"No positional argument is defined" Error in HaplotypeCaller
Hi there,
I am trying to run HaplotypeCaller on some bam files, using this command:
./gatk HaplotypeCaller \
- R Rflav_transcriptome_sequences.fa \
- I SRR5341585.bam \
- O 85variants.g.vcf \
- ERC GVCF
but on the first bam file I tried to do, I am received this error:
A USER ERROR has occurred: 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.
GATK version: 4.1.9.0
Any ideas on how to fix this? Thank you!
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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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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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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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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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Julianne Radford great! Thank you for posting your solution, I am sure it will be helpful for other GATK users.
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