Creating dictionary for fasta reeference file

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Priyadarshini Thirunavukkarasu

• July 30, 2021 09:24
• Edited

If you are seeing an error, please provide(REQUIRED) : 
a) GATK version used: 4.2.0.0
b) Exact command used: gatk CreateSequenceDictionary GCF_000001405.26_GRCh38_genomic.fna

c) Entire error log: Illegal argument value: Positional arguments were provided ',GCF_000001405.26_GRCh38_genomic.fna}' but no positional argument is defined for this tool.
Tool returned:
1


If not an error, choose a category for your question(REQUIRED):
a)How do I (......)? 
b) What does (.Illegal argument value: Positional arguments were provided ',GCF_000001405.26_GRCh38_genomic.fna}' but no positional argument is defined for this tool.
Tool returned:
1.) mean? 
c) Why do I see (......)? 
d) Where do I find (......)? 
e) Will (......) be in future releases?

0

• 

  Genevieve Brandt (she/her)

  • August 02, 2021 18:06

  Hi Priyadarshini Thirunavukkarasu,

  When running CreateSequenceDictionary, you need to provide your reference file with the -R argument. You can read more about the CreateSequenceDictionary tool here and details on the gatk command line here.

  Hope this helps!

  Best,

  Genevieve

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