VariantsToTable positional argument eror

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Owen Hudson

• December 14, 2021 17:22

If you are seeing an error, please provide(REQUIRED) :
a) GATK version used: 4.1.9.0
b) Exact command used: gatk VariantsToTable \ -V file.vcf.gz \ -F CHROM -F ID -F REF -F ALT \ -O c10output.table
c) Entire error log:

A USER ERROR has occurred: Illegal argument value: Positional arguments were provided ', -V{c10select.vcf.gz{ -F{CHROM{ -O{c10output.table}' but no positional argument is defined for this tool.

I dont know what positional arguments are provided and so don't know what to change.

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  Pamela Bretscher

  • December 15, 2021 14:31

  Hi Owen Hudson,

  This type of error generally happens when you have some sort of type in your command that prevents the tool from reading it properly, such as extra or missing spaces. From the error message, it looks like you might have an extra space before your file arguments (-F and -O). Could you check the full command you ran for any errors?

  Kind regards,

  Pamela

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