Error when trying reading gnomAD using HAIL - connection issues?
I'm trying to read the gnomad datasets like in the HAIL tutorial, but it keeps failing after a few minutes, due to connectivity issues, and i need to create a new environment each time, but then it fails again after a few commands.
e.g
hl.init(default_reference = "GRCh38", log = 'gnomAD-with-Hail.log')
sites_only_ht = "gs://gnomad-public-requester-pays/release/3.1/ht/genomes/gnomad.genomes.v3.1.sites.ht"
sites_only_table = hl.read_table(sites_only_ht)
but then i get an error:
2021-07-15 02:21:34::ERROR An error occurred while trying to connect to the Java server (127.0.0.1:44317)
Traceback (most recent call last):
File "/usr/local/lib/python3.7/dist-packages/py4j/java_gateway.py", line 982, in _get_connection
connection = self.deque.pop()
IndexError: pop from an empty deque
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/usr/local/lib/python3.7/dist-packages/py4j/java_gateway.py", line 1120, in start
self.socket.connect((self.address, self.port))
ConnectionRefusedError: [Errno 111] Connection refused
is there some enviroment/connection issues?
i'm using the default HAIL configuration for the cloud enviroment,
along with 2 CPUs, 75GB memory, and 50GB disk size
Comments
1 comment
Hi Yaron Einhorn,
Thanks for reaching out. Can you please share a screenshot of the error you are receiving and provide the following details?
Terra account email address
Terra billing project for cloud environment runtime
Cluster ID (visit https://app.terra.bio/#clusters, click Details, and see Name field)
Screenshot of your cloud environment configuration (gear icon at the top-right of workspace)
Approximate time issue first occurred
If possible, can you also share your workspace with GROUP_FireCloud-Support@firecloud.org by clicking the Share button in your workspace? We'll take a look at the issue and get back to you as soon as we can!
Best,
Samantha
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