{"action":"opened","issue":{"url":"https://api.github.com/repos/rhinempi/sparkhit/issues/3","repository_url":"https://api.github.com/repos/rhinempi/sparkhit","labels_url":"https://api.github.com/repos/rhinempi/sparkhit/issues/3/labels{/name}","comments_url":"https://api.github.com/repos/rhinempi/sparkhit/issues/3/comments","events_url":"https://api.github.com/repos/rhinempi/sparkhit/issues/3/events","html_url":"https://github.com/rhinempi/sparkhit/issues/3","id":364496978,"node_id":"MDU6SXNzdWUzNjQ0OTY5Nzg=","number":3,"title":"java.lang.IllegalStateException","user":{"login":"BoredMa","id":25764447,"node_id":"MDQ6VXNlcjI1NzY0NDQ3","avatar_url":"https://avatars1.githubusercontent.com/u/25764447?v=4","gravatar_id":"","url":"https://api.github.com/users/BoredMa","html_url":"https://github.com/BoredMa","followers_url":"https://api.github.com/users/BoredMa/followers","following_url":"https://api.github.com/users/BoredMa/following{/other_user}","gists_url":"https://api.github.com/users/BoredMa/gists{/gist_id}","starred_url":"https://api.github.com/users/BoredMa/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/BoredMa/subscriptions","organizations_url":"https://api.github.com/users/BoredMa/orgs","repos_url":"https://api.github.com/users/BoredMa/repos","events_url":"https://api.github.com/users/BoredMa/events{/privacy}","received_events_url":"https://api.github.com/users/BoredMa/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":0,"created_at":"2018-09-27T14:14:04Z","updated_at":"2018-09-27T14:14:04Z","closed_at":null,"author_association":"NONE","body":"I ran the command as follow:\r\n./bin/sparkhit piper --master yarn --deploy-mode client --num-executors 5 --executor-cores 30 --executor-memory 10g -fastq /biodata/bwa/ERR764952.fastq  -outfile  /biodata/bwa/output  -tool \"/usr/local/hk_soft/bwa-0.7.17/bwa mem\" -toolparam \"/biodata/bwa/reference.fasta\".\r\n\r\nbut i met this error.Did i do anything wrong? I have copied bwa tools to all nodes, and fastq fasta files in hdfs.\r\n\r\nCaused by: java.lang.IllegalStateException: Subprocess exited with status 1. Command ran: /usr/local/hk_soft/bwa-0.7.17/bwa mem /biodata/bwa/reference.fasta\r\n\tat org.apache.spark.rdd.PipedRDD$$anon$1.hasNext(PipedRDD.scala:178)\r\n\tat scala.collection.Iterator$$anon$11.hasNext(Iterator.scala:408)\r\n\tat org.apache.spark.rdd.PairRDDFunctions$$anonfun$saveAsHadoopDataset$1$$anonfun$13$$anonfun$apply$7.apply$mcV$sp(PairRDDFunctions.scala:1210)\r\n\tat org.apache.spark.rdd.PairRDDFunctions$$anonfun$saveAsHadoopDataset$1$$anonfun$13$$anonfun$apply$7.apply(PairRDDFunctions.scala:1210)\r\n\tat org.apache.spark.rdd.PairRDDFunctions$$anonfun$saveAsHadoopDataset$1$$anonfun$13$$anonfun$apply$7.apply(PairRDDFunctions.scala:1210)\r\n\tat org.apache.spark.util.Utils$.tryWithSafeFinallyAndFailureCallbacks(Utils.scala:1341)\r\n\tat org.apache.spark.rdd.PairRDDFunctions$$anonfun$saveAsHadoopDataset$1$$anonfun$13.apply(PairRDDFunctions.scala:1218)\r\n\tat org.apache.spark.rdd.PairRDDFunctions$$anonfun$saveAsHadoopDataset$1$$anonfun$13.apply(PairRDDFunctions.scala:1197)\r\n\tat org.apache.spark.scheduler.ResultTask.runTask(ResultTask.scala:87)\r\n\tat org.apache.spark.scheduler.Task.run(Task.scala:99)\r\n\tat org.apache.spark.executor.Executor$TaskRunner.run(Executor.scala:322)\r\n\tat java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)\r\n\tat java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)\r\n\tat java.lang.Thread.run(Thread.java:748)\r\n"}}
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