Bug Bulletin: we have identified a bug that affects indexing when producing gzipped VCFs. This will be fixed in the upcoming 3.2 release; in the meantime you need to reindex gzipped VCFs using Tabix.

PrintReads, Yet another ArrayIndexOutOfBoundsException

KarlJVKarlJV Posts: 4Member

Hi,

I'm trying to apply my recalibrated quality values with the following command:

java -jar GenomeAnalysisTK.jar -T PrintReads -R genome_noHap.fa -I realigned.bam -BQSR realigned.recal_data.grp -o realigned.recal.bam -nct 25

And get the following error. I couldn't find it elsewhere. Would be happy if I could get some advice.

Let me know if you need more info.

Best,

Karl

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

java.lang.ArrayIndexOutOfBoundsException: 0
at org.broadinstitute.sting.utils.recalibration.BaseRecalibration.recalibrateRead(BaseRecalibration.java:151)
at org.broadinstitute.sting.utils.recalibration.BQSRReadTransformer.apply(BQSRReadTransformer.java:93)
at org.broadinstitute.sting.gatk.walkers.readutils.PrintReads.map(PrintReads.java:251)
at org.broadinstitute.sting.gatk.walkers.readutils.PrintReads.map(PrintReads.java:98)
at org.broadinstitute.sting.gatk.traversals.TraverseReadsNano$TraverseReadsMap.apply(TraverseReadsNano.java:230)
at org.broadinstitute.sting.gatk.traversals.TraverseReadsNano$TraverseReadsMap.apply(TraverseReadsNano.java:218)
at org.broadinstitute.sting.utils.nanoScheduler.NanoScheduler$ReadMapReduceJob.run(NanoScheduler.java:471)
at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:471)
at java.util.concurrent.FutureTask$Sync.innerRun(FutureTask.java:334)
at java.util.concurrent.FutureTask.run(FutureTask.java:166)
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1145)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:615)
at java.lang.Thread.run(Thread.java:722)

ERROR ------------------------------------------------------------------------------------------
ERROR A GATK RUNTIME ERROR has occurred (version 2.4-3-g2a7af43):
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: 0
ERROR ------------------------------------------------------------------------------------------

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