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google / deepsomatic

DeepSomatic is an analysis pipeline that uses a deep neural network to call somatic variants from tumor-normal and tumor-only sequencing data.
BSD 3-Clause "New" or "Revised" License
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Unsuccessful TensorSliceReader constructor: Failed to find any matching files #9

Closed lixingqiancs closed 8 months ago

lixingqiancs commented 8 months ago

I got this error when I used singularity to run deepsomatic.

tensorflow.python.framework.errors_impl.NotFoundError: Unsuccessful TensorSliceReader constructor: Failed to find any matching files for /opt/models/deepsomatic/wgs

Please give me some suggestion, thanks!

image

kishwarshafin commented 8 months ago

@lixingqiancs ,

Can you please provide the command you are running which results in this error?

lixingqiancs commented 8 months ago

@lixingqiancs ,

Can you please provide the command you are running which results in this error?

INPUT_DIR="/mnt/dt2_dc2stor_data202/my/"

singularity exec -B ${INPUT_DIR} /mnt/dt2_dc2stor_data202/my/software/deepvariant/v1.6/deepvariant_1.6.0.sif run_deepsomatic --model_type WGS --ref ${INPUT_DIR}/database/deepvariant/reference/GRCh38_no_alt_analysis_set.fasta --reads_normal=${normal_bam} --reads_tumor=${tumor_bam} --output_vcf ${workdir}/output.vcf.gz --output_gvcf ${workdir}/output.g.vcf.gz --sample_name_tumor="tumor" --sample_name_normal="normal" --num_shards $1 --logging_dir=${workdir}/logs --intermediate_results_dir ${workdir}/intermediate_results_dir

kishwarshafin commented 8 months ago

@lixingqiancs ,

Looks like a file mounting issue. call_variants can't find the model file located in /opt/. Can you please add this to your singularity command and see if that helps:

-B /usr/lib/locale/:/usr/lib/locale/
lixingqiancs commented 8 months ago

@lixingqiancs ,

Looks like a file mounting issue. call_variants can't find the model file located in /opt/. Can you please add this to your singularity command and see if that helps:

-B /usr/lib/locale/:/usr/lib/locale/

I checked the docker image. It seems don't have the somatic model. Could you help me to check?

image image

kishwarshafin commented 8 months ago

Ah, you are using the wrong docker. Sorry I missed it the first time:

Please use:

docker pull google/deepsomatic:1.6.0
lixingqiancs commented 8 months ago

Ah, you are using the wrong docker. Sorry I missed it the first time:

Please use:

docker pull google/deepsomatic:1.6.0

That's work!!! Thanks so much for your important suggestion.