Name Tag Error while running Base Recaliberator

Hi!

I am running into an error while running BaseRecaliberator, I also googled it up and tried a lot of suggestion but nothing helped.

Here is what I am doing:

java -jar GenomeAnalysisTK.jar -T BaseRecalibrator -R hg19.fa -I Realigned_Mydata.sort.MarkDup.RG.bam -knownSites dbsnp_137.hg19.vcf.done -knownSites Mills_and_1000G_gold_standard.indels.hg19.vcf -o Recal.table_289

The error that I get is

INFO  09:53:40,686 HelpFormatter - -------------------------------------------------------------------------------- 
INFO  09:53:40,703 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.2-2-gec30cee, Compiled 2014/07/17 15:22:03 
INFO  09:53:40,706 HelpFormatter - Copyright (c) 2010 The Broad Institute 
INFO  09:53:40,709 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk 
INFO  09:53:40,746 HelpFormatter - Program Args: -T BaseRecalibrator -R hg19.fa -I Realigned_Mydata.sort.MarkDup.RG.bam -knownSites dbsnp_137.hg19.vcf.done -knownSites Mills_and_1000G_gold_standard.indels.hg19.vcf -o Recal.table_289 
INFO  09:53:40,765 HelpFormatter - Executing as [email protected] on Linux 3.12.21-gentoo-r1 amd64; Java HotSpot(TM) 64-Bit Server VM 1.7.0_55-b13. 
INFO  09:53:40,767 HelpFormatter - Date/Time: 2014/08/29 09:53:40 
INFO  09:53:40,768 HelpFormatter - -------------------------------------------------------------------------------- 
INFO  09:53:40,769 HelpFormatter - -------------------------------------------------------------------------------- 
INFO  09:53:49,753 GATKRunReport - Uploaded run statistics report to AWS S3 
##### ERROR ------------------------------------------------------------------------------------------
##### ERROR A USER ERROR has occurred (version 3.2-2-gec30cee): 
##### ERROR
##### ERROR This means that one or more arguments or inputs in your command are incorrect.
##### ERROR The error message below tells you what is the problem.
##### ERROR
##### ERROR If the problem is an invalid argument, please check the online documentation guide
##### ERROR (or rerun your command with --help) to view allowable command-line arguments for this tool.
##### ERROR
##### ERROR Visit our website and forum for extensive documentation and answers to 
##### ERROR commonly asked questions http://www.broadinstitute.org/gatk
##### ERROR
##### ERROR Please do NOT post this error to the GATK forum unless you have really tried to fix it yourself.
##### ERROR
##### ERROR MESSAGE: Invalid command line: No tribble type was provided on the command line and the type of the file could not be determined dynamically. Please add an explicit type tag :NAME listing the correct type from among the supported types:
##### ERROR          Name        FeatureType   Documentation
##### ERROR          BCF2     VariantContext   (this is an external codec and is not documented within GATK)
##### ERROR        BEAGLE      BeagleFeature   (this is an external codec and is not documented within GATK)
##### ERROR           BED         BEDFeature   (this is an external codec and is not documented within GATK)
##### ERROR      BEDTABLE       TableFeature   (this is an external codec and is not documented within GATK)
##### ERROR EXAMPLEBINARY            Feature   (this is an external codec and is not documented within GATK)
##### ERROR      GELITEXT    GeliTextFeature   (this is an external codec and is not documented within GATK)
##### ERROR      OLDDBSNP    OldDbSNPFeature   (this is an external codec and is not documented within GATK)
##### ERROR     RAWHAPMAP   RawHapMapFeature   (this is an external codec and is not documented within GATK)
##### ERROR        REFSEQ      RefSeqFeature   (this is an external codec and is not documented within GATK)
##### ERROR     SAMPILEUP   SAMPileupFeature   (this is an external codec and is not documented within GATK)
##### ERROR       SAMREAD     SAMReadFeature   (this is an external codec and is not documented within GATK)
##### ERROR         TABLE       TableFeature   (this is an external codec and is not documented within GATK)
##### ERROR           VCF     VariantContext   (this is an external codec and is not documented within GATK)
##### ERROR          VCF3     VariantContext   (this is an external codec and is not documented within GATK)
##### ERROR ------------------------------------------------------------------------------------------

Please suggest an edit in the command to fix this.

Thank you

Best Answer

Answers

  • My suggestion is to use -knownSites dbsnp_137.hg19.vcf instead of -knownSites dbsnp_137.hg19.vcf.done

  • AbhisheknlAbhisheknl NetherlandsMember

    It still throws up the same error :(

  • AbhisheknlAbhisheknl NetherlandsMember

    Now, the explaination you gave was helpful. Indeed very helpful, the first file was having problem, it runs fine now. Hope to see the results soon.

  • ibseqibseq United KingdomMember

    @pdexheimer said:
    Huh. That error means that GATK couldn't figure out the format of one of the RODs you gave it (in this case, the only RODs are the ones specified via -knownSites). Since both of them now have an extension of vcf, that means that one of them doesn't "look like" a VCF. First step is to narrow down which file is the problem (by running the command with only one file at a time), and then to examine that file and figure out why it looks wrong - Is it actually a compressed file, for instance?

    Hello
    got the same error by running :
    not sure if i can use a list for my bam as I would like to do the recalibration with all my samples at the same time.
    any advice?

    error log:
    INFO 08:33:35,999 HelpFormatter - --------------------------------------------------------------------------------
    INFO 08:33:36,002 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.3-0-g37228af, Compiled 2014/10/24 01:07:22
    INFO 08:33:36,003 HelpFormatter - Copyright (c) 2010 The Broad Institute
    INFO 08:33:36,003 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
    INFO 08:33:36,009 HelpFormatter - Program Args: -T BaseRecalibrator -R ../newpacbio.fasta -I bam.list -knownSites known.vcf -o recalibration.table
    INFO 08:33:36,012 HelpFormatter - Executing as [email protected] on Linux 3.2.0-105-generic amd64; Java HotSpot(TM) 64-Bit Server VM 1.7.0_07-b10.
    INFO 08:33:36,014 HelpFormatter - Date/Time: 2017/02/13 08:33:35
    INFO 08:33:36,015 HelpFormatter - --------------------------------------------------------------------------------
    INFO 08:33:36,015 HelpFormatter - --------------------------------------------------------------------------------

    ERROR ------------------------------------------------------------------------------------------
    ERROR A USER ERROR has occurred (version 3.3-0-g37228af):
    ERROR
    ERROR This means that one or more arguments or inputs in your command are incorrect.
    ERROR The error message below tells you what is the problem.
    ERROR
    ERROR If the problem is an invalid argument, please check the online documentation guide
    ERROR (or rerun your command with --help) to view allowable command-line arguments for this tool.
    ERROR
    ERROR Visit our website and forum for extensive documentation and answers to
    ERROR commonly asked questions http://www.broadinstitute.org/gatk
    ERROR
    ERROR Please do NOT post this error to the GATK forum unless you have really tried to fix it yourself.
    ERROR
    ERROR MESSAGE: Invalid command line: No tribble type was provided on the command line and the type of the file could not be determined dynamically. Please add an explicit type tag :NAME listing the correct type from among the supported types:
    ERROR Name FeatureType Documentation
    ERROR BCF2 VariantContext (this is an external codec and is not documented within GATK)
    ERROR BEAGLE BeagleFeature (this is an external codec and is not documented within GATK)
    ERROR BED BEDFeature (this is an external codec and is not documented within GATK)
    ERROR BEDTABLE TableFeature (this is an external codec and is not documented within GATK)
    ERROR EXAMPLEBINARY Feature (this is an external codec and is not documented within GATK)
    ERROR GELITEXT GeliTextFeature (this is an external codec and is not documented within GATK)
    ERROR OLDDBSNP OldDbSNPFeature (this is an external codec and is not documented within GATK)
    ERROR RAWHAPMAP RawHapMapFeature (this is an external codec and is not documented within GATK)
    ERROR REFSEQ RefSeqFeature (this is an external codec and is not documented within GATK)
    ERROR SAMPILEUP SAMPileupFeature (this is an external codec and is not documented within GATK)
    ERROR SAMREAD SAMReadFeature (this is an external codec and is not documented within GATK)
    ERROR TABLE TableFeature (this is an external codec and is not documented within GATK)
    ERROR VCF VariantContext (this is an external codec and is not documented within GATK)
    ERROR VCF3 VariantContext (this is an external codec and is not documented within GATK)
    ERROR ------------------------------------------------------------------------------------------

    (END)

    thanks
    ibseq

  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie

    Yes you can give BaseRecalibrator a list of bams. But that has nothing to do with VCF format errors. What is actually the problem you encountered here?

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