I’m running the following code: import hail as hl hl.init() all_genomes_mt = hl.read_matrix_table( f'gs://{genomes_mt_path}' ) result = hl.vep(all_genomes_mt) And getting the following error: hail.utils.java.FatalError: HailException: VEP command '/vep --format vcf --json --everything --allele_nu…

Hey @dlcotter ! My apologies! This should be fixed in latest Hail 0.2.123. The issue with some more information about root cause is #12936 .

Docker error when running VEP

danking Split this topic October 4, 2023, 2:25pm 3

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