ValueError: NOT_FOUND: Pangenome path ids not found for pangenome sample name: GRCh38 when running run_pangenome_aware_deepvariant

[MarionPerrier]

Have you checked the FAQ? https://github.com/google/deepvariant/blob/r1.8/docs/FAQ.md: Yes

Describe the issue:
Hi!
I am trying to call variants on a non-human organism (fungi). I run for that /opt/deepvariant/bin/run_pangenome_aware_deepvariant according to the tutorial here: https://github.com/google/deepvariant/blob/r1.8/docs/pangenome-aware-wgs-vg-case-study.md, however I have this error:

Traceback (most recent call last):
  File "/tmp/Bazel.runfiles_wsluf8vf/runfiles/com_google_deepvariant/deepvariant/make_examples_pangenome_aware_dv.py", line 388, in <module>
    app.run(main)
  File "/tmp/Bazel.runfiles_wsluf8vf/runfiles/absl_py/absl/app.py", line 312, in run
    _run_main(main, args)
  File "/tmp/Bazel.runfiles_wsluf8vf/runfiles/absl_py/absl/app.py", line 258, in _run_main
    sys.exit(main(argv))
  File "/tmp/Bazel.runfiles_wsluf8vf/runfiles/com_google_deepvariant/deepvariant/make_examples_pangenome_aware_dv.py", line 377, in main
    make_examples_core.make_examples_runner(options)
  File "/tmp/Bazel.runfiles_wsluf8vf/runfiles/com_google_deepvariant/deepvariant/make_examples_core.py", line 3027, in make_examples_runner
    region_processor.process(region, region_n)
  File "/tmp/Bazel.runfiles_wsluf8vf/runfiles/com_google_deepvariant/deepvariant/make_examples_core.py", line 1983, in process
    sample_reads = self.region_reads_norealign(
  File "/tmp/Bazel.runfiles_wsluf8vf/runfiles/com_google_deepvariant/deepvariant/make_examples_core.py", line 2112, in region_reads_norealign
    reads = itertools.chain(reads, sam_reader.query(region))
  File "/tmp/Bazel.runfiles_wsluf8vf/runfiles/com_google_deepvariant/third_party/nucleus/io/genomics_reader.py", line 249, in query
    return self._reader.query(region)
ValueError: NOT_FOUND: Pangenome path ids not found for pangenome sample name: GRCh38

Because I am not using GRCh38 as a reference genome, I am therefore wondering if the issue could be because run_pangenome_aware_deepvariant is not suitable for other species?

Setup

• Operating system: Linux on an HPC
• DeepVariant version: 1.8.0
• Installation method (Docker, built from source, etc.): Singularity image
• Type of data: (sequencing instrument, reference genome, anything special that is unlike the case studies?) short-reads Illumina simulated reads from fungi

Steps to reproduce:

• Command:

BIN_VERSION="pangenome_aware_deepvariant-1.8.0"

singularity run -B /vast/marion/:/vast/marion/ \
  docker://google/deepvariant:"${BIN_VERSION}" \
  /opt/deepvariant/bin/run_pangenome_aware_deepvariant \
  --model_type=WGS \
  --ref=$FOLDER/00_additional_ref/Genome_ref_renamed.fasta \
  --reads=$FOLDER/01_align/20250109_simReads.sort.bam \
  --pangenome=$FULL_REF/20241017_26pg.pg.full.gbz \
  --output_vcf=$FOLDER/02_deepVariant_pg/output.vcf.gz \
  --output_gvcf=$FOLDER/02_deepVariant_pg/output.g.vcf.gz \
  --num_shards=24

• Error trace: error_trace.txt

I can't publicly share the .gbz of my organism as of now, but I can probably send them to you by mail if necessary.

Does the quick start test work on your system?
Yes, the quickstart works. I also tried the deepvariant example for reads aligned with vg here, and it works fine.
No, the issue is not reproducible with the tutorial's data nor the quickstart.

Any additional context:
NA

[kishwarshafin]

hi @MarionPerrier ,

That is correct. The current implementation relies on HPRC_v1.1 graph and GRCh38 reference paths to extract the pangenome graph sequences.

[MarionPerrier]

Ok, thank you very much for your answer.