--sparkMaster yarn failed: org.apache.spark.SparkException: Could not parse Master URL: 'yarn'

Hi all,

I tried to play with the GATK4 on our Spark cluster. I tried the PrintReadsSpark with --sparkMaster yarn but was given following error:

17/11/22 13:41:44 ERROR SparkContext: Error initializing SparkContext.
org.apache.spark.SparkException: Could not parse Master URL: 'yarn'
at org.apache.spark.SparkContext$.org$apache$spark$SparkContext$$createTaskScheduler(SparkContext.scala:2759)
at org.apache.spark.SparkContext.(SparkContext.scala:522)
at org.apache.spark.api.java.JavaSparkContext.(JavaSparkContext.scala:59)
at org.broadinstitute.hellbender.engine.spark.SparkContextFactory.createSparkContext(SparkContextFactory.java:178)
at org.broadinstitute.hellbender.engine.spark.SparkContextFactory.getSparkContext(SparkContextFactory.java:110)
at org.broadinstitute.hellbender.engine.spark.SparkCommandLineProgram.doWork(SparkCommandLineProgram.java:36)
at org.broadinstitute.hellbender.cmdline.CommandLineProgram.runTool(CommandLineProgram.java:119)
at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMainPostParseArgs(CommandLineProgram.java:176)
at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:195)
at org.broadinstitute.hellbender.Main.runCommandLineProgram(Main.java:137)
at org.broadinstitute.hellbender.Main.mainEntry(Main.java:158)
at org.broadinstitute.hellbender.Main.main(Main.java:239)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:498)
at org.apache.spark.deploy.SparkSubmit$.org$apache$spark$deploy$SparkSubmit$$runMain(SparkSubmit.scala:738)
at org.apache.spark.deploy.SparkSubmit$.doRunMain$1(SparkSubmit.scala:181)
at org.apache.spark.deploy.SparkSubmit$.submit(SparkSubmit.scala:206)
at org.apache.spark.deploy.SparkSubmit$.main(SparkSubmit.scala:121)
at org.apache.spark.deploy.SparkSubmit.main(SparkSubmit.scala)
17/11/22 13:41:44 INFO ContextHandler: stopped o.s.j.s.ServletContextHandler{/stages/stage/kill,null}
17/11/22 13:41:44 INFO ContextHandler: stopped o.s.j.s.ServletContextHandler{/api,null}

I built the GATK4 from the latest git repos. I am wondering what I have missed?

Cheers,
Derrick

Issue · Github
by Sheila

Issue Number
2704
State
closed
Last Updated
Assignee
Array
Milestone
Array
Closed By
vdauwera

Best Answer

  • Accepted Answer

    Hi guys, it turned out to be all OK after I put everything in single line... I think something not parsed properly when the command was constructed in multiple lines. Anyway I am happy with just single line command. :) thanks

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