Hi!
I have Hail and VEP installed as modules on an HPC cluster, and I am trying to perform functional annotation on an imported VCF using VEP through Hail in order to distribute the task across multiple nodes. However, while VEP 111 works with Hail, VEP 114 and VEP 115 are hanging indefinitely even for a small VCF file. From what I have seen, the setup between VEP 111 and VEP 114/115 are identical, so I am not sure whether this is an issue with Hail or VEP. I have shared the code I am trying to test below:
import hail as hl
hl.init(log = 'tmp.log')
rg = hl.get_reference('GRCh38')
mt = hl.import_vcf('data/HG001_GIAB.vcf', reference_genome = rg)
mt = hl.vep(mt, 'data/vep-config.json', csq = True)
mt.describe()
Can you please help me with troubleshooting this issue in Hail? I can share the log files and some example data if needed, but I would prefer to send it privately to an email ID due to our organization policy.