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Variant Discovery in High-Throughput Sequencing Data

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Developed in the Data Sciences Platform at the Broad Institute, the toolkit offers a wide variety of tools with a primary focus on variant discovery and genotyping. Its powerful processing engine and high-performance computing features make it capable of taking on projects of any size. Learn more

"No positional argument is defined" Error in HaplotypeCaller

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    Genevieve Brandt (she/her)

    Hi Julianne Radford,

    Could you share your complete stack trace so we can look into your issue further?

    Please see this resource: https://gatk.broadinstitute.org/hc/en-us/articles/360053424571-How-to-Write-a-Post

    Genevieve

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    Julianne Radford

    Hi Genevieve Brandt (she/her)

    Yes thank you for replying. Here is the stack trace: 

    org.broadinstitute.barclay.argparser.CommandLineException$BadArgumentValue: Illegal argument value: Positional arguments were provided ',-{R{Rflav_transcriptome_sequences.fa{-{I{SRR5341585.bam{-{O{85variants.g.vcf{-{ERC{GVCF}' but no positional argument is defined for this tool.

    at org.broadinstitute.barclay.argparser.CommandLineArgumentParser.propagateParsedValues(CommandLineArgumentParser.java:507)

    at org.broadinstitute.barclay.argparser.CommandLineArgumentParser.parseArguments(CommandLineArgumentParser.java:170)

    at org.broadinstitute.hellbender.cmdline.CommandLineProgram.parseArgs(CommandLineProgram.java:233)

    at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:207)

    at org.broadinstitute.hellbender.Main.runCommandLineProgram(Main.java:160)

    at org.broadinstitute.hellbender.Main.mainEntry(Main.java:203)

    at org.broadinstitute.hellbender.Main.main(Main.java:289)


    Julianne

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    Genevieve Brandt (she/her)

    Hi Julianne Radford, could you include the entire stack trace, not just the error message? use --java-options '-DGATK_STACKTRACE_ON_USER_EXCEPTION=true' to see the entire stack trace.

    Thanks,

    Genevieve

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    Julianne Radford

    Hi Genevieve Brandt (she/her)

    I fixed the issue. I had a space between "-" and the characters (i.e. R, I, O, ERC). By deleting the space this resolved that problem.

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    Genevieve Brandt (she/her)

    Julianne Radford great! Thank you for posting your solution, I am sure it will be helpful for other GATK users.

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