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problem in UnifiedGenotyper

mahyarheymahyarhey BostonPosts: 50Member
edited October 2013 in Ask the GATK team

I run the UnifiedGenotyper with 3 samples. After almost 4 hours I got the following ERROR. What is this error mean? How I can to fix the problem? Thanks

ERROR ------------------------------------------------------------------------------------------
ERROR A GATK RUNTIME ERROR has occurred (version 2.2-4-g4a174fb):
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: -1 does not represent a valid base character
Post edited by Geraldine_VdAuwera on

Answers

  • Geraldine_VdAuweraGeraldine_VdAuwera Posts: 7,533Administrator, GATK Developer admin

    Hi Mahyar,

    Can you please post the full stack trace? The stack trace is the part of the console output that details the problem, just before the ERROR block.

    Geraldine Van der Auwera, PhD

  • mahyarheymahyarhey BostonPosts: 50Member

    Hi Geraldine,
    Unfortunately, I deleted the log file.

  • Geraldine_VdAuweraGeraldine_VdAuwera Posts: 7,533Administrator, GATK Developer admin

    Then I'm afraid you'll have to re-run it. Try running with -l DEBUG, it will give more information about what is wrong. Be sure to save the log file, as I can't do anything without that information.

    Geraldine Van der Auwera, PhD

  • mahyarheymahyarhey BostonPosts: 50Member

    Hi Geraldine,
    I run the UnifiedGenotyper for my all 42 samples and I got the VCF file for all sites. In the 4th column of the VCF file I have QUAL-value which is range between 0 to 25000. What would be the threshold of selection QUAL. (e.g. 50, 100, 1000, etc). Please advise>thanks

  • Geraldine_VdAuweraGeraldine_VdAuwera Posts: 7,533Administrator, GATK Developer admin

    Please read the Best Practices documentation > http://www.broadinstitute.org/gatk/guide/best-practices

    Geraldine Van der Auwera, PhD

  • mahyarheymahyarhey BostonPosts: 50Member

    Hi Gerladine, I Used "HaplotypeCaller" for calling variant of one of my Bam file. However, after 3 hours it created the VCF file, but there is no information in the file and just heading. In below, you can see my commands: What is wrong? please advise, Thanks

    java -jar GenomeAnalysisTK-2.2-4/GenomeAnalysisTK.jar
    -R ucsc.hg19.fasta
    -T HaplotypeCaller
    -I 15V_post_reorder_GROUP.rg.bam
    --dbsnp dbsnp_137.hg19.vcf
    -gt_mode GENOTYPE_GIVEN_ALLELES
    -out_mode EMIT_ALL_SITES
    --out 15V_post_afterQC.vcf

  • Geraldine_VdAuweraGeraldine_VdAuwera Posts: 7,533Administrator, GATK Developer admin

    Hi @mahyarhey,

    For one thing, you set HC to genotype given alleles, but didn't provide any alleles. That doesn't explain why you have no output though -- did the run complete without error? It can be helpful to post the output log.

    Geraldine Van der Auwera, PhD

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