Hi everyone,

first of all thank you for your your amazing work providing and maintaining a tool like GATK. Since I am pretty new to the field I wanted to try running my first workflow on Microsoft Azure. To be more precise I tried to run a GenomicsDBImport Task as shown in the below .wdl file. After a while I am always running into the same User Error: 

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

Regardless of how I change my command within my task I cant get it to run and therefore reaching out to the community for some help or ideas. 

Many thank in advance!

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

4.4.0.0

b) Exact command used (.wdl file): 

version 1.0

workflow GenomicsDBImport {

input {

File input_patient

File input_mother

File input_father

File bed_file

String output_dir

String tmp_dir

String gatk_docker = "broadinstitute/gatk:latest"

String gatk_path = "/gatk/gatk"

}




call JoinedGenotyping {

input:

input_patient = input_patient,

input_mother = input_mother,

input_father = input_father,

bed_file = bed_file,

output_dir = output_dir,

tmp_dir = tmp_dir,

docker = gatk_docker,

gatk_path = gatk_path

}

}

task JoinedGenotyping {

input {

# Command Parameters

File input_patient

File input_mother

File input_father

File bed_file

String output_dir

String tmp_dir

String gatk_path




# Runtime Parameters

String docker

Int addtional_disk_space_gb = 10

Int machine_mem_gb = 32

Int preemptible_attempts = 3




Int disk_space_gb = 40 + addtional_disk_space_gb

}

command {

~{gatk_path} --java-options "-Xmx16g -Xms16g" \

GenomicsDBImport \

    -V ~{input_patient} \

    -V ~{input_mother} \

    -V ~{input_father} \

    --genomicsdb-workspace-path ~{output_dir} \

    --tmp-dir ~{tmp_dir} \

    -L ~{bed_file} \

    --merge-input-intervals true \

    --max-num-intervals-to-import-in-parallel 1000 \

    --verbosity DEBUG
}

runtime {

docker: docker

memory: machine_mem_gb + " GB"

disk: disk_space_gb + " GB"

preemptible: true

maxRetries: preemptible_attempts

}

}

c) Entire program log (in stderr):

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

***********************************************************************
Set the system property GATK_STACKTRACE_ON_USER_EXCEPTION (--java-options '-DGATK_STACKTRACE_ON_USER_EXCEPTION=true') to print the stack trace.
Using GATK jar /gatk/gatk-package-4.4.0.0-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 -Xmx16g -Xms16g -jar /gatk/gatk-package-4.4.0.0-local.jar GenomicsDBImport \udcc2\udca0 \udcc2\udca0 -V /cromwell-executions/GenomicsDBImport/a2925592-9ea4-4725-a810-83f15608b220/call-JoinedGenotyping/input_patient.gvcf.gz \udcc2\udca0 \udcc2\udca0 -V /cromwell-executions/GenomicsDBImport/a2925592-9ea4-4725-a810-83f15608b220/call-JoinedGenotyping/input_father.gvcf.gz \udcc2\udca0 \udcc2\udca0 -V /cromwell-executions/GenomicsDBImport/a2925592-9ea4-4725-a810-83f15608b220/call-JoinedGenotyping/input_mother.gvcf.gz \udcc2\udca0 \udcc2\udca0 --genomicsdb-workspace-path mydatalake/output/ \udcc2\udca0 \udcc2\udca0 --tmp-dir mydatalake/tmp/ \udcc2\udca0 \udcc2\udca0 -L /cromwell-executions/GenomicsDBImport/a2925592-9ea4-4725-a810-83f15608b220/call-JoinedGenotyping/my.bed \udcc2\udca0 \udcc2\udca0 --merge-input-intervals true --max-num-intervals-to-import-in-parallel 1000 --verbosity DEBUG

Edit: I am almost sure that the highlighted parts - generated during runtime/cromwell-execution - are causing the issue. This is also true when I try to run "CombineGVCFs". It might be due to the encoding of the "\"