RemoteException file doesn't exist

Hail Query & hailctl
1

Hail Version: Hail version: 0.2.61-3c86d3ba497a

Error: Error summary: RemoteException: File does not exist: /header.g.vcf.gz

Using the run_combiner tool below (from a docker image with Hail installed) – and the Header_File is being passed in as a local file path “/header.g.vcf.gz” (and I can confirm it exists at that location with a quick ls). What’s the best way to interpret that error?

hl.experimental.run_combiner(
    gvcf_list,
    sample_names=samples_list,
    header=HEADER_FILE,
    out_file=args.output_cloud_path,
    tmp_path=args.tmp_bucket,
    key_by_locus_and_alleles=True,
    overwrite=args.overwrite_existing,
    reference_genome='GRCh38',
    use_exome_default_intervals=True,
    target_records=10000
)
2

I’m not familiar with the combiner, but I’d try file:///header.g.vcf.gz. It’s possible this is a Hadoop filesystem vs. local file system issue. RemoteException sounds to me like a Java exception (meaning that the root cause is Hail’s Java backend which indeed uses the Hadoop filesystem). The full stack trace would indicate if the issue arose in Java/Scala code or not.

1 Like