{"action":"created","issue":{"url":"https://api.github.com/repos/citiususc/SparkBWA/issues/6","repository_url":"https://api.github.com/repos/citiususc/SparkBWA","labels_url":"https://api.github.com/repos/citiususc/SparkBWA/issues/6/labels{/name}","comments_url":"https://api.github.com/repos/citiususc/SparkBWA/issues/6/comments","events_url":"https://api.github.com/repos/citiususc/SparkBWA/issues/6/events","html_url":"https://github.com/citiususc/SparkBWA/issues/6","id":161070749,"number":6,"title":"Cannot satrt SparkBWA ","user":{"login":"xubo245","id":8759816,"avatar_url":"https://avatars.githubusercontent.com/u/8759816?v=3","gravatar_id":"","url":"https://api.github.com/users/xubo245","html_url":"https://github.com/xubo245","followers_url":"https://api.github.com/users/xubo245/followers","following_url":"https://api.github.com/users/xubo245/following{/other_user}","gists_url":"https://api.github.com/users/xubo245/gists{/gist_id}","starred_url":"https://api.github.com/users/xubo245/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/xubo245/subscriptions","organizations_url":"https://api.github.com/users/xubo245/orgs","repos_url":"https://api.github.com/users/xubo245/repos","events_url":"https://api.github.com/users/xubo245/events{/privacy}","received_events_url":"https://api.github.com/users/xubo245/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":22,"created_at":"2016-06-19T12:25:03Z","updated_at":"2016-06-24T08:13:40Z","closed_at":null,"body":"shell:\r\n\r\n```\r\nspark-submit --class SparkBWA \\\r\n--master local \\\r\n--driver-memory 1500m \\\r\n--executor-memory 1500m \\\r\n--executor-cores 1 \\\r\n--archives bwa.zip \\\r\n--verbose \\\r\n--num-executors 32 \\\r\nSparkBWA.jar \\\r\n-algorithm mem -reads paired \\\r\n-index /home/hadoop/xubo/ref/GRCH38L1Index/GRCH38chr1L3556522.fasta \\\r\n-partitions 3 \\\r\n/xubo/alignment/sparkBWA/GRCH38chr1L3556522N10L50paired1.fastq /xubo/alignment/sparkBWA/GRCH38chr1L3556522N10L50paired2.fastq \\\r\n/xubo/alignment/output/sparkBWA/datatest1\r\n```\r\n\r\nerror:\r\n\r\n```\r\n16/06/19 20:23:03 ERROR Executor: Exception in task 1.0 in stage 3.0 (TID 4)\r\njava.lang.UnsatisfiedLinkError: no bwa in java.library.path\r\n\tat java.lang.ClassLoader.loadLibrary(ClassLoader.java:1886)\r\n\tat java.lang.Runtime.loadLibrary0(Runtime.java:849)\r\n\tat java.lang.System.loadLibrary(System.java:1088)\r\n\tat BwaJni.<clinit>(BwaJni.java:44)\r\n\tat Bwa.run(Bwa.java:443)\r\n\tat BwaRDD$BwaAlignment.call(BwaRDD.java:283)\r\n\tat BwaRDD$BwaAlignment.call(BwaRDD.java:173)\r\n\tat org.apache.spark.api.java.JavaPairRDD$$anonfun$toScalaFunction2$1.apply(JavaPairRDD.scala:1024)\r\n\tat org.apache.spark.api.java.JavaRDDLike$$anonfun$mapPartitionsWithIndex$1.apply(JavaRDDLike.scala:102)\r\n\tat org.apache.spark.api.java.JavaRDDLike$$anonfun$mapPartitionsWithIndex$1.apply(JavaRDDLike.scala:102)\r\n\tat org.apache.spark.rdd.RDD$$anonfun$mapPartitionsWithIndex$1$$anonfun$apply$18.apply(RDD.scala:727)\r\n\tat org.apache.spark.rdd.RDD$$anonfun$mapPartitionsWithIndex$1$$anonfun$apply$18.apply(RDD.scala:727)\r\n\tat org.apache.spark.rdd.MapPartitionsRDD.compute(MapPartitionsRDD.scala:38)\r\n\tat org.apache.spark.rdd.RDD.computeOrReadCheckpoint(RDD.scala:300)\r\n\tat org.apache.spark.rdd.RDD.iterator(RDD.scala:264)\r\n\tat org.apache.spark.scheduler.ResultTask.runTask(ResultTask.scala:66)\r\n\tat org.apache.spark.scheduler.Task.run(Task.scala:88)\r\n\tat org.apache.spark.executor.Executor$TaskRunner.run(Executor.scala:214)\r\n\tat java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1145)\r\n\tat java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:615)\r\n\tat java.lang.Thread.run(Thread.java:745)\r\n16/06/19 20:23:03 ERROR Executor: Exception in task 0.0 in stage 3.0 (TID 3)\r\njava.lang.NoClassDefFoundError: Could not initialize class BwaJni\r\n\tat Bwa.run(Bwa.java:443)\r\n\tat BwaRDD$BwaAlignment.call(BwaRDD.java:283)\r\n\tat BwaRDD$BwaAlignment.call(BwaRDD.java:173)\r\n\tat org.apache.spark.api.java.JavaPairRDD$$anonfun$toScalaFunction2$1.apply(JavaPairRDD.scala:1024)\r\n\tat org.apache.spark.api.java.JavaRDDLike$$anonfun$mapPartitionsWithIndex$1.apply(JavaRDDLike.scala:102)\r\n\tat org.apache.spark.api.java.JavaRDDLike$$anonfun$mapPartitionsWithIndex$1.apply(JavaRDDLike.scala:102)\r\n\tat org.apache.spark.rdd.RDD$$anonfun$mapPartitionsWithIndex$1$$anonfun$apply$18.apply(RDD.scala:727)\r\n\tat org.apache.spark.rdd.RDD$$anonfun$mapPartitionsWithIndex$1$$anonfun$apply$18.apply(RDD.scala:727)\r\n\tat org.apache.spark.rdd.MapPartitionsRDD.compute(MapPartitionsRDD.scala:38)\r\n\tat org.apache.spark.rdd.RDD.computeOrReadCheckpoint(RDD.scala:300)\r\n\tat org.apache.spark.rdd.RDD.iterator(RDD.scala:264)\r\n\tat org.apache.spark.scheduler.ResultTask.runTask(ResultTask.scala:66)\r\n\tat org.apache.spark.scheduler.Task.run(Task.scala:88)\r\n\tat org.apache.spark.executor.Executor$TaskRunner.run(Executor.scala:214)\r\n\tat java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1145)\r\n\tat java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:615)\r\n\tat java.lang.Thread.run(Thread.java:745)\r\n16/06/19 20:23:03 ERROR SparkUncaughtExceptionHandler: Uncaught exception in thread Thread[Executor task launch worker-1,5,main]\r\njava.lang.UnsatisfiedLinkError: no bwa in java.library.path\r\n\tat java.lang.ClassLoader.loadLibrary(ClassLoader.java:1886)\r\n\tat java.lang.Runtime.loadLibrary0(Runtime.java:849)\r\n\tat java.lang.System.loadLibrary(System.java:1088)\r\n\r\n```\r\n\r\nHow to solve the error ?please"},"comment":{"url":"https://api.github.com/repos/citiususc/SparkBWA/issues/comments/228284456","html_url":"https://github.com/citiususc/SparkBWA/issues/6#issuecomment-228284456","issue_url":"https://api.github.com/repos/citiususc/SparkBWA/issues/6","id":228284456,"user":{"login":"Nav15","id":11848244,"avatar_url":"https://avatars.githubusercontent.com/u/11848244?v=3","gravatar_id":"","url":"https://api.github.com/users/Nav15","html_url":"https://github.com/Nav15","followers_url":"https://api.github.com/users/Nav15/followers","following_url":"https://api.github.com/users/Nav15/following{/other_user}","gists_url":"https://api.github.com/users/Nav15/gists{/gist_id}","starred_url":"https://api.github.com/users/Nav15/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/Nav15/subscriptions","organizations_url":"https://api.github.com/users/Nav15/orgs","repos_url":"https://api.github.com/users/Nav15/repos","events_url":"https://api.github.com/users/Nav15/events{/privacy}","received_events_url":"https://api.github.com/users/Nav15/received_events","type":"User","site_admin":false},"created_at":"2016-06-24T08:13:40Z","updated_at":"2016-06-24T08:13:40Z","body":"Ran  successfully in **cluster mode** as well. Please close."}}
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