Running GenomicsDBImport/CombineGVCFs on Azure leads to User Error: Illegal argument value
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 "\"
-
Solved by getting rid of the "\" within the command section.
-
hi Martin Danner,
May I know which part of the script you delete the '\'? delete all these '\' in the following part?
~{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
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