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.<init>(SparkContext.scala:373)
at org.apache.spark.api.java.JavaSparkContext.<init>(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$.<init>(package.scala:204)
at org.apache.spark.internal.config.package$.<clinit>(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
