Variant Transforms returns same bug please resolve

[hze...@gmail.com]

Dear GCP Lifesciences team

variant transforms returns error please resolve this the configurations area as under

#!/bin/bash

# Parameters to replace:

# The GOOGLE_CLOUD_PROJECT is the project that contains your BigQuery dataset.

GOOGLE_CLOUD_PROJECT=genomic-analysis-255208

INPUT_PATTERN=gs://genomic-analysis-255208-vtgenomics/*.vcf

OUTPUT_TABLE=genomic-analysis-255208:genomicscovid19.deep_variant

TEMP_LOCATION=gs://genomic-analysis-255208-vtgenomics/temp

COMMAND="vcf_to_bq \

    --input_pattern ${INPUT_PATTERN} \

    --output_table ${OUTPUT_TABLE} \

    --temp_location ${TEMP_LOCATION} \

    --job_name vcf-to-bigquery \

    --runner DataflowRunner"

docker run -v ~/.config:/root/.config \

    gcr.io/cloud-lifesciences/gcp-variant-transforms \

    --project "${GOOGLE_CLOUD_PROJECT}" \

    --zones us-west1-b \

    "${COMMAND}"

the error details are:

getopt: unrecognized option '--zones' --project 'genomic-analysis-255208' -- 'us-west1-b' 'vcf_to_bq --input_pattern gs://genomic-analysis-255208-vtgenomics/*.vcf --output_table genomic-analysis-255208:genomicscovid19.deep_variant --temp_location gs://genomic-analysis-255208-vtgenomics/temp --job_name vcf-to-bigquery --runner DataflowRunner'

if replaced by region as --region us-central1  and at link of dataflow it said worker-regionor worker-zone to be used because zone is depreciated that is in a link :

https://cloud.google.com/sdk/gcloud/reference/dataflow/jobs/run

then it returns error

--project 'genomic-analysis-255208' --region 'us-central1' -- 'vcf_to_bq --input_pattern gs://genomic-analysis-255208-vtgenomics/*.vcf --output_table genomic-analysis-255208:genomicscovid19.deep_variant --temp_location gs://genomic-analysis-255208-vtgenomics/temp --job_name vcf-to-bigquery --runner DataflowRunner'

Please set the temp_location using flag --temp_location.

is it bug in variant transforms

on the other hand,

while  https://www.qwiklabs.com/focuses/10210?parent=catalog

running lab it returns no error

so tell me what is the problem

because i followed the links

https://cloud.google.com/life-sciences/docs/how-tos/load-variants

https://cloud.google.com/life-sciences/docs/how-tos/vcf-preprocessor

thanks in advance

Haroon Zeb Khan

[Saman Vaisipour]

Hi Haroon,

You need to update your command as follows:

COMMAND="vcf_to_bq \
    --input_pattern ${INPUT_PATTERN} \
    --output_table ${OUTPUT_TABLE} \

    --job_name vcf-to-bigquery \
    --runner DataflowRunner"

docker run -v ~/.config:/root/.config \
    gcr.io/cloud-lifesciences/gcp-variant-transforms \
    --project "${GOOGLE_CLOUD_PROJECT}" \

    --temp_location ${TEMP_LOCATION} \
    --region us-west1 \
    "${COMMAND}"

 

Note there are two changes:

• Instead of --zones in your docker run command you need to set a GCP region using --region (here I used us-west1).
• The temp_location flag must be set in the docker run command instead of your COMMAND.

Please follow these instructions for more information on how to run Variant Transforms.

Thanks for letting us know about those outdated documents, we will update them soon.

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Saman Vaisipour |

Software Eng |

sam...@google.com |

519-513-5756