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Multiple metadata directories for CNVPipeline?

jfarrelljfarrell Member ✭✭

Can more than one metadata directory be specified for the CNVPipeline? When I specify multiple -md parameters I get this error.

org.broadinstitute.gatk.utils.exceptions.UserException$CannotExecuteQScript: Unable to execute QScript: CNVDiscoveryPipeline.script() threw the following exception: java.lang.IllegalArgumentException: Only one metadataLocation must be specified
        at org.broadinstitute.gatk.queue.QCommandLine$$anonfun$execute$5.apply(QCommandLine.scala:159)
        at org.broadinstitute.gatk.queue.QCommandLine$$anonfun$execute$5.apply(QCommandLine.scala:147)
        at scala.collection.Iterator$class.foreach(Iterator.scala:727)
        at scala.collection.AbstractIterator.foreach(Iterator.scala:1157)
        at scala.collection.IterableLike$class.foreach(IterableLike.scala:72)
        at scala.collection.AbstractIterable.foreach(Iterable.scala:54)
        at org.broadinstitute.gatk.queue.QCommandLine.execute(QCommandLine.scala:147)
        at org.broadinstitute.gatk.utils.commandline.CommandLineProgram.start(CommandLineProgram.java:248)
        at org.broadinstitute.gatk.utils.commandline.CommandLineProgram.start(CommandLineProgram.java:155)
        at org.broadinstitute.gatk.queue.QCommandLine$.main(QCommandLine.scala:62)
        at org.broadinstitute.gatk.queue.QCommandLine.main(QCommandLine.scala)
Caused by: java.lang.IllegalArgumentException: **Only one metadataLocation must be specified**
        at org.broadinstitute.sv.qscript.SVQScript.metaDataLocation(SVQScript.q:195)
        at org.broadinstitute.sv.qscript.SVQScript$DependsOnMetaData$class.$init$(SVQScript.q:442)
        at org.broadinstitute.sv.qscript.SVQScript$CreateMergedBamHeaders.<init>(SVQScript.q:1196)
        at org.broadinstitute.sv.qscript.SVQScript.mergeBamHeaders(SVQScript.q:1207)
        at CNVDiscoveryPipeline.script(CNVDiscoveryPipeline.q:91)

Is is supported? If so, what is the correct syntax?

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