The frontline support team will be slow on the forum because we are occupied with the GATK Workshop on March 21st and 22nd 2019. We will be back and more available to answer questions on the forum on March 25th 2019.

I can't run GATK4 BwaSpark tool on a yarn cluster

hmushtaqhmushtaq NetherlandsMember

I am trying to run the gatk BwaSpark tool on Microsoft Azure cloud, by issuing the following command (Note that I am a bit unsure about how many / should I put with hdfs:. If my file is in /data/gatk4input, is hdfs:///data/gatk4input, the right way to do it?).

./gatk BwaSpark -I hdfs:///data/gatk4input/input.bam -O hdfs:///data/gatk4output/bwa.bam -R hdfs:///data/filesB37/human_g1k_v37_decoy.fasta --disable-sequence-dictionary-validation true -- --spark-master yarn

But, I get the following error. Any idea, what is the problem here. Every other Spark program that I wrote myself, runs absolutely fine on my cluster.

18/03/12 17:30:01 ERROR SparkContext: Error initializing SparkContext.
org.apache.spark.SparkException: Unable to load YARN support
at org.apache.spark.deploy.SparkHadoopUtil$.liftedTree1$1(SparkHadoopUtil.scala:417)
at org.apache.spark.deploy.SparkHadoopUtil$.yarn$lzycompute(SparkHadoopUtil.scala:412)
at org.apache.spark.deploy.SparkHadoopUtil$.yarn(SparkHadoopUtil.scala:412)
at org.apache.spark.deploy.SparkHadoopUtil$.get(SparkHadoopUtil.scala:437)
at org.apache.spark.util.Utils$.getSparkOrYarnConfig(Utils.scala:2303)
at org.apache.spark.SparkEnv$.create(SparkEnv.scala:320)
at org.apache.spark.SparkEnv$.createDriverEnv(SparkEnv.scala:165)
at org.apache.spark.SparkContext.createSparkEnv(SparkContext.scala:256)
at org.apache.spark.SparkContext.(SparkContext.scala:420)


Sign In or Register to comment.