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Not sure if bug or user error

I am using the GATK best practices for germline SNPs and Indels in Whole Genomes and Exomes and I get the following error when I try to use this command: os.system('java -Xmx6g -Djava.io.tmpdir=/Users/seyfim/tmp -jar /Users/seyfim/software/GenomeAnalysisTK-3.7-0/GenomeAnalysisTK.jar -T GenotypeGVCFs -R /Users/seyfim/Directory/Marilyn/hg19.fa --variant '+n+'.sample.raw.vcf -o ALL_SAMPLES.vcf -V '+rest)

Error:

ERROR --
ERROR stack trace

java.lang.NullPointerException
at org.broadinstitute.gatk.utils.commandline.ArgumentTypeDescriptor.parseRodBindingCollectionSource(ArgumentTypeDescriptor.java:448)
at org.broadinstitute.gatk.utils.commandline.RodBindingCollectionArgumentTypeDescriptor.parse(ArgumentTypeDescriptor.java:671)
at org.broadinstitute.gatk.utils.commandline.CompoundArgumentTypeDescriptor.parse(ArgumentTypeDescriptor.java:834)
at org.broadinstitute.gatk.utils.commandline.ArgumentTypeDescriptor.parse(ArgumentTypeDescriptor.java:137)
at org.broadinstitute.gatk.utils.commandline.ArgumentSource.parse(ArgumentSource.java:119)
at org.broadinstitute.gatk.utils.commandline.ParsingEngine.loadValueIntoObject(ParsingEngine.java:509)
at org.broadinstitute.gatk.utils.commandline.ParsingEngine.loadArgumentsIntoObject(ParsingEngine.java:429)
at org.broadinstitute.gatk.utils.commandline.ParsingEngine.loadArgumentsIntoObject(ParsingEngine.java:403)
at org.broadinstitute.gatk.utils.commandline.CommandLineProgram.loadArgumentsIntoObject(CommandLineProgram.java:279)
at org.broadinstitute.gatk.engine.CommandLineExecutable.execute(CommandLineExecutable.java:112)
at org.broadinstitute.gatk.utils.commandline.CommandLineProgram.start(CommandLineProgram.java:256)
at org.broadinstitute.gatk.utils.commandline.CommandLineProgram.start(CommandLineProgram.java:158)
at org.broadinstitute.gatk.engine.CommandLineGATK.main(CommandLineGATK.java:108)

ERROR ------------------------------------------------------------------------------------------
ERROR A GATK RUNTIME ERROR has occurred (version 3.7-0-gcfedb67):
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 https://software.broadinstitute.org/gatk
ERROR
ERROR MESSAGE: Code exception (see stack trace for error itself)
ERROR ------------------------------------------------------------------------------------------

Best Answer

Answers

  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie admin

    Can you show the command line recorded in the console output?

  • INFO 10:41:22,293 HelpFormatter - --------------------------------------------------------------------------------
    INFO 10:41:22,294 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.7-0-gcfedb67, Compiled 2016/12/12 11:21:18
    INFO 10:41:22,294 HelpFormatter - Copyright (c) 2010-2016 The Broad Institute
    INFO 10:41:22,294 HelpFormatter - For support and documentation go to https://software.broadinstitute.org/gatk
    INFO 10:41:22,294 HelpFormatter - [Mon Aug 21 10:41:22 EDT 2017] Executing on Mac OS X 10.12.6 x86_64
    INFO 10:41:22,294 HelpFormatter - Java HotSpot(TM) 64-Bit Server VM 1.8.0_131-b11
    INFO 10:41:22,297 HelpFormatter - Program Args: -T GenotypeGVCFs -R /Users/seyfim/Directory/Marilyn/hg19.fa --variant /Users/seyfim/working/bwa_working/CCS3-46871919_2.sample.raw.vcf -o ALL_SAMPLES.vcf -V
    INFO 10:41:22,302 HelpFormatter - Executing as [email protected] on Mac OS X 10.12.6 x86_64; Java HotSpot(TM) 64-Bit Server VM 1.8.0_131-b11.
    INFO 10:41:22,302 HelpFormatter - Date/Time: 2017/08/21 10:41:22
    INFO 10:41:22,302 HelpFormatter - --------------------------------------------------------------------------------
    INFO 10:41:22,302 HelpFormatter - --------------------------------------------------------------------------------

  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie admin

    It looks like your command is incomplete: there is no value provided to the last -V argument. My guess is that the rest variable in your script is coming out empty.

  • Here's the full command with -V and rest:

    rest=' -V '.join([ i for i in os.listdir('.') if i.endswith('.vcf')])
    os.system('java -Xmx6g -Djava.io.tmpdir=/Users/seyfim/tmp -jar /Users/seyfim/software/GenomeAnalysisTK-3.7-0/GenomeAnalysisTK.jar -T GenotypeGVCFs -R /Users/seyfim/Directory/Marilyn/hg19.fa --variant '+n+'.sample.raw.vcf -o ALL_SAMPLES.vcf -V '+rest)

    I tried running the tool individually with hard-coding the --variant file and it worked so I am not sure what is wrong

  • Thank you very much, I figured out that the rest variable was empty as you had stated!

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