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MuTect error

uthrabalajiuthrabalaji DALLASMember
edited March 2015 in Ask the GATK team

Hi,

I am running MuTect version 1.14 and I get the following error

ERROR ------------------------------------------------------------------------------------------
ERROR stack trace

org.broadinstitute.sting.utils.exceptions.ReviewedStingException: Unable to create iterator for rod named cosmic
at org.broadinstitute.sting.gatk.datasources.rmd.ReferenceOrderedQueryDataPool.createIteratorFromResource(ReferenceOrderedDataSource.java:247)
at org.broadinstitute.sting.gatk.datasources.rmd.ReferenceOrderedQueryDataPool.createIteratorFromResource(ReferenceOrderedDataSource.java:184)
at org.broadinstitute.sting.gatk.datasources.rmd.ResourcePool.iterator(ResourcePool.java:92)
at org.broadinstitute.sting.gatk.datasources.rmd.ReferenceOrderedDataSource.seek(ReferenceOrderedDataSource.java:167)
at org.broadinstitute.sting.gatk.datasources.providers.ManagingReferenceOrderedView.(ManagingReferenceOrderedView.java:42)
at org.broadinstitute.sting.gatk.traversals.TraverseLociNano.traverse(TraverseLociNano.java:61)
at org.broadinstitute.sting.gatk.traversals.TraverseLociNano.traverse(TraverseLociNano.java:23)
at org.broadinstitute.sting.gatk.executive.ShardTraverser.call(ShardTraverser.java:73)
at java.util.concurrent.FutureTask$Sync.innerRun(FutureTask.java:334)
at java.util.concurrent.FutureTask.run(FutureTask.java:166)
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1146)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:615)
at java.lang.Thread.run(Thread.java:701)
Caused by: java.io.IOException: Invalid argument
at java.io.FileInputStream.readBytes(Native Method)
at java.io.FileInputStream.read(FileInputStream.java:239)
at org.broad.tribble.util.SeekableFileStream.read(SeekableFileStream.java:83)
at org.broad.tribble.TribbleIndexedFeatureReader$BlockStreamWrapper.read(TribbleIndexedFeatureReader.java:405)
at java.io.InputStream.read(InputStream.java:101)
at org.broad.tribble.readers.PositionalBufferedStream.fill(PositionalBufferedStream.java:141)
at org.broad.tribble.readers.PositionalBufferedStream.peek(PositionalBufferedStream.java:132)
at org.broad.tribble.readers.PositionalBufferedStream.isDone(PositionalBufferedStream.java:116)
at org.broad.tribble.TribbleIndexedFeatureReader$QueryIterator.readNextRecord(TribbleIndexedFeatureReader.java:316)
at org.broad.tribble.TribbleIndexedFeatureReader$QueryIterator.(TribbleIndexedFeatureReader.java:258)
at org.broad.tribble.TribbleIndexedFeatureReader.query(TribbleIndexedFeatureReader.java:128)
at org.broadinstitute.sting.gatk.refdata.tracks.RMDTrack.query(RMDTrack.java:117)
at org.broadinstitute.sting.gatk.datasources.rmd.ReferenceOrderedQueryDataPool.createIteratorFromResource(ReferenceOrderedDataSource.java:240)
... 12 more

ERROR ------------------------------------------------------------------------------------------
ERROR A GATK RUNTIME ERROR has occurred (version 2.2-25-g2a68eab):
ERROR
ERROR Please visit the wiki to see if this is a known problem
ERROR If not, please post the error, 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
ERROR MESSAGE: Unable to create iterator for rod named cosmic
ERROR ------------------------------------------------------------------------------------------

I read somewhere to try a different version of GATK for a similar error. I am not sure how I can change the versions of GATK. I have GATK-2.6 and GATK-3.3.0 both installed. I apologize if this is a very basic question. I would appreciate any input on how to get past this error.

Thanks in advance for all the help,
Uthra

Post edited by uthrabalaji on

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