PrintReads, Yet another ArrayIndexOutOfBoundsException

KarlJV

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 ------------------------------------------------------------------------------------------

Geraldine_VdAuwera

Looks like a bug, we've had a few other similar reports this morning. We'll look into it and post any status updates here:

http://gatkforums.broadinstitute.org/discussion/2346/bug-in-various-tools-2-4-7-arrayindexoutofboundsexception#latest

ebanks

Hi Karl,

Thanks for uploading the helpful data. The problem here is that you have a read that doesn't have its base sequence stored (there's a "*" instead of the bases). While technically valid according to the SAM specification, this isn't something we support. I'm updating the GATK to filter out such reads, but in the meantime you'll need to do that on your own.

Geraldine_VdAuwera

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

KarlJV

Hi Geraldine,

I've uploaded a file to your ftp:

bugreport_karljv_130314.tar.gz

Hope everything is there.

Looking forward to hear what you get out of it.

Geraldine_VdAuwera

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

KarlJV

Thanks for the help.

KarlJV

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 :)

KarlJV

It worked...

Geraldine_VdAuwera

Glad to hear it, Karl. Thanks for letting us know about your workaround. In the future the workaround won't be necessary anymore but in the meantime it may be useful to others as well.