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?