Hi,
I’m trying to run a hail sample QC pipeline locally and I’m getting the following error:
Java stack trace:
org.apache.spark.SparkException: Job aborted due to stage failure: Task 9 in stage 46.0 failed 1 times, most recent failure: Lost task 9.0 in stage 46.0 (TID 2426) (192.168.0.8 executor driver): java.lang.NoClassDefFoundError: Could not initialize class is.hail.methods.IBSFFI$
I’ve read that this may be due to a mismatch between the architecture the library is compiled for, and my system architecture, and that one way to solve it is to recompiling Hail…? Could you explain me how to do that?
Some info that you may need:
$uname -a
Darwin wm8e6-415 22.6.0 Darwin Kernel Version 22.6.0: Thu Nov 2 07:43:25 PDT 2023; root:xnu-8796.141.3.701.17~6/RELEASE_ARM64_T6020 arm64
$pip3 show hail
Name: hail
Version: 0.2.126
Summary: Scalable library for exploring and analyzing genomic data.
Home-page: https://hail.is
Author: Hail Team
Author-email: hail@broadinstitute.org
License:
Location: /Users/ldomenec/anaconda3/lib/python3.11/site-packages
Requires: aiodns, aiohttp, asyncinit, avro, azure-identity, azure-mgmt-storage, azure-storage-blob, bokeh, boto3, botocore, decorator, Deprecated, dill, frozenlist, google-auth, google-auth-oauthlib, humanize, janus, jproperties, nest-asyncio, numpy, orjson, pandas, parsimonious, plotly, protobuf, pyspark, python-json-logger, pyyaml, requests, rich, scipy, sortedcontainers, tabulate, typer, uvloop
$python3 -V
Python 3.11.5
$ java -version
java version “11.0.22” 2024-01-16 LTS
Java™ SE Runtime Environment 18.9 (build 11.0.22+9-LTS-219)
Java HotSpot™ 64-Bit Server VM 18.9 (build 11.0.22+9-LTS-219, mixed mode)
$ echo $JAVA_HOME
/Library/Java/JavaVirtualMachines/jdk-11.jdk/Contents/Home
Let me know if you need anything else.
Many thanks!
Laura