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tkdagdelen / gnocchi_old

Apache License 2.0
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Consolidated Changes #51

Open Georgehe4 opened 7 years ago

Georgehe4 commented 7 years ago

Updated to Adam 0.20.1-SNAPSHOT and Spark 2.0+

May be better to merge into a separate branch to track only adam 0.20.1 and spark udpates

Merged in the following branches

Georgehe4 commented 7 years ago

This version is experiencing crypto errors with VCF2Adam on the Hadoop cluster. Stack trace:

Exception in thread "main" 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)