broadinstitute/seqr-loading-pipelines

Pipeline failed during allele registry step because of no response variants matching reference genome.

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2024-07-08 16:54:27 - allele_registry - INFO - Calling the ClinGen Allele Registry
ERROR: [pid 59761] Worker Worker(salt=7496661520, workers=1, host=seqr-airflow2-37-v03-pipeline-snv-indel-m, username=root, pid=59761) failed    WriteNewVariantsTableTask(reference_genome=GRCh37, dataset_type=SNV_INDEL, sample_type=WGS, callset_paths=["gs://fc-bc11f445-8ba8-43c9-8b6a-81074b535bf5/uploads/CRWGS23/CR.genotypes.filtered.vcf.gz"], project_guids=["R0806_costarica_wgs23"], project_remap_paths=["gs://seqr-datasets/v02/GRCh37/AnVIL_WGS/R0806_costarica_wgs23/base/R0806_costarica_wgs23_remap.tsv"], project_pedigree_paths=["gs://seqr-datasets/v02/GRCh37/AnVIL_WGS/R0806_costarica_wgs23/base/R0806_costarica_wgs23_subsetted_pedigree.tsv"], imputed_sex_paths=null, ignore_missing_samples_when_remapping=False, validate=True, force=False, liftover_ref_path=gs://hail-common/references/grch38_to_grch37.over.chain.gz, run_id=manual__2024-07-08T14-18-30.518750+00-00)
Traceback (most recent call last):
  File "/tmp/UpdateVariantAnnotationsTableWithNewSamplesTask_F4HOC/pyscripts.zip/v03_pipeline/lib/misc/allele_registry.py", line 71, in register_alleles_in_chunks
    yield register_alleles(chunk_ht, reference_genome, base_url)
  File "/tmp/UpdateVariantAnnotationsTableWithNewSamplesTask_F4HOC/pyscripts.zip/v03_pipeline/lib/misc/allele_registry.py", line 105, in register_alleles
    return handle_api_response(res, base_url, reference_genome)
  File "/tmp/UpdateVariantAnnotationsTableWithNewSamplesTask_F4HOC/pyscripts.zip/v03_pipeline/lib/misc/allele_registry.py", line 163, in handle_api_response
    allele_info = next(
StopIteration