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via GitHub by Georgehe4
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java.io.IOException: Stream closed	at org.apache.hadoop.crypto.CryptoOutputStream.checkStream(CryptoOutputStream.java:250)	at org.apache.hadoop.crypto.CryptoOutputStream.flush(CryptoOutputStream.java:237)	at java.io.FilterOutputStream.flush(FilterOutputStream.java:140)	at java.io.DataOutputStream.flush(DataOutputStream.java:123)	at org.bdgenomics.adam.rdd.VCFHeaderUtils$.write(VCFHeaderUtils.scala:75)	at org.bdgenomics.adam.rdd.VCFHeaderUtils$.write(VCFHeaderUtils.scala:46)	at org.bdgenomics.adam.rdd.MultisampleAvroGenomicRDD.saveMetadata(GenomicRDD.scala:827)	at org.bdgenomics.adam.rdd.AvroGenomicRDD.saveAsParquet(GenomicRDD.scala:913)	at org.bdgenomics.adam.rdd.AvroGenomicRDD.saveAsParquet(GenomicRDD.scala:883)	at org.bdgenomics.adam.cli.Vcf2ADAM.run(Vcf2ADAM.scala:74)	at net.fnothaft.gnocchi.cli.RegressPhenotypes.loadGenotypes(RegressPhenotypes.scala:152)	at net.fnothaft.gnocchi.cli.RegressPhenotypes.run(RegressPhenotypes.scala:118)	at org.bdgenomics.utils.cli.BDGSparkCommand$class.run(BDGCommand.scala:55)	at net.fnothaft.gnocchi.cli.RegressPhenotypes.run(RegressPhenotypes.scala:110)	at net.fnothaft.gnocchi.cli.GnocchiMain$.main(GnocchiMain.scala:48)	at net.fnothaft.gnocchi.cli.GnocchiMain.main(GnocchiMain.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:731)	at org.apache.spark.deploy.SparkSubmit$.doRunMain$1(SparkSubmit.scala:181)	at org.apache.spark.deploy.SparkSubmit$.submit(SparkSubmit.scala:206)	at org.apache.spark.deploy.SparkSubmit$.main(SparkSubmit.scala:121)	at org.apache.spark.deploy.SparkSubmit.main(SparkSubmit.scala)