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ASEReadCounter not accepting VCF file as input

I'm trying to run ASEReadCounter, but it's not accepting a VCF file as input. I'm getting the following error:

##### ERROR MESSAGE: Invalid command line: No tribble type was provided on the command line and the type of the file '/gpfs/commons/home/phoffman/ALS/2019_06/ase/vcfs/CGND-HRA-00013_header.vcf.gz' 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  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 ------------------------------------------------------------------------------------------

I've tried searching for a way to solve this, but nothing appears on either Google or the GATK Forum that actually fixes the error.

Answers

  • bshifawbshifaw Member, Broadie, Moderator admin
    edited September 25

    Hi @mojaveazure

    Please provide the full error stacktrace as well as the exact command.
    You may want to try validating the vcf with ValidateVariants

  • mojaveazuremojaveazure New YorkMember
    Running ASEReadCounter
    INFO  23:40:13,245 HelpFormatter - -------------------------------------------------------------------------------- 
    INFO  23:40:13,249 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.7-0-gcfedb67, Compiled 2016/12/12 11:21:18 
    INFO  23:40:13,249 HelpFormatter - Copyright (c) 2010-2016 The Broad Institute 
    INFO  23:40:13,249 HelpFormatter - For support and documentation go to https://software.broadinstitute.org/gatk 
    INFO  23:40:13,249 HelpFormatter - [Tue Sep 24 23:40:13 EDT 2019] Executing on Linux 3.10.0-957.el7.x86_64 amd64 
    INFO  23:40:13,249 HelpFormatter - Java HotSpot(TM) 64-Bit Server VM 1.8.0_45-b14 
    INFO  23:40:13,255 HelpFormatter - Program Args: -R /gpfs/commons/home/phoffman/ssc/reference/GRCh38_canonical_chromosomes_only_prim
    INFO  23:40:13,260 HelpFormatter - Executing as [email protected] on Linux 3.10.0-957.el7.x86_64 amd64; Java HotSp
    INFO  23:40:13,261 HelpFormatter - Date/Time: 2019/09/24 23:40:13 
    INFO  23:40:13,261 HelpFormatter - -------------------------------------------------------------------------------- 
    INFO  23:40:13,261 HelpFormatter - -------------------------------------------------------------------------------- 
    ##### ERROR ------------------------------------------------------------------------------------------
    ##### ERROR A USER ERROR has occurred (version 3.7-0-gcfedb67): 
    ##### 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 https://software.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 '/gpfs/commons/
    ##### ERROR Name      FeatureType   Documentation
    ##### ERROR BCF2   VariantContext   (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 ------------------------------------------------------------------------------------------
    

    ValidateVariants provides the same error

    INFO  11:28:46,732 HelpFormatter - --------------------------------------------------------------------------------- 
    INFO  11:28:46,736 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.7-0-gcfedb67, Compiled 2016/12/12 11:21:18 
    INFO  11:28:46,736 HelpFormatter - Copyright (c) 2010-2016 The Broad Institute 
    INFO  11:28:46,736 HelpFormatter - For support and documentation go to https://software.broadinstitute.org/gatk 
    INFO  11:28:46,736 HelpFormatter - [Wed Sep 25 11:28:46 EDT 2019] Executing on Linux 3.10.0-957.1.3.el7.x86_64 amd64 
    INFO  11:28:46,736 HelpFormatter - Java HotSpot(TM) 64-Bit Server VM 1.8.0_45-b14 
    INFO  11:28:46,739 HelpFormatter - Program Args: -T ValidateVariants --variant vcfs/CGND-HRA-00532_header.vcf.gz 
    INFO  11:28:46,744 HelpFormatter - Executing as [email protected] on Linux 3.10.0-957.1.3.el7.x86_64 amd64; Java HotSpot(TM) 64-Bit Server VM 1.8.0_45-b14. 
    INFO  11:28:46,745 HelpFormatter - Date/Time: 2019/09/25 11:28:46 
    INFO  11:28:46,745 HelpFormatter - --------------------------------------------------------------------------------- 
    INFO  11:28:46,745 HelpFormatter - --------------------------------------------------------------------------------- 
    ##### ERROR ------------------------------------------------------------------------------------------
    ##### ERROR A USER ERROR has occurred (version 3.7-0-gcfedb67): 
    ##### 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 https://software.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 'vcfs/CGND-HRA-00532_header.vcf.gz' 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  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 ------------------------------------------------------------------------------------------
    
  • bshifawbshifaw Member, Broadie, Moderator admin

    This looks like GATK3, please use the latest version of GATK4 and let us know if you still come across the same error.

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