test-guac-run

/hpc/users/ahujaa01/spark/spark-1.6.2-bin-hadoop2.6/bin/spark-submit 
   --master yarn-client 
   --executor-memory 18g 
   --driver-memory 12g 
   --num-executors 100 
   --executor-cores 8 
   --class org.hammerlab.guacamole.Main 
   --conf spark.default.parallelism=10000 
   --conf spark.yarn.executor.memoryOverhead=3024 
   --conf spark.shuffle.service.enabled=true 
   --conf spark.memory.storageFraction=0.15 
   --conf spark.app.name=Guacamole 
   --conf spark.kryoserializer.buffer.max=256m 
   --conf spark.core.connection.ack.wait.timeout=1120 
   --conf spark.executor.extra JavaOptions=-XX:+UseCompressedOops 
   --conf spark.eventLog.dir=hdfs://demeter-nn1.demeter.hpc.mssm.edu:8020/user/spark/applicationHistory 
   --conf spark.eventLog.enabled=true -
   -jars /demeter/users/ahujaa01/src/hammerlab/guacamole/target/guacamole-deps-0.0.1-SNAPSHOT.jar 
   --driver-java-options '-Dyarn.resourcemanager.am.max-attempts=1 -Dlog4j.configuration=file:///demeter/users/ahujaa01/src/internal-tools/scripts/guacamole/log4j.properties' /demeter/users/ahujaa01/src/hammerlab/guacamole/target/guacamole-0.0.1-SNAPSHOT.jar 
   somatic-standard 
   --loci-partitioner micro-regions 
  --reference /hpc/users/ahujaa01/ksinai-demeter/b37decoy-reference-genome/hs37d5.fasta 
  --min-mapq 1 
  --min-normal-read-depth 8 
  --min-tumor-read-depth 8 
  --max-tumor-read-depth 250 
  --min-tumor-alternate-read-depth 1 
  --min-average-mapping-quality 25 
  --min-average-base-quality 15 
  --odds 1000 
  --min-likelihood 75 
  --min-lod 0 
  --max-median-mismatches 10 
  --filter-multi-allelic 
  --min-vaf 5 
  --normal-reads hdfs://demeter-nn1.demeter.hpc.mssm.edu/datasets/dream/data/synthetic-challenge-2/synthetic.challenge.set2.normal.wit
hMDTags.bam 
  --tumor-reads hdfs://demeter-nn1.demeter.hpc.mssm.edu/datasets/dream/data/synthetic-challenge-2/synthetic.challenge.set2.tumor.withMDTags.bam 
  --out /user/ahujaa01/dreamtests/synth2-739078877fc39ecade08a84fc37d6e9ff68221d7.vcf