GenomicsDBImport java error

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TONG ZHOU TAO

• May 04, 2021 06:33

When I use GenomicsDBImport,it comes out like that:

java.lang.IndexOutOfBoundsException: Index: 0
at java.util.Collections$EmptyList.get(Collections.java:4454)
at org.genomicsdb.model.GenomicsDBImportConfiguration$ImportConfiguration.getColumnPartitions(GenomicsDBImportConfiguration.java:2083)
at org.genomicsdb.importer.GenomicsDBImporter.<init>(GenomicsDBImporter.java:203)
at org.broadinstitute.hellbender.tools.genomicsdb.GenomicsDBImport.traverse(GenomicsDBImport.java:745)
at org.broadinstitute.hellbender.engine.GATKTool.doWork(GATKTool.java:1049)
at org.broadinstitute.hellbender.cmdline.CommandLineProgram.runTool(CommandLineProgram.java:140)
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)

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  Genevieve Brandt (she/her)

  • May 04, 2021 16:27

  Hello, for posts regarding GATK issues, we require three items to be included in the post.

  1. GATK version number
  2. Exact command used
  3. Complete Stack Trace/Error log [Use -DSTACK_TRACE_ON_USEREXCEPTION to print the stack trace.] How to submit java arguments.

  Your post is missing these items that must be included so that we can thoroughly look into the problem. Please read our forum guidelines for more information.

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