inputFileIndexCache isn't defined error?

I am running the local example test run found in the cookbook. I have downloaded and unpacked all files properly.

I have edited the necessary files to call the proper file folders.

On each run, the error stack trace keeps popping up.

    INFO  10:40:43,569 QScriptManager - Compiling 2 QScripts 
    INFO  10:40:46,606 QScriptManager - Compilation complete 
    ##### ERROR --
    ##### ERROR stack trace 
    org.broadinstitute.gatk.utils.commandline.InvalidArgumentException: 
    Argument with name 'inputFileIndexCache' isn't defined.
        at org.broadinstitute.gatk.utils.commandline.ParsingEngine.validate(ParsingEngine.java:307)
        at org.broadinstitute.gatk.utils.commandline.ParsingEngine.validate(ParsingEngine.java:280)
        at org.broadinstitute.gatk.utils.commandline.CommandLineProgram.start(CommandLineProgram.java:225)
        at org.broadinstitute.gatk.utils.commandline.CommandLineProgram.start(CommandLineProgram.java:158)
        at org.broadinstitute.gatk.queue.QCommandLine$.main(QCommandLine.scala:61)
        at org.broadinstitute.gatk.queue.QCommandLine.main(QCommandLine.scala)

Any suggestions as to potential mistakes I am making?

Answers

  • edited November 2017
  • bhandsakerbhandsaker Member, Broadie, Moderator

    Please post the Genome STRiP version number (for completeness) and the exact command line you are running.

  • edited November 2017

    USER:~/svtoolkit/cookbook/genotyping/1000G_phase1_local$ scripts/genotype_sites.sh example/1000G_MERGED_DEL_2_99615.vcf rundir
    INFO 11:03:31,800 QScriptManager - Compiling 2 QScripts
    INFO 11:03:35,648 QScriptManager - Compilation complete

    ERROR --
    ERROR stack trace

    org.broadinstitute.gatk.utils.commandline.InvalidArgumentException:
    Argument with name 'inputFileIndexCache' isn't defined.
    at org.broadinstitute.gatk.utils.commandline.ParsingEngine.validate(ParsingEngine.java:307)
    at org.broadinstitute.gatk.utils.commandline.ParsingEngine.validate(ParsingEngine.java:280)
    at org.broadinstitute.gatk.utils.commandline.CommandLineProgram.start(CommandLineProgram.java:225)
    at org.broadinstitute.gatk.utils.commandline.CommandLineProgram.start(CommandLineProgram.java:158)
    at org.broadinstitute.gatk.queue.QCommandLine$.main(QCommandLine.scala:61)
    at org.broadinstitute.gatk.queue.QCommandLine.main(QCommandLine.scala)

    ERROR ------------------------------------------------------------------------------------------
    ERROR A GATK RUNTIME ERROR has occurred (version 3.7.GS-r1748-0-g74bfe0b):
    ERROR
    ERROR This might be a bug. Please check the documentation guide to see if this is a known problem.
    ERROR If not, please post the error message, with stack trace, to the GATK forum.
    ERROR Visit our website and forum for extensive documentation and answers to
    ERROR commonly asked questions https://software.broadinstitute.org/gatk
    ERROR
    ERROR MESSAGE: Argument with name 'inputFileIndexCache' isn't defined.
    ERROR ------------------------------------------------------------------------------------------

    INFO 11:03:35,701 QCommandLine - Shutting down jobs. Please wait...

  • Genome STRiP (svtoolkit) version 2.00.1774

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