Error in pbrun deepvariant_germline command. (with --prealign-helper-thread option)

Hi,
I am using pbrun deepvariant_germline command (with --prealign-helper-thread option):
(NVIDIA Parabricks Container 4.2.0-1)

pbrun deepvariant_germline
–prealign-helper-thread
–ref /workdir/parabricks_sample/Ref/Homo_sapiens_assembly38.fasta
–in-fq /workdir/parabricks_sample/Data/sample_1.fq.gz
/workdir/parabricks_sample/Data/sample_2.fq.gz
–out-variants /outputdir/deepvariant_germline.vcf
–out-bam /outputdir/deepvariant_germline.bam

I get the following output (message):

usage: pbrun deepvariant
Help: pbrun deepvariant -h
pbrun: error: unrecognized arguments: --prealign_helper_thread

Wrong option?
Please advise.

Hi @M.Fukasawa,

I am running the same command as you with the same data, but I’m not having issues with that flag.

Input files

DOCKER_IMAGE=“nvcr.io/nvidia/clara/clara-parabricks:4.2.0-1
DATA_DIR=“/home/me/parabricks/parabricks_sample”
SAMPLE_1=“${DATA_DIR}/Data/sample_1.fq.gz”
SAMPLE_2=“${DATA_DIR}/Data/sample_2.fq.gz”
REF=“${DATA_DIR}/Ref/Homo_sapiens_assembly38.fasta”

Output files

OUT_DIR=“${DATA_DIR}/output”
OUT_BAM=“${OUT_DIR}/output.bam”
OUT_VCF=“${OUT_DIR}/output.vcf”

docker run -v ${DATA_DIR}:${DATA_DIR}
-w ${DATA_DIR}
–gpus all
${DOCKER_IMAGE}
pbrun deepvariant_germline
–ref ${REF}
–in-fq ${SAMPLE_1} ${SAMPLE_2}
–prealign-helper-thread
–out-bam ${OUT_BAM}
–out-variants ${OUT_VCF}

Can you confirm that your entire script looks like this?

Hi @gburnett, Thank you for your answer.
I did what you instructed me to do, but the result was the same. :(
deepvariant_germline.log (22.1 KB)

Please check this log. (especially the last 3 lines)

There should be dashes instead of udnerscores:

–prealign-helper-thread not --prealign_helper_thread