java.util.NoSuchElementException when running SingleStudy

Hi all, I just tested your project but sadly got an exception[0]. For testing purposes I used the chromosome 9 of the 1000genome project(phase 3) [1] and the corresponding panel[2]. I renamed the vcf and panel for personal organization preferences. I have a spark(v2.1.1) and hdfs(v2.8.0) standalone on my workstation installed. Both work just fine (I'm currently using them via pyspark). Attached you'll find my config[3] and the command[4] I'm running on the cli.

Best, 1Tilly

[0]

ERROR SingleStudy$: Something went wrong, exit java.util.NoSuchElementException: None.get at scala.None$.get(Option.scala:347) at scala.None$.get(Option.scala:345) at org.dizhang.seqspark.worker.Samples$$anonfun$9.apply(Samples.scala:148) at org.dizhang.seqspark.worker.Samples$$anonfun$9.apply(Samples.scala:148) at scala.collection.TraversableLike$$anonfun$map$1.apply(TraversableLike.scala:234) at scala.collection.TraversableLike$$anonfun$map$1.apply(TraversableLike.scala:234) at scala.collection.IndexedSeqOptimized$class.foreach(IndexedSeqOptimized.scala:33) at scala.collection.mutable.ArrayOps$ofRef.foreach(ArrayOps.scala:186) at scala.collection.TraversableLike$class.map(TraversableLike.scala:234) at scala.collection.mutable.ArrayOps$ofRef.map(ArrayOps.scala:186) at org.dizhang.seqspark.worker.Samples$.titv(Samples.scala:148) at org.dizhang.seqspark.worker.QualityControl$.cleanVCF(QualityControl.scala:110) at org.dizhang.seqspark.SingleStudy$.run(SingleStudy.scala:171) at org.dizhang.seqspark.SingleStudy$.main(SingleStudy.scala:57) at org.dizhang.seqspark.SingleStudy.main(SingleStudy.scala) at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62) at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.lang.reflect.Method.invoke(Method.java:498) at org.apache.spark.deploy.SparkSubmit$.org$apache$spark$deploy$SparkSubmit$$runMain(SparkSubmit.scala:743) at org.apache.spark.deploy.SparkSubmit$.doRunMain$1(SparkSubmit.scala:187) at org.apache.spark.deploy.SparkSubmit$.submit(SparkSubmit.scala:212) at org.apache.spark.deploy.SparkSubmit$.main(SparkSubmit.scala:126) at org.apache.spark.deploy.SparkSubmit.main(SparkSubmit.scala) 17/07/12 16:09:26 INFO SparkContext: Invoking stop() from shutdown hook

[1] ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/release/20130502/ALL.chr9.phase3_shapeit2_mvncall_integrated_v5a.20130502.genotypes.vcf.gz

[2] ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/release/20130502/integrated_call_samples_v3.20130502.ALL.panel

[3]

seqspark {
  project = demo2
  pipeline = [ "qualityControl" ]
  input {
      genotype.path = "chr9ph31k.vcf.gz"
      phenotype.path = "ph31k.panel"

  }
  qualityControl {
      genotypes = ["DP >= 1 and GQ >= 1"]
      summaries = ["pca", "titv"]
    }
}

[4]./bin/seqspark SingleStudy conf/demo2.conf

statgenetics / seqspark

java.util.NoSuchElementException when running SingleStudy #2