Impot VCF from dbSNP

Hi, I wished to import dbSNP latest version in Hail. The official (GRCh38) VCF is available on NCBI FTP (

Notably contig names in this VCF file are RefSeq accession IDs ( i.e. NC_000001.11 for chr1) and it also includes all alternative contigs…
Thus seeking to import this VCF as a hail matrixtable, I am using hl.import_vcf with the option contig_recoding and skip_invalid_loci


mt = hl.import_vcf('s3://.../GCF_000001405.39.gz', 
              reference_genome='GRCh38', force_bgz=True, 
              contig_recoding=contigs_map, skip_invalid_loci=True)

I get a warning - but that should not be a problem, right ?

Hail: WARN: expected input file '...' to end in .vcf[.bgz, .gz]

More problematic, I also get the following error

An error was encountered:
IllegalArgumentException: requirement failed
Hail version: 0.2.80-4ccfae1ff293
Error summary: IllegalArgumentException: requirement failed

Any idea what might be wrong ? and/or how to trouble shoot this shortcoming

what’s the full stack trace here?