Getting "ValueError: NOT_FOUND: Could not open" when running the DeepVariant pipeline
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10 weeks ago
langziv ▴ 20

Hi.
I followed the instruction on how to use DeepVariant with docker, and used the following command:

BIN_VERSION="1.4.0"
sudo docker run \
  -v "input":"/input" \
  -v "output":"/output" \
  google/deepvariant:"${BIN_VERSION}" \
  /opt/deepvariant/bin/run_deepvariant \
  --model_type=WES \
  --ref=/input/GCF_000001405.26_GRCh38_genomic1.fa.gz \
  --reads=/input/1115492_23181_0_0.cram \
  --regions "chr3:10,049,322-10,156,156" \
  --output_vcf=/output/output.vcf.gz \
  --output_gvcf=/output/output.g.vcf.gz \
  --num_shards=5 

Does anyone has an idea why I might be getting this error?
Thanks.

variant-calling DeepVariant docker • 418 views
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Don't know the exact problem here, but it may not be a good idea to run docker as sudo. That is in fact how they suggest it for this program. Beyond that, an obvious thing to check is whether all your input files are present, and whether you have the permission to write in output directory.

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Thanks. The problem persists.

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this question was already solved. Crosspost

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