Have you checked the FAQ? https://github.com/google/deepvariant/blob/r1.6/docs/FAQ.md:

Describe the issue:
When variant is not detected, the program will freeze in the last step；

Setup

• Operating system:Centos7.6
• DeepVariant version: 1.6
• Installation method (Docker, built from source, etc.): singularity
• Type of data: (sequencing instrument, reference genome, anything special that is unlike the case studies?) PACBIO-SMART；A reference sequence for a normal person；

Steps to reproduce:

• Command: /bin/singularity run -B /work/:/work/ /work/deepvariant.sif /opt/deepvariant/bin/run_deepvariant --model_type=PACBIO --ref=human_geneA_reference.fa --reads=reference.align.bam --output_vcf=out.vcf --output_gvcf=out.gvcf --num_shards=32
• Error trace: Last line： I0119 11:43:53.450599 47012502976320 call_variants.py:623] Complete: call_variants（Stuck at this step）.

Does the quick start test work on your system?
Please test with https://github.com/google/deepvariant/blob/r1.6/docs/deepvariant-quick-start.md.
Is there any way to reproduce the issue by using the quick start?

Any additional context:

deepvariant_1.6.pdf