The current GATK version is 3.7-0
Examples: Monday, today, last week, Mar 26, 3/26/04

Howdy, Stranger!

It looks like you're new here. If you want to get involved, click one of these buttons!

Did you remember to?


1. Search using the upper-right search box, e.g. using the error message.
2. Try the latest version of tools.
3. Include tool and Java versions.
4. Tell us whether you are following GATK Best Practices.
5. Include relevant details, e.g. platform, DNA- or RNA-Seq, WES (+capture kit) or WGS (PCR-free or PCR+), paired- or single-end, read length, expected average coverage, somatic data, etc.
6. For tool errors, include the error stacktrace as well as the exact command.
7. For format issues, include the result of running ValidateSamFile for BAMs or ValidateVariants for VCFs.
8. For weird results, include an illustrative example, e.g. attach IGV screenshots according to Article#5484.
9. For a seeming variant that is uncalled, include results of following Article#1235.

Did we ask for a bug report?


Then follow instructions in Article#1894.

Formatting tip!


Surround blocks of code, error messages and BAM/VCF snippets--especially content with hashes (#)--with lines with three backticks ( ``` ) each to make a code block.
Powered by Vanilla. Made with Bootstrap.
Picard 2.9.0 is now available. Download and read release notes here.
GATK 3.7 is here! Be sure to read the Version Highlights and optionally the full Release Notes.

ReduceReads Code exception

dcittarodcittaro Member Posts: 31

Hi there, I've tried to run ReduceReads for the first time and I got this error:

`$ java -Xmx8g -jar /lustre1/tools/bin/GenomeAnalysisTK-2.3-6.jar -T ReduceReads -R /lustre1/genomes/hg19/fa/hg19.fa -I filein.bam -o fileout.bam
[…]

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

java.lang.NullPointerException
at org.broadinstitute.sting.gatk.walkers.compression.reducereads.SingleSampleCompressor.closeVariantRegions(SingleSampleCompressor.java:83)
at org.broadinstitute.sting.gatk.walkers.compression.reducereads.MultiSampleCompressor.closeVariantRegionsInAllSamples(MultiSampleCompressor.java:94)
at org.broadinstitute.sting.gatk.walkers.compression.reducereads.MultiSampleCompressor.addAlignment(MultiSampleCompressor.java:76)
at org.broadinstitute.sting.gatk.walkers.compression.reducereads.ReduceReadsStash.compress(ReduceReadsStash.java:67)
at org.broadinstitute.sting.gatk.walkers.compression.reducereads.ReduceReads.reduce(ReduceReads.java:387)
at org.broadinstitute.sting.gatk.walkers.compression.reducereads.ReduceReads.reduce(ReduceReads.java:87)
at org.broadinstitute.sting.gatk.traversals.TraverseReadsNano$TraverseReadsReduce.apply(TraverseReadsNano.java:226)
at org.broadinstitute.sting.gatk.traversals.TraverseReadsNano$TraverseReadsReduce.apply(TraverseReadsNano.java:215)
at org.broadinstitute.sting.utils.nanoScheduler.NanoScheduler.executeSingleThreaded(NanoScheduler.java:254)
at org.broadinstitute.sting.utils.nanoScheduler.NanoScheduler.execute(NanoScheduler.java:219)
at org.broadinstitute.sting.gatk.traversals.TraverseReadsNano.traverse(TraverseReadsNano.java:91)
at org.broadinstitute.sting.gatk.traversals.TraverseReadsNano.traverse(TraverseReadsNano.java:55)
at org.broadinstitute.sting.gatk.executive.LinearMicroScheduler.execute(LinearMicroScheduler.java:83)
at org.broadinstitute.sting.gatk.GenomeAnalysisEngine.execute(GenomeAnalysisEngine.java:281)
at org.broadinstitute.sting.gatk.CommandLineExecutable.execute(CommandLineExecutable.java:113)
at org.broadinstitute.sting.commandline.CommandLineProgram.start(CommandLineProgram.java:237)
at org.broadinstitute.sting.commandline.CommandLineProgram.start(CommandLineProgram.java:147)
at org.broadinstitute.sting.gatk.CommandLineGATK.main(CommandLineGATK.java:91)

ERROR ------------------------------------------------------------------------------------------
ERROR A GATK RUNTIME ERROR has occurred (version 2.3-6-gebbba25):
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: Code exception (see stack trace for error itself)
ERROR ------------------------------------------------------------------------------------------

`
Is there something wrong with running RR with multiple samples?

d

Tagged:

Answers

Sign In or Register to comment.