These are the errors:
log4j:ERROR A "org.apache.log4j.ConsoleAppender" object is not assignable to a "org.apache.log4j.Appender" variable.
log4j:ERROR The class "org.apache.log4j.Appender" was loaded by
log4j:ERROR [sun.misc.Launcher$AppClassLoader@7e6cbb7a] whereas object of type
log4j:ERROR "org.apache.log4j.ConsoleAppender" was loaded by [org.apache.spark.util.ChildFirstURLClassLoader@5ef60048].
log4j:ERROR Could not instantiate appender named "console".
log4j:ERROR A "org.apache.log4j.ConsoleAppender" object is not assignable to a "org.apache.log4j.Appender" variable.
log4j:ERROR The class "org.apache.log4j.Appender" was loaded by
log4j:ERROR [sun.misc.Launcher$AppClassLoader@7e6cbb7a] whereas object of type
log4j:ERROR "org.apache.log4j.ConsoleAppender" was loaded by [org.apache.spark.util.ChildFirstURLClassLoader@5ef60048].
log4j:ERROR Could not instantiate appender named "console".
While running this command:
./gatk-launch BaseRecalibratorSpark -I gs://mybucket/example.bam -R gs://mybucket/example.fasta -knownSites sample.vcf.gz -O test.spark.table -apiKey $APIKEY -- --sparkRunner GCS --cluster samplecluster --num-executors 5 --executor-cores 2 --executor-memory 4g