diff --git a/utils-cli/src/main/scala/org/bdgenomics/utils/cli/BDGCommand.scala b/utils-cli/src/main/scala/org/bdgenomics/utils/cli/BDGCommand.scala index 6e73aca..9704ec8 100644 --- a/utils-cli/src/main/scala/org/bdgenomics/utils/cli/BDGCommand.scala +++ b/utils-cli/src/main/scala/org/bdgenomics/utils/cli/BDGCommand.scala @@ -18,10 +18,8 @@ package org.bdgenomics.utils.cli import java.io.{ StringWriter, PrintWriter } -import org.apache.hadoop.mapreduce.Job import org.apache.spark.{ SparkConf, Logging, SparkContext } import org.bdgenomics.utils.instrumentation._ -import org.bdgenomics.utils.misc.HadoopUtil trait BDGCommandCompanion { val commandName: String @@ -42,7 +40,7 @@ trait BDGCommand extends Runnable { trait BDGSparkCommand[A <: Args4jBase] extends BDGCommand with Logging { protected val args: A - def run(sc: SparkContext, job: Job) + def run(sc: SparkContext) def run() { val start = System.nanoTime() @@ -51,9 +49,8 @@ trait BDGSparkCommand[A <: Args4jBase] extends BDGCommand with Logging { conf.setMaster("local[%d]".format(Runtime.getRuntime.availableProcessors())) } val sc = new SparkContext(conf) - val job = HadoopUtil.newJob() val metricsListener = initializeMetrics(sc) - run(sc, job) + run(sc) val totalTime = System.nanoTime() - start printMetrics(totalTime, metricsListener) }