"2016-07-26T18:14:44Z","closed_at":null,"body":"Running the command in the README:\r\n\r\n```\r\n$ scripts/guacamole somatic-joint     \\\r\n  src/test/resources/synth1.normal.100k-200k.withmd.bam \\     \r\n  src/test/resources/synth1.tumor.100k-200k.withmd.bam    \\\r\n   --reference-fasta ~/sinai/data/b37.fasta    \\\r\n   --out /tmp/out.vcf\r\n```\r\n\r\nGives me:\r\n\r\n```\r\nFound guac jar: target/guacamole-0.0.1-SNAPSHOT.jar\r\nJava HotSpot(TM) 64-Bit Server VM warning: ignoring option MaxPermSize=512m; support was removed in 8.0\r\n--> [Tue Jul 26 14:13:15 EDT 2016]: Guacamole starting.\r\n2016-07-26 14:13:16 WARN  NativeCodeLoader:62 - Unable to load native-hadoop library for your platform... using builtin-java classes where applicable\r\n2016-07-26 14:13:16 ERROR SparkContext:95 - Error initializing SparkContext.\r\ncom.typesafe.config.ConfigException$Missing: No configuration setting found for key 'akka.version'\r\n\tat com.typesafe.config.impl.SimpleConfig.findKey(SimpleConfig.java:124)\r\n\tat com.typesafe.config.impl.SimpleConfig.find(SimpleConfig.java:145)\r\n\tat com.typesafe.config.impl.SimpleConfig.find(SimpleConfig.java:151)\r\n\tat com.typesafe.config.impl.SimpleConfig.find(SimpleConfig.java:159)\r\n\tat com.typesafe.config.impl.SimpleConfig.find(SimpleConfig.java:164)\r\n\tat com.typesafe.config.impl.SimpleConfig.getString(SimpleConfig.java:206)\r\n\tat akka.actor.ActorSystem$Settings.<init>(ActorSystem.scala:169)\r\n\tat akka.actor.ActorSystemImpl.<init>(ActorSystem.scala:505)\r\n\tat akka.actor.ActorSystem$.apply(ActorSystem.scala:142)\r\n\tat akka.actor.ActorSystem$.apply(ActorSystem.scala:119)\r\n\tat org.apache.spark.util.AkkaUtils$.org$apache$spark$util$AkkaUtils$$doCreateActorSystem(AkkaUtils.scala:121)\r\n\tat org.apache.spark.util.AkkaUtils$$anonfun$1.apply(AkkaUtils.scala:53)\r\n\tat org.apache.spark.util.AkkaUtils$$anonfun$1.apply(AkkaUtils.scala:52)\r\n\tat org.apache.spark.util.Utils$$anonfun$startServiceOnPort$1.apply$mcVI$sp(Utils.scala:1988)\r\n\tat scala.collection.immutable.Range.foreach$mVc$sp(Range.scala:141)\r\n\tat org.apache.spark.util.Utils$.startServiceOnPort(Utils.scala:1979)\r\n\tat org.apache.spark.util.AkkaUtils$.createActorSystem(AkkaUtils.scala:55)\r\n\tat org.apache.spark.SparkEnv$.create(SparkEnv.scala:266)\r\n\tat org.apache.spark.SparkEnv$.createDriverEnv(SparkEnv.scala:193)\r\n\tat org.apache.spark.SparkContext.createSparkEnv(SparkContext.scala:288)\r\n\tat org.apache.spark.SparkContext.<init>(SparkContext.scala:457)\r\n\tat org.hammerlab.guacamole.commands.SparkCommand.createSparkContext(SparkCommand.scala:65)\r\n\tat org.hammerlab.guacamole.commands.SparkCommand.run(SparkCommand.scala:10)\r\n\tat org.hammerlab.guacamole.commands.Command.run(Command.scala:46)\r\n\tat org.hammerlab.guacamole.Main$.main(Main.scala:68)\r\n\tat org.hammerlab.guacamole.Main.main(Main.scala)\r\nException in thread \"main\" com.typesafe.config.ConfigException$Missing: No configuration setting found for key 'akka.version'\r\n\tat com.typesafe.config.impl.SimpleConfig.findKey(SimpleConfig.java:124)\r\n\tat com.typesafe.config.impl.SimpleConfig.find(SimpleConfig.java:145)\r\n\tat com.typesafe.config.impl.SimpleConfig.find(SimpleConfig.java:151)\r\n\tat com.typesafe.config.impl.SimpleConfig.find(SimpleConfig.java:159)\r\n\tat com.typesafe.config.impl.SimpleConfig.find(SimpleConfig.java:164)\r\n\tat com.typesafe.config.impl.SimpleConfig.getString(SimpleConfig.java:206)\r\n\tat akka.actor.ActorSystem$Settings.<init>(ActorSystem.scala:169)\r\n\tat akka.actor.ActorSystemImpl.<init>(ActorSystem.scala:505)\r\n\tat akka.actor.ActorSystem$.apply(ActorSystem.scala:142)\r\n\tat akka.actor.ActorSystem$.apply(ActorSystem.scala:119)\r\n\tat org.apache.spark.util.AkkaUtils$.org$apache$spark$util$AkkaUtils$$doCreateActorSystem(AkkaUtils.scala:121)\r\n\tat org.apache.spark.util.AkkaUtils$$anonfun$1.apply(AkkaUtils.scala:53)\r\n\tat org.apache.spark.util.AkkaUtils$$anonfun$1.apply(AkkaUtils.scala:52)\r\n\tat org.apache.spark.util.Utils$$anonfun$startServiceOnPort$1.apply$mcVI$sp(Utils.scala:1988)\r\n\tat scala.collection.immutable.Range.foreach$mVc$sp(Range.scala:141)\r\n\tat org.apache.spark.util.Utils$.startServiceOnPort(Utils.scala:1979)\r\n\tat org.apache.spark.util.AkkaUtils$.createActorSystem(AkkaUtils.scala:55)\r\n\tat org.apache.spark.SparkEnv$.create(SparkEnv.scala:266)\r\n\tat org.apache.spark.SparkEnv$.createDriverEnv(SparkEnv.scala:193)\r\n\tat org.apache.spark.SparkContext.createSparkEnv(SparkContext.scala:288)\r\n\tat org.apache.spark.SparkContext.<init>(SparkContext.scala:457)\r\n\tat org.hammerlab.guacamole.commands.SparkCommand.createSparkContext(SparkCommand.scala:65)\r\n\tat org.hammerlab.guacamole.commands.SparkCommand.run(SparkCommand.scala:10)\r\n\tat org.hammerlab.guacamole.commands.Command.run(Command.scala:46)\r\n\tat org.hammerlab.guacamole.Main$.main(Main.scala:68)\r\n\tat org.hammerlab.guacamole.Main.main(Main.scala)\r\n        2.09 real         2.46 user         0.23 sys"}}
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