GATK SortSamSpark error: Failed to load org.broadinstitute.hellbender.Main

Question

[dragon940401]

Hi, I'm studing gatk tool for WGS data(fastq mapping, sam to bam file)

I did align fastq file. so I got sam file. And I would Implement sortsamspark for converting sam file to bam file.

But Error message has occurred.

Error: Failed to load org.broadinstitute.hellbender.Main: org/apache/logging/log4j/core/appender/AbstractAppender

21/06/26 01:53:04 INFO ShutdownHookManager: Shutdown hook called

21/06/26 01:53:04 INFO ShutdownHookManager: Deleting directory/tmp/spark-691a0c68-b46a-47d9-9ac4-648fe5faa28f

How can i fix it? Thanks.

My code is below.

    gatk SortSamSpark \
-I /home/path/GATK/RNA_data/Alignment_ref_hg38_ERR1088639.sam \
-O /home/path/GATK/RNA_data/Sort_ERR1088639.bam \
-SO coordinate \
-- \
--spark-runner SPARK \
--jars $GATK_SPARKJAR_LOCATION \
--spark-master URL \
--driver-cores 2 \
--deploy-mode client \
--driver-memory 32g \
--driver-java-options "-Xss16g" \
--num-executors 3 \
--executor-cores 2 \
--executor-memory 10g \
--conf spark.dynamicAllocation.enabled=false \
--conf spark.kryoserializer.buffer.max=512m \
--conf spark.executor.extraJavaOptions="-DGATK_STACKTRACE_ON_USER_EXCEPTION=true" \
--conf spark.executor.memoryOverhead=10000 \
--conf spark.executor.extraJavaOptions="-Xms10g" \
--conf spark.memory.offHeap.enabled=true \
--conf spark.memory.offHeap.size=8g \
--java-options "-DGATK_STACKTRACE_ON_USER_EXCEPTION=true" \
--verbose

My env. and tool version are below.

~/.bashrc

gatk

export PATH=$PATH:/home/edu1/tools/gatk-4.1.9.0

export GATK_SPARKJAR_LOCATION=/home/path/gatk-4.1.9.0/gatk-package-4.1.9.0-spark.jar

export GATK_LOCALJAR_LOCATION=/home/path/gatk-4.1.9.0/gatk-package-4.1.9.0-local.jar

export PATH=$PATH:/home/path/gatk-4.1.9.0/gatk-completion.sh

JAVA

export JAVA_HOME=/home/path/jdk-1.8.0_231

export PATH=$PATH:$JAVA_HOME/bin

export CLASSPATH=$CLASSPATH:$JAVA_HOME/lib

tools version

1. gatk : 4.1.9.0
2. java -version openjdk version "1.8.0_262" OpenJDK Runtime Environment (build 1.8.0_262-b10) OpenJDK 64-Bit Server VM (build 25.262-b10, mixed mode)
3. apache spark : spark-3.1.1-bin-hadoop2.7