Hi there,
I am trying to run hail gnomad tutorial for ancestry. It is convulated for my skills.
I have installed all tools, dependencies, set jar path and other things.
import sys
print(sys.path)
sys.path.append(‘/sc/arion/projects/gapslab/team_folders/sanjeev/projects/TARCC/ancestry_estimation/pip_python3.12/’)
import osjava_home_path=“/hpc/packages/minerva-rocky9/java/21.0.4/jdk-21.0.4/” # Replace with the actual path to your JDK
os.environ[“JAVA_HOME”] = java_home_path
import hail as hl
import gnomad
Error step:
these are intermediate files that helped with running the script faster - not included in the main list of files
unrelateds_mt_preoutlier = hl.read_matrix_table(‘gs://hgdp-1kg/tutorial_datasets/pca/temp_files/unrel_preout.mt’)
relateds_mt_preoutlier = hl.read_matrix_table(‘gs://hgdp-1kg/tutorial_datasets/pca/temp_files/rel_preout.mt’)
I run into error for socketexception network is unreachable.
I’ve enabled proxies in the cluster.
Can you please help me with this?