GATK BaseRecalibrator - Null Pointer Exception

Question

[nrk_02]

Hello!

I am using Gatk 4.1.3 , and getting Null Pointer Exception.

Command:

gatk BaseRecalibrator -R F.fna -I V.bam --known-sites X.vcf.gz --known-sites Y.vcf.gz --known-sites Z.vcf.gz --known-sites R.vcf.gz -O T.table

Error:

java.lang.NullPointerException
        at org.broadinstitute.hellbender.utils.recalibration.RecalUtils.parsePlatformForRead(RecalUtils.java:495)
        at org.broadinstitute.hellbender.utils.recalibration.BaseRecalibrationEngine.processRead(BaseRecalibrationEngine.java:122)
        at org.broadinstitute.hellbender.tools.walkers.bqsr.BaseRecalibrator.apply(BaseRecalibrator.java:185)
        at org.broadinstitute.hellbender.engine.ReadWalker.lambda$traverse$0(ReadWalker.java:96)
        at java.util.stream.ForEachOps$ForEachOp$OfRef.accept(ForEachOps.java:183)
        at java.util.stream.ReferencePipeline$3$1.accept(ReferencePipeline.java:193)
        at java.util.stream.ReferencePipeline$2$1.accept(ReferencePipeline.java:175)
        at java.util.stream.ReferencePipeline$3$1.accept(ReferencePipeline.java:193)
        at java.util.Iterator.forEachRemaining(Iterator.java:116)
        at java.util.Spliterators$IteratorSpliterator.forEachRemaining(Spliterators.java:1801)
        at java.util.stream.AbstractPipeline.copyInto(AbstractPipeline.java:482)
        at java.util.stream.AbstractPipeline.wrapAndCopyInto(AbstractPipeline.java:472)
        at java.util.stream.ForEachOps$ForEachOp.evaluateSequential(ForEachOps.java:150)
        at java.util.stream.ForEachOps$ForEachOp$OfRef.evaluateSequential(ForEachOps.java:173)
        at java.util.stream.AbstractPipeline.evaluate(AbstractPipeline.java:234)
        at java.util.stream.ReferencePipeline.forEach(ReferencePipeline.java:485)
        at org.broadinstitute.hellbender.engine.ReadWalker.traverse(ReadWalker.java:94)
        at org.broadinstitute.hellbender.engine.GATKTool.doWork(GATKTool.java:1048)
        at org.broadinstitute.hellbender.cmdline.CommandLineProgram.runTool(CommandLineProgram.java:139)
        at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMainPostParseArgs(CommandLineProgram.java:191)
        at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:210)
        at org.broadinstitute.hellbender.Main.runCommandLineProgram(Main.java:162)
        at org.broadinstitute.hellbender.Main.mainEntry(Main.java:205)
        at org.broadinstitute.hellbender.Main.main(Main.java:291)
Using GATK jar /tools/gatk/4.1.3.0/gatk-package-4.1.3.0-local.jar

I am not sure what to pay attention to solve the problem - any help is appreciated, thanks!

[brunobsouzaa]

For the command you've posted, your -R argument should point to a fasta file. Also, make sure you are using the -Xmx argument. Also, I don't see a input file!

[nrk_02]

It was like that actually, I updated the entry, Thanks!

[brunobsouzaa]

Can you post the full log info? I mean, what's the info before this error?