Error message when running a GATK SelectVariants: no positional argument is defined for this tool

Question

[mohsamir2016]

Dear all,

I am stuck at one step in whihc I am trying to select SNPs or INDELS from a raw VCF file. I have used this comand

gatk SelectVariants \
 -R Ref/GCF_000002315.5_GRCg6a_genomic.fna\
 -V Raw_variant/ L11A_rawvariant.vcf\
 --select-type-to-include SNP \
 -O Raw_variant/ L11A_SNP.vcf

When I run this line, I got an error :

A USER ERROR has occurred: Illegal argument value: Positional arguments were provided ',L11A_rawvariant.vcf{L11A_SNP.vcf}' but no positional argument is defined for this tool.

Below it it says

Set the system property GATK_STACKTRACE_ON_USER_EXCEPTION (--java-options '-DGATK_STACKTRACE_ON_USER_EXCEPTION=true') to print the stack trace.

Could you please explain to me what this means. I checked the recent documentation of GATK for current version (4.4.0) also for my version 4.3.0, but it did not say anything, and it also recommend writing the code the way I have done as shown in this link for the recent GATK https://gatk.broadinstitute.org/hc/en-us/articles/13832694334235-SelectVariants

Could you please help me fix this ? What do I need to include ?

I tried to get the stack trace, by running --java-options '-DGATK_STACKTRACE_ON_USER_EXCEPTION=true' but it says

--java-options: command not found

Thanks

Answer 1

[GenoMax]

-O Raw_variant/ L11A_SNP.vcf

You appear to have an extra space between the variant/ and L11. Remove that.

[mohsamir2016]

Hi, I tried it now with no space, but it pops up the same error. There should be another thing, ...!

[GenoMax]

Raw_variant/ L11A_rawvariant.vcf

Another extra space in this option.

[mohsamir2016]

Thank you... that was the problem ...Extra space. Thanks

[Ram]

Accept GenoMax's answer to mark this post as solved.