2018-10-31

跑gatk FindBadGenomicKmersSpark的时候出现一个问题

Exception in thread "main" java.lang.ExceptionInInitializerError
        at org.apache.spark.SparkConf.validateSettings(SparkConf.scala:546)
        at org.apache.spark.SparkContext.(SparkContext.scala:373)
        at org.apache.spark.api.java.JavaSparkContext.(JavaSparkContext.scala:58)
        at org.broadinstitute.hellbender.engine.spark.SparkContextFactory.createSparkContext(SparkContextFactory.java:178)
        at org.broadinstitute.hellbender.engine.spark.SparkContextFactory.getSparkContext(SparkContextFactory.java:110)
        at org.broadinstitute.hellbender.engine.spark.SparkCommandLineProgram.doWork(SparkCommandLineProgram.java:28)
        at org.broadinstitute.hellbender.cmdline.CommandLineProgram.runTool(CommandLineProgram.java:139)
        at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMainPostParseArgs(CommandLineProgram.java:192)
        at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:211)
        at org.broadinstitute.hellbender.Main.runCommandLineProgram(Main.java:160)
        at org.broadinstitute.hellbender.Main.mainEntry(Main.java:203)
        at org.broadinstitute.hellbender.Main.main(Main.java:289)
Caused by: java.net.UnknownHostException: niushen: niushen: 域名解析暂时失败
        at java.net.InetAddress.getLocalHost(InetAddress.java:1505)
        at org.apache.spark.util.Utils$.findLocalInetAddress(Utils.scala:891)
        at org.apache.spark.util.Utils$.org$apache$spark$util$Utils$$localIpAddress$lzycompute(Utils.scala:884)
        at org.apache.spark.util.Utils$.org$apache$spark$util$Utils$$localIpAddress(Utils.scala:884)
        at org.apache.spark.util.Utils$$anonfun$localHostName$1.apply(Utils.scala:941)
        at org.apache.spark.util.Utils$$anonfun$localHostName$1.apply(Utils.scala:941)
        at scala.Option.getOrElse(Option.scala:121)
        at org.apache.spark.util.Utils$.localHostName(Utils.scala:941)
        at org.apache.spark.internal.config.package$.(package.scala:204)
        at org.apache.spark.internal.config.package$.(package.scala)
        ... 12 more
Caused by: java.net.UnknownHostException: niushen: 域名解析暂时失败
        at java.net.Inet6AddressImpl.lookupAllHostAddr(Native Method)
        at java.net.InetAddress$2.lookupAllHostAddr(InetAddress.java:928)
        at java.net.InetAddress.getAddressesFromNameService(InetAddress.java:1323)
        at java.net.InetAddress.getLocalHost(InetAddress.java:1500)
        ... 21 more

原因是Linux找不到主机名
解决办法：
修改/etc/hosts文件

127.0.0.1 主机名 localhost.localdomain localhost

比如

127.0.0.1   localhost localhost.localdomain localhost4 localhost4.localdomain4
::1         localhost localhost.localdomain localhost6 localhost6.localdomain6
127.0.0.1 niushen localhost.localdomain localhost

之后可以正常运行