Heads up:
We’re moving the GATK website, docs and forum to a new platform. Read the full story and breakdown of key changes on this blog.
If you happen to see a question you know the answer to, please do chime in and help your fellow community members. We encourage our fourm members to be more involved, jump in and help out your fellow researchers with their questions. GATK forum is a community forum and helping each other with using GATK tools and research is the cornerstone of our success as a genomics research community.We appreciate your help!

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

Check out this blog post to learn how you can get started with GATK and try out the pipelines in preconfigured workspaces (with a user-friendly interface!) without having to install anything.

Error running CNV module using latest version 2.0.1665

marcpmarcp new yorkMember

I'm running the CNVDiscoveryPipeline using the latest version of GenomeSTrip 2.0.1665.
And I'm getting the following error:
INFO 20:00:36,839 QCommandLine - Scripting CNVDiscoveryPipeline
INFO 20:00:36,920 QCommandLine - Done with errors

ERROR ------------------------------------------------------------------------------------------
ERROR stack trace
org.broadinstitute.gatk.utils.exceptions.UserException$CannotExecuteQScript: Unable to execute QScript: CNVDiscoveryPipeline.script() threw the following exception: java.lang.IllegalArgumentException: Only one metadataLocation must be specified
at org.broadinstitute.gatk.queue.QCommandLine
at scala.collection.Iterator$class.foreach(Iterator.scala:727)
at scala.collection.AbstractIterator.foreach(Iterator.scala:1157)
at scala.collection.IterableLike$class.foreach(IterableLike.scala:72)
at scala.collection.AbstractIterable.foreach(Iterable.scala:54)
at org.broadinstitute.gatk.queue.QCommandLine.execute(QCommandLine.scala:146)
at org.broadinstitute.gatk.utils.commandline.CommandLineProgram.start(CommandLineProgram.java:248)
at org.broadinstitute.gatk.utils.commandline.CommandLineProgram.start(CommandLineProgram.java:155)
at org.broadinstitute.gatk.queue.QCommandLine$.main(QCommandLine.scala:61)
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:201)
at org.broadinstitute.sv.qscript.SVQScript$CreateMergedBamHeaders.(SVQScript.q:1253)
at org.broadinstitute.sv.qscript.SVQScript.mergeBamHeaders(SVQScript.q:1263)
at CNVDiscoveryPipeline.script(CNVDiscoveryPipeline.q:104)
at org.broadinstitute.gatk.queue.QCommandLine$$anonfun$execute$5.apply(QCommandLine.scala:155)
... 10 more

ERROR ------------------------------------------------------------------------------------------
ERROR A GATK RUNTIME ERROR has occurred (version 3.5.GS-r1661-0-g49c0dfe):
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 http://www.broadinstitute.org/gatk
ERROR MESSAGE: Unable to execute QScript: CNVDiscoveryPipeline.script() threw the following exception: java.lang.IllegalArgumentException: Only one metadataLocation must be specified
ERROR ------------------------------------------------------------------------------------------
Could you please help with that?
Thanks a lot in advance.
Any help would be much appreciated.
Best Regards.

Sign In or Register to comment.