Errors on testing DeepTrio on PacBio samples about deepvariant

[kishwarshafin]

@aheravi ,

Can you please share the command you are using?

[aheravi]

Hi @kishwarshafin ,
Here is the command I used:

BIN_VERSION="1.6.0"

singularity run -B /deepvariant/ \
  docker://google/deepvariant:deeptrio-"${BIN_VERSION}" \
  /opt/deepvariant/bin/deeptrio/run_deeptrio \
  --model_type PACBIO \
  --ref ./reference/GRCh38_no_alt_analysis_set.fasta \
  --reads_child ./input/HG002.pfda_challenge.grch38.phased.chr20.bam \
  --reads_parent1 ./input/HG003.pfda_challenge.grch38.phased.chr20.bam \
  --reads_parent2 ./input/HG004.pfda_challenge.grch38.phased.chr20.bam \
  --output_vcf_child ./output/HG002.output.vcf.gz \
  --output_vcf_parent1 ./output/HG003.output.vcf.gz \
  --output_vcf_parent2 ./output/HG004.output.vcf.gz \
  --sample_name_child 'HG002' \
  --sample_name_parent1 'HG003' \
  --sample_name_parent2 'HG004' \
  --num_shards $(nproc) \
  --intermediate_results_dir ./output/intermediate_results_dir \
  --output_gvcf_child ./output/HG002.g.vcf.gz \
  --output_gvcf_parent1 ./output/HG003.g.vcf.gz \
  --output_gvcf_parent2 ./output/HG004.g.vcf.gz \
  --regions chr20

[kishwarshafin]

@aheravi ,

Just to see if it works, can you please run the command without using:

--intermediate_results_dir ./output/intermediate_results_dir

And see if it works? Meanwhile, I will try to reproduce it locally.

[aheravi]

Thanks, @kishwarshafin.
Sounds working.