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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.

I'm not able to run this program on my Mac

OliverOliver Posts: 0
edited October 2012 in Ask the GATK team

Hi I´ve a strange problem with the GATK. Everytime I try to run it my Console shows the following error Message.

30.10.12 15:10:06   [0x0-0xe20e2].com.apple.JarLauncher[1114]   ##### ERROR ------------------------------------------------------------------------------------------
30.10.12 15:10:06   [0x0-0xe20e2].com.apple.JarLauncher[1114]   ##### ERROR A USER ERROR has occurred (version 2.1-13-g0f021e6): 
30.10.12 15:10:06   [0x0-0xe20e2].com.apple.JarLauncher[1114]   ##### ERROR The invalid arguments or inputs must be corrected before the GATK can proceed
30.10.12 15:10:06   [0x0-0xe20e2].com.apple.JarLauncher[1114]   ##### ERROR Please do not post this error to the GATK forum
30.10.12 15:10:06   [0x0-0xe20e2].com.apple.JarLauncher[1114]   ##### ERROR
30.10.12 15:10:06   [0x0-0xe20e2].com.apple.JarLauncher[1114]   ##### ERROR See the documentation (rerun with -h) for this tool to view allowable command-line arguments.
30.10.12 15:10:06   [0x0-0xe20e2].com.apple.JarLauncher[1114]   ##### ERROR Visit our website and forum for extensive documentation and answers to 
30.10.12 15:10:06   [0x0-0xe20e2].com.apple.JarLauncher[1114]   ##### ERROR commonly asked questions http://www.broadinstitute.org/gatk
30.10.12 15:10:06   [0x0-0xe20e2].com.apple.JarLauncher[1114]   ##### ERROR
30.10.12 15:10:06   [0x0-0xe20e2].com.apple.JarLauncher[1114]   ##### ERROR MESSAGE: Argument with name '--analysis_type' (-T) is missing.
30.10.12 15:10:06   [0x0-0xe20e2].com.apple.JarLauncher[1114]   ##### ERROR ------------------------------------------------------------------------------------------

Can you show me my mistakes please?
With regards Oliver

Post edited by Geraldine_VdAuwera on

Best Answer

  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAPosts: 11,743 admin
    Accepted Answer

    Hi Oliver,

    The error message says it all: your command is missing an argument. Please read the documentation (such as this one and this one to start with) for solutions.

    In future please try to read the documentation first before posting a User Error in the forum.

    Geraldine Van der Auwera, PhD

Answers

  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAPosts: 11,743 admin
    Accepted Answer

    Hi Oliver,

    The error message says it all: your command is missing an argument. Please read the documentation (such as this one and this one to start with) for solutions.

    In future please try to read the documentation first before posting a User Error in the forum.

    Geraldine Van der Auwera, PhD

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