No_et and proxy errors

Hi All,

I have a no_et key for GATK but when I try and use it with mutect I am encountering the following error:

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

org.broadinstitute.sting.utils.exceptions.ReviewedStingException: Could not locate the GATK public key GATK_public.key in the classpath
at org.broadinstitute.sting.utils.crypt.CryptUtils.loadGATKDistributedPublicKey(CryptUtils.java:278)
at org.broadinstitute.sting.gatk.CommandLineExecutable.authorizeGATKRun(CommandLineExecutable.java:137)
at org.broadinstitute.sting.gatk.CommandLineExecutable.execute(CommandLineExecutable.java:85)
at org.broadinstitute.sting.commandline.CommandLineProgram.start(CommandLineProgram.java:236)
at org.broadinstitute.sting.commandline.CommandLineProgram.start(CommandLineProgram.java:146)
at org.broadinstitute.sting.gatk.CommandLineGATK.main(CommandLineGATK.java:93)

We are behind a tight firewall and so running muTect with:
java -Dhttp.proxyHost=localhost -Dhttp.noProxyHosts=”localhost” -Dhttp.proxyPort=3128
did not work either with mutect producing the following exception:
HttpMethodDirector - I/O exception (java.net.ConnectException) caught when processing request: Connection refused

Thanks for your time,

Jason

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Best Answer

Answers

  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie admin

    Hi Jason,

    Your GATK key should just work with MuTect. Have you tested that it works with GATK?

  • jelluljellul Member

    Hi Geraldine,

    Yes we use it routinely with GATK v1.5 and v2 without a problem.

    Cheers,

    Jason

  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie admin

    Hmm. Can you post the full command line you were using when you got the error?

  • jelluljellul Member
    edited March 2013

    Hi Geraldine,

    Here you go:

    [[email protected] alignCustom]$ java -jar /home/ClusterSetup/binaries/all_arch/mutect/muTect-1.1.4/muTect-1.1.4.jar -T MuTect -et no_et -K /home/ClusterSetup/binaries/all_arch/mutect/muTect-1.1.4/maria.doyle_petermac.org.key -I:tumor /home/pmc-bioinf02/NGS_USERS/Hunter/IC289T/IC289T.bam -I:normal /home/pmc-bioinf02/NGS_USERS/Hunter/IC289T/IC289G.bam -o /dev/null -vcf /home/pmc-bioinf02/NGS_USERS/Hunter/IC289T/Combined_callers_SNVs/IC289T_mutect.vcf -nt 8 --cosmic /home/data/databases/Cosmic/Cosmic_v54/hg19_cosmic_v54_120711.vcf --dbsnp /home/data/databases/dbSNP/dbSNP134/00-All.vcf -L /home/data/reference/bed_files/NimbleGen_v2/SeqCap_EZ_Exome_v2_target_regions_MERGED.bed -R /galaxy/indexes/human/g1k_v37/picard/human_g1k_v37.fasta
    
    INFO  13:00:14,212 ArgumentTypeDescriptor - Dynamically determined type of /home/data/reference/bed_files/NimbleGen_v2/SeqCap_EZ_Exome_v2_target_regions_MERGED.bed to be BED 
    INFO  13:00:14,279 HelpFormatter - --------------------------------------------------------------------------------- 
    INFO  13:00:14,279 HelpFormatter - The Genome Analysis Toolkit (GATK) v2.2-25-g2a68eab, Compiled 2012/11/08 10:30:02 
    INFO  13:00:14,279 HelpFormatter - Copyright (c) 2010 The Broad Institute 
    INFO  13:00:14,279 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk 
    INFO  13:00:14,283 HelpFormatter - Program Args: -T MuTect -et no_et -K /home/ClusterSetup/binaries/all_arch/mutect/muTect-1.1.4/maria.doyle_petermac.org.key -I:tumor /home/pmc-bioinf02/NGS_USERS/Hunter/IC289T/IC289T.bam -I:normal /home/pmc-bioinf02/NGS_USERS/Hunter/IC289T/IC289G.bam -o /dev/null -vcf /home/pmc-bioinf02/NGS_USERS/Hunter/IC289T/Combined_callers_SNVs/IC289T_mutect.vcf -nt 8 --cosmic /home/data/databases/Cosmic/Cosmic_v54/hg19_cosmic_v54_120711.vcf --dbsnp /home/data/databases/dbSNP/dbSNP134/00-All.vcf -L /home/data/reference/bed_files/NimbleGen_v2/SeqCap_EZ_Exome_v2_target_regions_MERGED.bed -R /galaxy/indexes/human/g1k_v37/picard/human_g1k_v37.fasta 
    INFO  13:00:14,283 HelpFormatter - Date/Time: 2013/03/04 11:00:14 
    INFO  13:00:14,284 HelpFormatter - --------------------------------------------------------------------------------- 
    INFO  13:00:14,284 HelpFormatter - --------------------------------------------------------------------------------- 
    ##### ERROR ------------------------------------------------------------------------------------------
    ##### ERROR stack trace 
    org.broadinstitute.sting.utils.exceptions.ReviewedStingException: Could not locate the GATK public key GATK_public.key in the classpath
        at org.broadinstitute.sting.utils.crypt.CryptUtils.loadGATKDistributedPublicKey(CryptUtils.java:278)
        at org.broadinstitute.sting.gatk.CommandLineExecutable.authorizeGATKRun(CommandLineExecutable.java:137)
        at org.broadinstitute.sting.gatk.CommandLineExecutable.execute(CommandLineExecutable.java:85)
        at org.broadinstitute.sting.commandline.CommandLineProgram.start(CommandLineProgram.java:236)
        at org.broadinstitute.sting.commandline.CommandLineProgram.start(CommandLineProgram.java:146)
        at org.broadinstitute.sting.gatk.CommandLineGATK.main(CommandLineGATK.java:93)
    ##### ERROR ------------------------------------------------------------------------------------------
    ##### ERROR A GATK RUNTIME ERROR has occurred (version 2.2-25-g2a68eab):
    ##### 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: Could not locate the GATK public key GATK_public.key in the classpath
    ##### ERROR ------------------------------------------------------------------------------------------
    

    Thanks

    Jason

  • jelluljellul Member

    Thanks Geraldine.

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