diff --git a/src/gentropy/config.py b/src/gentropy/config.py index 0a76b2c84..8c876bb6d 100644 --- a/src/gentropy/config.py +++ b/src/gentropy/config.py @@ -343,7 +343,7 @@ class FinemapperConfig(StepConfig): output_path: str = MISSING locus_radius: int = MISSING locus_l: int = MISSING - _target_: str = "gentropy.susie_finemapping.SusieFineMapperStep" + _target_: str = "gentropy.susie_finemapper.SusieFineMapperStep" @dataclass diff --git a/src/gentropy/susie_finemapper.py b/src/gentropy/susie_finemapper.py index 5a0fa31f3..ceb5fbb34 100644 --- a/src/gentropy/susie_finemapper.py +++ b/src/gentropy/susie_finemapper.py @@ -5,6 +5,7 @@ import time from typing import Any +import hail as hl import numpy as np import pandas as pd import pyspark.sql.functions as f @@ -49,6 +50,7 @@ def __init__( locus_radius (int): Radius of base-pair window around the locus, default is 500_000 locus_l (int): Maximum number of causal variants in locus, default is 10 """ + hl.init(sc=session.spark.sparkContext, log="/dev/null") # Read studyLocus study_locus = ( StudyLocus.from_parquet(session, study_locus_collected_path)