The current GATK version is 3.4-46

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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.

Best,

Karl

##### ERROR stack trace

java.lang.ArrayIndexOutOfBoundsException: 0
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)

##### ERROR ------------------------------------------------------------------------------------------
Tagged:

Hi Karl, could you please upload a snippet of your bam where the error is occurring? To debug and fix this we need to reproduce the error locally. Detailed instructions here: http://www.broadinstitute.org/gatk/guide/article?id=1894

Geraldine Van der Auwera, PhD

• Posts: 4Member

Hi Geraldine,

bugreport_karljv_130314.tar.gz

Hope everything is there.

Looking forward to hear what you get out of it.

Thanks Karl. We'll try to get this fixed asap.

Geraldine Van der Auwera, PhD

• Posts: 4Member

Thanks for the help.

• Posts: 4Member
edited March 2013

I've traced this back through my pipeline and it seems to come from the gem-mapper and the not-primary hits

It works by applying -rf NotPrimaryAlignment. I know for sure in ~ 10h

Post edited by KarlJV on
• Posts: 4Member

It worked...