gistfile1.txt

$ adam-submit --driver-memory 20g --executor-memory 20g --verbose -- transformGenotypes test_vcf_files/90k.chr21.merged.subset.VEP.dbNSFP.ClinVar.HGMD.vcf.gz test_vcf_files/90k.chr21.merged.subset.VEP.dbNSFP.ClinVar.HGMD.adam

It runs for some time before crashing as it attempts to convert the string “nan” to a float. Here’s some of the stack trace of the crash, first line is what appears to be normal processing:

18/10/15 18:40:19 INFO InternalParquetRecordWriter: Flushing mem columnStore to file. allocated memory: 104944123
18/10/15 18:40:38 ERROR Utils: Aborting task
java.lang.NumberFormatException: For input string: "nan"
        at sun.misc.FloatingDecimal.readJavaFormatString(FloatingDecimal.java:2043)
        at sun.misc.FloatingDecimal.parseFloat(FloatingDecimal.java:122)
        at java.lang.Float.parseFloat(Float.java:451)
        at scala.collection.immutable.StringLike$class.toFloat(StringLike.scala:280)
        at scala.collection.immutable.StringOps.toFloat(StringOps.scala:29)
        at org.bdgenomics.adam.converters.VariantContextConverter$$anonfun$org$bdgenomics$adam$converters$VariantContextConverter$$toFloat$2.apply(VariantContextConverter.scala:1311)
        at org.bdgenomics.adam.converters.VariantContextConverter$$anonfun$org$bdgenomics$adam$converters$VariantContextConverter$$toFloat$2.apply(VariantContextConverter.scala:1305)
        at org.bdgenomics.adam.converters.VariantContextConverter.org$bdgenomics$adam$converters$VariantContextConverter$$tryAndCatchStringCast(VariantContextConverter.scala:956)
        at org.bdgenomics.adam.converters.VariantContextConverter.org$bdgenomics$adam$converters$VariantContextConverter$$toFloat(VariantContextConverter.scala:1303)
        at org.bdgenomics.adam.converters.VariantContextConverter$$anonfun$org$bdgenomics$adam$converters$VariantContextConverter$$lineToVariantContextExtractor$4$$anonfun$apply$51.apply(VariantContextConverter.scala:                                                      1468)
        at org.bdgenomics.adam.converters.VariantContextConverter$$anonfun$org$bdgenomics$adam$converters$VariantContextConverter$$lineToVariantContextExtractor$4$$anonfun$apply$51.apply(VariantContextConverter.scala:                                                      1468)
        at scala.Option.map(Option.scala:146)
        at org.bdgenomics.adam.converters.VariantContextConverter.org$bdgenomics$adam$converters$VariantContextConverter$$variantContextFieldExtractor(VariantContextConverter.scala:1437)
        at org.bdgenomics.adam.converters.VariantContextConverter$$anonfun$org$bdgenomics$adam$converters$VariantContextConverter$$lineToVariantContextExtractor$4.apply(VariantContextConverter.scala:1468)
        at org.bdgenomics.adam.converters.VariantContextConverter$$anonfun$org$bdgenomics$adam$converters$VariantContextConverter$$lineToVariantContextExtractor$4.apply(VariantContextConverter.scala:1466)
        at org.bdgenomics.adam.converters.VariantContextConverter$$anonfun$76.apply(VariantContextConverter.scala:1742)
        at org.bdgenomics.adam.converters.VariantContextConverter$$anonfun$76.apply(VariantContextConverter.scala:1742)
        at scala.collection.TraversableLike$$anonfun$flatMap$1.apply(TraversableLike.scala:241)
        at scala.collection.TraversableLike$$anonfun$flatMap$1.apply(TraversableLike.scala:241)
        at scala.collection.mutable.ResizableArray$class.foreach(ResizableArray.scala:59)
        at scala.collection.mutable.ArrayBuffer.foreach(ArrayBuffer.scala:48)
        at scala.collection.TraversableLike$class.flatMap(TraversableLike.scala:241)
        at scala.collection.AbstractTraversable.flatMap(Traversable.scala:104)
        at org.bdgenomics.adam.converters.VariantContextConverter.org$bdgenomics$adam$converters$VariantContextConverter$$convert$1(VariantContextConverter.scala:1742)
        at org.bdgenomics.adam.converters.VariantContextConverter$$anonfun$makeVariantFormatFn$1.apply(VariantContextConverter.scala:1756)
        at org.bdgenomics.adam.converters.VariantContextConverter$$anonfun$makeVariantFormatFn$1.apply(VariantContextConverter.scala:1756)
        at org.bdgenomics.adam.converters.VariantContextConverter.convert(VariantContextConverter.scala:353)
        at org.bdgenomics.adam.rdd.ADAMContext$$anonfun$loadVcf$1$$anonfun$apply$15.apply(ADAMContext.scala:2170)
        at org.bdgenomics.adam.rdd.ADAMContext$$anonfun$loadVcf$1$$anonfun$apply$15.apply(ADAMContext.scala:2170)
        at scala.collection.Iterator$$anon$12.nextCur(Iterator.scala:434)
        at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:440)
        at scala.collection.Iterator$$anon$12.hasNext(Iterator.scala:439)
        at scala.collection.Iterator$$anon$11.hasNext(Iterator.scala:408)
        at org.apache.spark.internal.io.SparkHadoopWriter$$anonfun$4.apply(SparkHadoopWriter.scala:124)
        at org.apache.spark.internal.io.SparkHadoopWriter$$anonfun$4.apply(SparkHadoopWriter.scala:123)
        at org.apache.spark.util.Utils$.tryWithSafeFinallyAndFailureCallbacks(Utils.scala:1411)
        at org.apache.spark.internal.io.SparkHadoopWriter$.org$apache$spark$internal$io$SparkHadoopWriter$$executeTask(SparkHadoopWriter.scala:135)
        at org.apache.spark.internal.io.SparkHadoopWriter$$anonfun$3.apply(SparkHadoopWriter.scala:79)
        at org.apache.spark.internal.io.SparkHadoopWriter$$anonfun$3.apply(SparkHadoopWriter.scala:78)
        at org.apache.spark.scheduler.ResultTask.runTask(ResultTask.scala:87)
        at org.apache.spark.scheduler.Task.run(Task.scala:109)
        at org.apache.spark.executor.Executor$TaskRunner.run(Executor.scala:345)
        at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149)
        at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624)
        at java.lang.Thread.run(Thread.java:748)