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GA4GHUtil fails with Spark 2.2.1 #353

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akmorrow13 opened this issue Jan 19, 2018 · 0 comments
Open

GA4GHUtil fails with Spark 2.2.1 #353

akmorrow13 opened this issue Jan 19, 2018 · 0 comments

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@akmorrow13
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When testing with python, you get the following error:

    Py4JJavaError: An error occurred while calling z:org.bdgenomics.mango.converters.GA4GHutil.alignmentRecordRDDtoJSON.
E                   : java.lang.NoClassDefFoundError: Could not initialize class org.apache.spark.sql.execution.datasources.parquet.ParquetSchemaConverter$
E                   	at org.apache.spark.sql.execution.datasources.parquet.ParquetFileFormat.buildReaderWithPartitionValues(ParquetFileFormat.scala:301)
E                   	at org.apache.spark.sql.execution.FileSourceScanExec.inputRDD$lzycompute(DataSourceScanExec.scala:285)
E                   	at org.apache.spark.sql.execution.FileSourceScanExec.inputRDD(DataSourceScanExec.scala:283)
E                   	at org.apache.spark.sql.execution.FileSourceScanExec.inputRDDs(DataSourceScanExec.scala:303)
E                   	at org.apache.spark.sql.execution.FilterExec.inputRDDs(basicPhysicalOperators.scala:124)
E                   	at org.apache.spark.sql.execution.ProjectExec.inputRDDs(basicPhysicalOperators.scala:42)
E                   	at org.apache.spark.sql.execution.WholeStageCodegenExec.doExecute(WholeStageCodegenExec.scala:386)
E                   	at org.apache.spark.sql.execution.SparkPlan$$anonfun$execute$1.apply(SparkPlan.scala:117)
E                   	at org.apache.spark.sql.execution.SparkPlan$$anonfun$execute$1.apply(SparkPlan.scala:117)
E                   	at org.apache.spark.sql.execution.SparkPlan$$anonfun$executeQuery$1.apply(SparkPlan.scala:138)
E                   	at org.apache.spark.rdd.RDDOperationScope$.withScope(RDDOperationScope.scala:151)
E                   	at org.apache.spark.sql.execution.SparkPlan.executeQuery(SparkPlan.scala:135)
E                   	at org.apache.spark.sql.execution.SparkPlan.execute(SparkPlan.scala:116)
E                   	at org.apache.spark.sql.execution.DeserializeToObjectExec.doExecute(objects.scala:95)
E                   	at org.apache.spark.sql.execution.SparkPlan$$anonfun$execute$1.apply(SparkPlan.scala:117)
E                   	at org.apache.spark.sql.execution.SparkPlan$$anonfun$execute$1.apply(SparkPlan.scala:117)
E                   	at org.apache.spark.sql.execution.SparkPlan$$anonfun$executeQuery$1.apply(SparkPlan.scala:138)
E                   	at org.apache.spark.rdd.RDDOperationScope$.withScope(RDDOperationScope.scala:151)
E                   	at org.apache.spark.sql.execution.SparkPlan.executeQuery(SparkPlan.scala:135)
E                   	at org.apache.spark.sql.execution.SparkPlan.execute(SparkPlan.scala:116)
E                   	at org.apache.spark.sql.execution.QueryExecution.toRdd$lzycompute(QueryExecution.scala:92)
E                   	at org.apache.spark.sql.execution.QueryExecution.toRdd(QueryExecution.scala:92)
E                   	at org.apache.spark.sql.Dataset.rdd$lzycompute(Dataset.scala:2586)
E                   	at org.apache.spark.sql.Dataset.rdd(Dataset.scala:2583)
E                   	at org.bdgenomics.adam.rdd.read.DatasetBoundAlignmentRecordRDD.rdd$lzycompute(AlignmentRecordRDD.scala:247)
E                   	at org.bdgenomics.adam.rdd.read.DatasetBoundAlignmentRecordRDD.rdd(AlignmentRecordRDD.scala:247)
E                   	at org.bdgenomics.mango.converters.GA4GHutil$.alignmentRecordRDDtoJSON(GA4GHutil.scala:63)
E                   	at org.bdgenomics.mango.converters.GA4GHutil.alignmentRecordRDDtoJSON(GA4GHutil.scala)
E                   	at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
E                   	at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
E                   	at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
E                   	at java.lang.reflect.Method.invoke(Method.java:497)
E                   	at py4j.reflection.MethodInvoker.invoke(MethodInvoker.java:244)
E                   	at py4j.reflection.ReflectionEngine.invoke(ReflectionEngine.java:357)
E                   	at py4j.Gateway.invoke(Gateway.java:280)
E                   	at py4j.commands.AbstractCommand.invokeMethod(AbstractCommand.java:132)
E                   	at py4j.commands.CallCommand.execute(CallCommand.java:79)
E                   	at py4j.GatewayConnection.run(GatewayConnection.java:214)
E                   	at java.lang.Thread.run(Thread.java:745)

I checked the 2.2.1 sql jar, which has this class.

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