gcsfuse: command not found

[case3526]

Model for calling whole genome sequencing data.

MODEL=gs://deepvariant/models/DeepVariant/0.8.0/DeepVariant-inception_v3-0.8.0+data-wgs_standard IMAGE_VERSION=0.8.0 DOCKER_IMAGE=gcr.io/deepvariant-docker/deepvariant:"${IMAGE_VERSION}" COMMAND="/opt/deepvariant_runner/bin/gcp_deepvariant_runner \ --project ${PROJECT_ID} \ --zones us-west1-* \ --docker_image ${DOCKER_IMAGE} \ --outfile ${OUTPUT_BUCKET}/${OUTPUT_FILE_NAME} \ --gvcf_outfile ${OUTPUT_BUCKET}/${OUTPUT_gVCF_FILE_NAME} \ --staging ${OUTPUT_BUCKET}/${STAGING_FOLDER_NAME} \ --model ${MODEL} \ --bam gs://files_jays/bam/bqsr.realign.markdup.sorted.merged.bam \ --bai gs://files_jays/bam/bqsr.realign.markdup.sorted.merged.bai \ --ref gs://genomics-public-data/references/GRCh38_Verily/GRCh38_Verily_v1.genome.fa \ --shards 512 \ --make_examples_workers 32 \ --make_examples_cores_per_worker 16 \ --make_examples_ram_per_worker_gb 60 \ --make_examples_disk_per_worker_gb 200 \ --call_variants_workers 32 \ --call_variants_cores_per_worker 32 \ --call_variants_ram_per_worker_gb 60 \ --call_variants_disk_per_worker_gb 50 \ --preemptible \ --max_preemptible_tries 5 \ --gcsfuse"

Run the pipeline.

gcloud alpha genomics pipelines run \ --project "${PROJECT_ID}" \ --service-account-scopes="https://www.googleapis.com/auth/cloud-platform" \ --logging "${OUTPUT_BUCKET}/${STAGING_FOLDER_NAME}/runnerlogs$(date +%Y%m%d_%H%M%S).log" \ --regions us-west1 \ --docker-image gcr.io/cloud-genomics-pipelines/gcp-deepvariant-runner \ --command-line "${COMMAND}"

logs on one of the VMs

/bin/bash: gcsfuse: command not found parallel: This job failed: mkdir -p ./input-gcsfused-0 && gcsfuse --implicit-dirs files_jays /input-gcsfused-0 /bin/bash: gcsfuse: command not found parallel: This job failed: mkdir -p ./input-gcsfused-1 && gcsfuse --implicit-dirs files_jays /input-gcsfused-1 /bin/bash: gcsfuse: command not found

[HagenC]

Just a guess- but add a white-space after --gcsfuse and " so i becomes --gcsfuse ", not --gcfuse".

[samanvp]

This is known issue, we will be releasing a new docker image later this week that will resolve it.

[case3526]

Thanks @samanvp!

[samanvp]

We just released a new docker image located at gcr.io/cloud-lifesciences/gcp-deepvariant-runner. Please let us know if you still observe gcsfuse issue using the latest release.