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RealignerTargetCreator : error message on format 1000G_phase1.indels.b37.vcf

TiphaineTiphaine Member
edited August 2012 in Ask the GATK team

Hi,

I would like to run RealignerTargetCreator with option --known and data 1000G_phase1.indels.b37.vcf ( from https://main.g2.bx.psu.edu/library_common/ldda_info?library_id=f9ba60baa2e6ba6d&show_deleted=False&cntrller=library&folder_id=709338dd4741c085&use_panels=False&id=93fcddc692e0986f ).
But I have an error message that I don't understand . Could you help me ?

INFO 14:07:09,205 HelpFormatter - ---------------------------------------------------------------------------------
INFO 14:07:09,209 HelpFormatter - The Genome Analysis Toolkit (GATK) v2.0-35-g2d70733, Compiled 2012/08/03 15:09:41
INFO 14:07:09,209 HelpFormatter - Copyright (c) 2010 The Broad Institute
INFO 14:07:09,209 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
INFO 14:07:09,210 HelpFormatter - Program Args: -I /scratch/cbrc/BWA/sample.bam.dedup.bam -R /scratch/cbrc/ref/b37/human_g1k_v37.fasta -T RealignerTargetCreator --out /scratch/cbrc/Z09_BrandNew/RealignerTarget/sample.intervals --known /scratch/cbrc/ref/b37/indels/1000G_phase1.indels.b37.vcf
INFO 14:07:09,210 HelpFormatter - Date/Time: 2012/08/13 14:07:09
INFO 14:07:09,210 HelpFormatter - ---------------------------------------------------------------------------------
INFO 14:07:09,210 HelpFormatter - ---------------------------------------------------------------------------------
INFO 14:07:09,244 ArgumentTypeDescriptor - Dynamically determined type of /scratch/cbrc/ref/b37/indels/1000G_phase1.indels.b37.vcf to be VCF
INFO 14:07:09,247 GenomeAnalysisEngine - Strictness is SILENT
INFO 14:07:30,816 HttpMethodDirector - I/O exception (java.net.ConnectException) caught when processing request: Connection timed out
INFO 14:07:30,816 HttpMethodDirector - Retrying request

Thanks,

Tiphaine

Best Answers

  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MA admin
    Accepted Answer

    I'm sorry, I don't understand what you are saying. Are you having another problem? From what you posted here it looks like it's running fine. There is no error message here, only an information message telling you that it identified the known file as being in VCF format. This is perfectly normal.

Answers

  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie admin

    Hi Tiphaine,

    Your problem stems from the Phone Home feature trying to send it report but failing to establish a network connection. Please see this article for details and solutions:
    http://gatkforums.broadinstitute.org/discussion/1250/what-is-phone-home-and-how-does-it-affect-me

  • TiphaineTiphaine Member
    edited August 2012

    Ok. I understand why I did not have about the same issue when I run by master node and a classic node in our cluster. I'm going to resquest key

    But I have had my issue on format of known indels :
    error message from my master node (run yesterday, 13/08/2012):

    #

    INFO 10:59:27,854 HelpFormatter - ---------------------------------------------------------------------------------

    INFO 10:59:27,856 HelpFormatter - The Genome Analysis Toolkit (GATK) v2.0-35-g2d70733, Compiled 2012/08/03 15:09:41

    INFO 10:59:27,856 HelpFormatter - Copyright (c) 2010 The Broad Institute

    INFO 10:59:27,856 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk

    INFO 10:59:27,856 HelpFormatter - Program Args: -I /scratch/cbrc/BWA/sample.bam.dedup.bam -R /scratch/cbrc/ref/b37/human_g1k_v37.fasta -T RealignerTargetCreator -o /scratch/cbrc/RealignerTarget/sample.intervals --known /scratch/cbrc/ref/b37/indels/1000G_phase1.indels.b37.vcf

    INFO 10:59:27,857 HelpFormatter - Date/Time: 2012/08/13 10:59:27

    INFO 10:59:27,857 HelpFormatter - ---------------------------------------------------------------------------------

    INFO 10:59:27,857 HelpFormatter - ---------------------------------------------------------------------------------

    INFO 10:59:27,865 ArgumentTypeDescriptor - Dynamically determined type of /scratch/cbrc/ref/b37/indels/1000G_phase1.indels.b37.vcf to be VCF

    INFO 10:59:27,868 GenomeAnalysisEngine - Strictness is SILENT

    INFO 10:59:29,236 GATKRunReport - Uploaded run statistics report to AWS S3

    #

    Could you help me ?

  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie admin
    Accepted Answer

    I'm sorry, I don't understand what you are saying. Are you having another problem? From what you posted here it looks like it's running fine. There is no error message here, only an information message telling you that it identified the known file as being in VCF format. This is perfectly normal.

  • TiphaineTiphaine Member
    edited August 2012

    It is me,I'm sorry. I thought that I have the error from VCF file because I can't produce the output file with RealignerTargetCreator. My issue does'nt come from the file of known indel... but

    ERROR ------------------------------------------------------------------------------------------
    ERROR A USER ERROR has occurred (version 2.0-35-g2d70733):
    ERROR The invalid arguments or inputs must be corrected before the GATK can proceed
    ERROR Please do not post this error to the GATK forum
    ERROR
    ERROR See the documentation (rerun with -h) for this tool to view allowable command-line arguments.
    ERROR Visit our website and forum for extensive documentation and answers to
    ERROR commonly asked questions http://www.broadinstitute.org/gatk
    ERROR
    ERROR MESSAGE: Invalid command line: Failed to load reference dictionary
    ERROR ------------------------------------------------------------------------------------------

    ... so I need to load the reference dictionary. I'm going to your forum because I don't know what it is

    Post edited by Tiphaine on
  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie admin

    Hi Tiphaine, these kinds of very basic questions are largely addressed in the documentation (Guide section). Please check it out and try to find the answers yourself as much as possible. Good luck!

  • TiphaineTiphaine Member

    It is ok, I found it. thanks

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