pangenome-aware-wgs-bwa-case doesn't run successfully.

[Jiawei-Shen]

I followed the pangenome-aware-wgs-bwa-case-study.md to run the code.
But since I am using LSF (Load Sharing Facility) cluster, I change the code

mkdir -p output
mkdir -p output/intermediate_results_dir

BIN_VERSION="pangenome_aware_deepvariant-1.8.0"

sudo docker pull google/deepvariant:"${BIN_VERSION}"

sudo docker run \
  -v "${PWD}/input":"/input" \
  -v "${PWD}/output":"/output" \
  -v "${PWD}/reference":"/reference" \
  --shm-size 12gb \
  google/deepvariant:"${BIN_VERSION}" \
  /opt/deepvariant/bin/run_pangenome_aware_deepvariant \
  --model_type WGS \
  --ref /reference/GRCh38_no_alt_analysis_set.fasta \
  --reads /input//HG003.novaseq.pcr-free.35x.dedup.grch38_no_alt.chr20.bam  \
  --pangenome /input/hprc-v1.1-mc-grch38.gbz \
  --output_vcf /output/HG003.output.vcf.gz \
  --output_gvcf /output/HG003.output.g.vcf.gz \
  --num_shards $(nproc) \
  --regions chr20 \
  --intermediate_results_dir /output/intermediate_results_dir

to

export LSF_DOCKER_SHM_SIZE=64g
bsub -Is -G compute-epigenome-condo -R 'gpuhost' -gpu "num=1" -q epigenome-interactive \
  -a 'docker(google/deepvariant:pangenome_aware_deepvariant-1.8.0)' \
  /opt/deepvariant/bin/run_pangenome_aware_deepvariant \
    --model_type WGS \
    --ref /reference/GRCh38_no_alt_analysis_set.fasta \
    --reads /input/HG003.novaseq.pcr-free.35x.dedup.grch38_no_alt.chr20.bam \
    --pangenome /input/hprc-v1.1-mc-grch38.gbz \
    --output_vcf /output/HG003.output.vcf.gz \
    --output_gvcf /output/HG003.output.g.vcf.gz \
    --num_shards 16 \
    --regions chr20 \
    --intermediate_results_dir /output/intermediate_results_dir

But the terminal outputs:

and no other outputs then.

I checked the share_memeory and it crushed like this.:

Do you know why this doesn't work?

[kishwarshafin]

Hi @Jiawei-Shen can you please share the full log? It doesn't look like the memory loading crashed, those are warnings that can be ignored. Are you seeing make_examples fail?

[kishwarshafin]

I am closing this issue due to inactivity. Please feel free to reopen.