Question: error while running realignerTargetCreator
0
gravatar for raya.girish
3.3 years ago by
raya.girish20
raya.girish20 wrote:

Hello All I have sample obtain from Ion torrent machines I looking for somatic mutations I already did preprocessing of samples but when i am running RealignerTargetCreator its giving me error I am not able to tackle it please help The error is

ERROR stack trace java.lang.ArrayIndexOutOfBoundsException: 1 at org.broadinstitute.gatk.utils.contexts.ReferenceContext.getBase(ReferenceContext.java:179) at org.broadinstitute.gatk.tools.walkers.indels.RealignerTargetCreator.map(RealignerTargetCreator.java:212) at org.broadinstitute.gatk.tools.walkers.indels.RealignerTargetCreator.map(RealignerTargetCreator.java:117) at org.broadinstitute.gatk.engine.traversals.TraverseLociNano$TraverseLociMap.apply(TraverseLociNano.java:267) at org.broadinstitute.gatk.engine.traversals.TraverseLociNano$TraverseLociMap.apply(TraverseLociNano.java:255) at org.broadinstitute.gatk.utils.nanoScheduler.NanoScheduler.executeSingleThreaded(NanoScheduler.java:274) at org.broadinstitute.gatk.utils.nanoScheduler.NanoScheduler.execute(NanoScheduler.java:245) at org.broadinstitute.gatk.engine.traversals.TraverseLociNano.traverse(TraverseLociNano.java:144) at org.broadinstitute.gatk.engine.traversals.TraverseLociNano.traverse(TraverseLociNano.java:92) at org.broadinstitute.gatk.engine.traversals.TraverseLociNano.traverse(TraverseLociNano.java:48) at org.broadinstitute.gatk.engine.executive.ShardTraverser.call(ShardTraverser.java:98) at java.util.concurrent.FutureTask.run(FutureTask.java:266) at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142) at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617) at java.lang.Thread.run(Thread.java:745)

ERROR ------------------------------------------------------------------------------------------
ERROR A GATK RUNTIME ERROR has occurred (version 3.6-0-g89b7209):
ERROR
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 https://www.broadinstitute.org/gatk
ERROR
ERROR MESSAGE: 1
ERROR ------------------------------------------------------------------------------------------
exome target gatk ion torrent • 791 views
ADD COMMENTlink modified 3.2 years ago by Biostar ♦♦ 20 • written 3.3 years ago by raya.girish20

The GATK forum might be a more appropriate place for this, in addition you probably should share the command you tried.

ADD REPLYlink written 3.3 years ago by WouterDeCoster43k

This errors occurs when there is a difference between the FASTA/chromosome sizes and the BED/BAM sizes.

ADD REPLYlink written 3.2 years ago by Pierre Lindenbaum126k
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