HailException: incompatible file format, supported version: 1.4.0, found 1.5.0

Hail Query & hailctl
1

Hi, I use vep_or_lookup_vep(ds, reference="GRCh38") to annotate my vcf file.
But it report error:

hail.utils.java.FatalError: HailException: incompatible file format when reading: gs://gnomad-public-requester-pays/resources/context/grch38_context_vep_annotated.ht
supported version: 1.4.0, found 1.5.0

Code I used is:

import hail as hl
hl.init(default_reference=‘GRCh38’)
from gnomad.utils.vep import vep_or_lookup_vep

ds = hl.import_vcf(‘gs://path/chr22.vcf.bgz’, reference_genome=“GRCh38”, drop_samples=True).rows()
ds = vep_or_lookup_vep(ds, reference=“GRCh38”)
ds.export(‘gs://path/chr22.gnomad.vep.tsv.bgz’)

hail version:

Running on Apache Spark version 2.4.5
Welcome to
__ __ <>__
/ // /__ __/ /
/ __ / _ `/ / /
// //_,/// version 0.2.49-11ae8408bad0

Any ideas? Thanks a lot.

2

This error message should be improved, but this means that you’re trying to use an older version of Hail to read a file written with a newer version. You can fix this by updating to the latest release.

1 Like
3

Thanks a lot, Tim. Now I see what was happening and I will try it.
btw, while I was waiting for answer, I tried hail.vep(), worked quite good as well.

4

Thanks for the clarification.

Our situation here is quite different. We have a team in different location who is working with hail version 0.2.72. They performed several QC steps on new data arrived from lab and sent the hail matrix table to other team in different location. The other team works with 0.2.42.

Since, the versions are different, they are not able to load new hail matrix table and it gives the above mentioned error. Is there any way that new hail matrix tables can be loaded using older versions?
Also, can you tell us at which version forward compatibility of loading hail matrix table is broken?

PS: We are trying to get every team upgraded to latest hail version.