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FATAL root error, RealignerTargetCreator

I keep getting the same error message when running a command in GATK. I am using GATK 3.3 Eventually I would like to call SNPs, but want to realign around InDels first.

To make sure that my input files are correct, I used Picard: java -jar /programs/ValidateSamFile.jar I=merged_sorted_fixed.bam No errors were found.

I wrote:
java -jar /programs/GenomeAnalysisTK/GenomeAnalysisTK.jar \
-T RealignerTargetCreator\
-R target_sequences.fasta
-o merged_output.intervals \
-I merged_sorted_fixed.bam \
--minReadsAtLocus 4 \
--mismatchFraction 0

And this is the output:

" Adding rod class GFF
Adding rod class dbSNP
Adding rod class HapMapAlleleFrequencies
Adding rod class SAMPileup
Adding rod class GELI
Adding rod class RefSeq
Adding rod class Table
Adding rod class PooledEM
Adding rod class 1KGSNPs
Adding rod class SangerSNP
Adding rod class HapMapGenotype
Adding rod class Intervals
Adding rod class Variants 76 [main] INFO org.broadinstitute.sting.gatk.WalkerManager - plugin directory: /scratch/atk25/programs/GenomeAnalysisTK/walkers 100 [main] INFO org.broadinstitute.sting.gatk.WalkerManager - * Adding module CountLoci 101 [main] INFO org.broadinstitute.sting.gatk.WalkerManager - * Adding module PrintReads 101 [main] INFO org.broadinstitute.sting.gatk.WalkerManager - * Adding module Pileup 101 [main] INFO org.broadinstitute.sting.gatk.WalkerManager - * Adding module DepthOfCoverage 105 [main] INFO org.broadinstitute.sting.gatk.WalkerManager - * Adding module ValidatingPileup 106 [main] INFO org.broadinstitute.sting.gatk.WalkerManager - * Adding module CountReads 139 [main] FATAL root - Exception caught by base Command Line Program, with message: null 139 [main] FATAL root - with cause: null java.lang.NullPointerException at org.broadinstitute.sting.gatk.WalkerManager.createWalkerByName(WalkerManager.java:93) at org.broadinstitute.sting.gatk.GenomeAnalysisEngine.getWalkerByName(GenomeAnalysisEngine.java:157) at org.broadinstitute.sting.gatk.CommandLineGATK.getArgumentSources(CommandLineGATK.java:117) at org.broadinstitute.sting.utils.cmdLine.CommandLineProgram.start(CommandLineProgram.java:199) at org.broadinstitute.sting.gatk.CommandLineGATK.main(CommandLineGATK.java:58) java.lang.RuntimeException: java.lang.NullPointerException at org.broadinstitute.sting.utils.cmdLine.CommandLineProgram.start(CommandLineProgram.java:279) at org.broadinstitute.sting.gatk.CommandLineGATK.main(CommandLineGATK.java:58) Caused by: java.lang.NullPointerException at org.broadinstitute.sting.gatk.WalkerManager.createWalkerByName(WalkerManager.java:93) at org.broadinstitute.sting.gatk.GenomeAnalysisEngine.getWalkerByName(GenomeAnalysisEngine.java:157) at org.broadinstitute.sting.gatk.CommandLineGATK.getArgumentSources(CommandLineGATK.java:117) at org.broadinstitute.sting.utils.cmdLine.CommandLineProgram.start(CommandLineProgram.java:199)

... 1 more

An error has occurred. Please check your command line arguments for any typos or inconsistencies."

I'd really appreciate any help!

Answers

  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie

    Hi there,

    This look completely different from normal GATK output. Are you using GATK through a pipelining service like Galaxy or similar?

  • AnnikaAnnika ArizonaMember

    No, I wrote it in linux.

  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie

    Hi @Annika,

    Can you please check which version of GATK you are using? Some of the code elements mentioned in the stack track you posted date from much older versions and are no longer present in GATK 3.3, so it's not possible that you are using that version.

  • AnnikaAnnika ArizonaMember

    Hi Geraldine,
    GATK 3.3 is the only version installed on the cluster I'm using: When I call module avail, it only lists gatk/3.3-0.

  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie

    Then I think you need to talk to your IT/sysadmin people, because the output you have there indicates you are running something close to version 1.0, which is downright ancient. My guess is someone made a mistake in your cluster setup and linked to the wrong program executable.

  • AnnikaAnnika ArizonaMember

    I'll talk to the IT person and let you know. Thank you for looking into it!

  • AnnikaAnnika ArizonaMember

    Hi Geraldine,
    Yes, it was an old version. With the new version it's running. Thank you for your advise!

  • HasaniHasani GermanyMember

    Dear GATK team,

    could you please explain the following case to me:
    I'm calling mutations out of RNA-Seq data, my command looks like this:

    java -Xms1024m -Xmx10g -jar $GATKPATH/GenomeAnalysisTK.jar \ -T RealignerTargetCreator \ -I $infile \ -o $out.indel.bam.list \ --filter_reads_with_N_cigar

    For some files, the command was executed normally, and the pipeline continued. However, in some cases I got the error of demanding a reference (Walker requires a reference but none was provided.)

    So could you please tell me what is going on? more importantly, if I should re-compute the successful ones?

    Thank you

  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie

    Hi @Hasani,

    Look closely at your command line: there is an argument missing. The error message helpfully tells you which one...

    I'm not sure why some of your commands are complete and some are not, but if I were you I'd check whatever script (or person) generates them.

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