Test-drive the GATK tools and Best Practices pipelines on Terra
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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?