Index_bgen zlib compression exception

Science
#1

I’m trying to index a bgen while on RAP.

get_bgen_path = lambda chrom: f'file:///mnt/project/Bulk/Exome sequences/Population level exome OQFE variants, BGEN format - interim 450k release/ukb23150_c{chrom}_b0_v1.bgen'
get_idx2_path = lambda chrom: f'{hail_dir}/exome/wes_450k/bgen/chr{chrom}.idx2'

chrom = 21
hl.index_bgen(
    path = get_bgen_path(chrom),
    index_file_map = {get_bgen_path(chrom): get_idx2_path(chrom)},
)

But I get HailException: Hail only supports zlib compression.

#2

Log: hail-20220505-0948-0.2.78-b17627756568.log (18.3 KB)

#3

We don’t support zstd compression, which was added after we wrote the BGEN importer. What BGEN is this? We can add this support but we’ve got a lot going on right now.

#4

How do I check the BGEN version? I can’t seem to get it with bgenix.

This isn’t a bottleneck for me, so no rush.

#5

I have the same problem, these are all of the UK Biobank genotype files (500K WES, as well as the older 450K WES).

1 Like
#6

Thanks for the ping, @orr. We’ve noted this as a key new feature for our users working with UKB. The team is very resource constrained these days, but we’ll do our best to get it done for y’all.

1 Like