Hello All
I have sample obtain from Ion torrent machines 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 ------------------------------------------------------------------------------------------
I running the latest version of GATK
my command is
java -Xmx4g -jar GenomeAnalysisTK.jar -T RealignerTargetCreator -U ALLOW_SEQ_DICT_INCOMPATIBILITY -R /media/Hg19/ucsc.hg19.fasta -I /home/samples/marked_duplicates_unprocessed.bam --known Mills_and_1000G_gold_standard.indels.hg19.sites.vcf -nt 4 -o marked_duplicates_unprocessed.bam.intervals
please help its urgent