Hi All,

When executed 'interactively' from the prompt, the command below behaves as expected:

# command1
gatk SelectVariants \
-R Homo_sapiens_assembly38.fasta \
-V in.vcf.gz \
-O out.vcf.gz \
--se AAC \
--select 'vc.getGenotype("AAC0009").isCalled() && ! vc.getGenotype("AAC0009").isHomRef()'

Similarly, when executed from a shell script with 'hardcoded' SampleIDs in the JEXL statement, it produces the expected output:

#!/bin/bash -e
module load GATK/4.6.2.0
gatk --java-options '-DGATK_STACKTRACE_ON_USER_EXCEPTION=true' SelectVariants \
-R Homo_sapiens_assembly38.fasta \
-V in.vcf.gz \
-O out.vcf.gz \
--se AAC \
--select 'vc.getGenotype("AAC0009").isCalled() && ! vc.getGenotype("AAC0009").isHomRef()'

Perplexingly, susbtituting the SampleIDs in the expression produces the following error (full stack trace below):

A USER ERROR has occurred: Illegal argument value: Positional arguments were provided ',&&{!{vc.getGenotype("AAC009").isHomRef()'}' but no positional argument is defined for this tool.

#!/bin/bash -e
PROBANDID=AAC0009
SelectionExpression="'vc.getGenotype(\"$PROBANDID\").isCalled() && ! vc.getGenotype(\"$PROBANDID\").isHomRef()'"
module load GATK/4.6.2.0-foss-2023a
gatk --java-options '-DGATK_STACKTRACE_ON_USER_EXCEPTION=true' SelectVariants -R Homo_sapiens_assembly38.fasta -V in.vcf.gz -O out.vcf.gz --se AAC --select $SelectionExpression
echo "From script: >"$SelectionExpression"<" # just to check successful substitution

This depite the variable substitution (apparently) generating the corrext JEXL string (enclosed in '><' to identify leading trailing non-char):

From script: >'vc.getGenotype("AAC0009").isCalled() && ! vc.getGenotype("AAC0009").isHomRef()'<

More perplexingly, copying and executing at the prompt the command returned by SelectVariants ('Running') after executing the failing script, works fine!

# command 4
gatk SelectVariants -R Homo_sapiens_assembly38.fasta -V in.vcf.gz -O out.vcf.gz --se AAC --select 'vc.getGenotype("AAC0009").isCalled() && ! vc.getGenotype("AAC0009").isHomRef()'

Yet command1 (working fine) and is identical to command4 (what gatk 'confirmed' when the failing script (substititued SampleIDs) was executed - 'diff' comfrms identity and both work!

I can't understand why the variable substitution creates a command resulting in a GATK error, while it (apparently) has substituted OK.

Any ideas??

Many thanks in advance!

REQUIRED for all errors and issues:
a) GATK version used: 4.6.2.0

b) Exact command used: see message

c) Entire program log (failing script):

bash Extract.sh
Using GATK jar /opt/nesi/zen3/GATK/4.6.2.0-foss-2023a/gatk-package-4.6.2.0-local.jar
Running:
   java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribble=false -Dsamjdk.compression_level=2 -DGATK_STACKTRACE_ON_USER_EXCEPTION=true -jar /opt/nesi/zen3/GATK/4.6.2.0-foss-2023a/gatk-package-4.6.2.0-local.jar SelectVariants -R Homo_sapiens_assembly38.fasta -V in.vcf.gz -O out.vcf.gz --se AAC --select 'vc.getGenotype("AAC009").isCalled() && ! vc.getGenotype("AAC009").isHomRef()'
USAGE: SelectVariants [arguments]

This tool makes it possible to select a subset of variants based on various criteria in order to facilitate certain
analyses. Examples include comparing and contrasting cases vs. controls, extracting variant or non-variant loci that
meet certain requirements, or troubleshooting some unexpected results, to name a few.
Version:4.6.2.0
Required Arguments:
--output,-O <GATKPath>        Path to which variants should be written  Required.
--variant,-V <GATKPath>       A VCF file containing variants  Required.
Optional Arguments: #omitted for brevity
***********************************************************************
A USER ERROR has occurred: Illegal argument value: Positional arguments were provided ',&&{!{vc.getGenotype("AAC009").isHomRef()'}' but no positional argument is defined for this tool.
***********************************************************************
org.broadinstitute.barclay.argparser.CommandLineException$BadArgumentValue: Illegal argument value: Positional arguments were provided ',&&{!{vc.getGenotype("AAC009").isHomRef()'}' but no positional argument is defined for this tool.
        at org.broadinstitute.barclay.argparser.CommandLineArgumentParser.propagateParsedValues(CommandLineArgumentParser.java:514)
        at org.broadinstitute.barclay.argparser.CommandLineArgumentParser.parseArguments(CommandLineArgumentParser.java:170)
        at org.broadinstitute.hellbender.cmdline.CommandLineProgram.parseArgs(CommandLineProgram.java:244)
        at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:218)
        at org.broadinstitute.hellbender.Main.runCommandLineProgram(Main.java:166)
        at org.broadinstitute.hellbender.Main.mainEntry(Main.java:209)
        at org.broadinstitute.hellbender.Main.main(Main.java:306)