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java.lang.ClassCastException: [I cannot be cast to [B while running BaseRecalibrator

anishanish Member
edited October 2015 in Ask the GATK team

Hi,

I'm doing pre-processing in Ion Torrent samples. But I'm getting an error while running BaseRecalibrator.

Here are the steps I followed:
1. Sort BAMs
2. Add or change RG from Picard tools
3. Indel Realignment from GATK
4. Base recalibration from GATK [ERROR]

This is the error I get:
##### ERROR ------------------------------------------------------------------------------------------
##### ERROR stack trace
java.lang.ClassCastException: [I cannot be cast to [B
at org.broadinstitute.gatk.engine.recalibration.RecalUtils.isColorSpaceConsistent(RecalUtils.java:888)
at org.broadinstitute.gatk.tools.walkers.bqsr.BaseRecalibrator.badSolidOffset(BaseRecalibrator.java:308)
at org.broadinstitute.gatk.tools.walkers.bqsr.BaseRecalibrator.calculateSkipArray(BaseRecalibrator.java:302)
at org.broadinstitute.gatk.tools.walkers.bqsr.BaseRecalibrator.map(BaseRecalibrator.java:267)
at org.broadinstitute.gatk.tools.walkers.bqsr.BaseRecalibrator.map(BaseRecalibrator.java:136)
at org.broadinstitute.gatk.engine.traversals.TraverseReadsNano$TraverseReadsMap.apply(TraverseReadsNano.java:228)
at org.broadinstitute.gatk.engine.traversals.TraverseReadsNano$TraverseReadsMap.apply(TraverseReadsNano.java:216)
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.TraverseReadsNano.traverse(TraverseReadsNano.java:102)
at org.broadinstitute.gatk.engine.traversals.TraverseReadsNano.traverse(TraverseReadsNano.java:56)
at org.broadinstitute.gatk.engine.executive.LinearMicroScheduler.execute(LinearMicroScheduler.java:108)
at org.broadinstitute.gatk.engine.GenomeAnalysisEngine.execute(GenomeAnalysisEngine.java:315)
at org.broadinstitute.gatk.engine.CommandLineExecutable.execute(CommandLineExecutable.java:121)
at org.broadinstitute.gatk.utils.commandline.CommandLineProgram.start(CommandLineProgram.java:248)
at org.broadinstitute.gatk.utils.commandline.CommandLineProgram.start(CommandLineProgram.java:155)
at org.broadinstitute.gatk.engine.CommandLineGATK.main(CommandLineGATK.java:106)
##### ERROR ------------------------------------------------------------------------------------------
##### ERROR A GATK RUNTIME ERROR has occurred (version 3.4-46-gbc02625):
##### 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 http://www.broadinstitute.org/gatk
##### ERROR
##### ERROR MESSAGE: [I cannot be cast to [B

Here is the code I have used:
java -XX:ParallelGCThreads=4 -Xmx4G -jar $GATK_HOME/GenomeAnalysisTK.jar -R $REF -T BaseRecalibrator -I $FILE -knownSites $KNOWN_SITES -o $BAMs/BaseRecalibration/$SAMPLE.recal.table

Does anyone know how to fix this?

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