FailedConsole Output

Skipping 3,121 KB.. Full Log
        :param name: the name of the member from which the answer comes from
            (e.g., *hello* in `object1.hello()`). Optional.
        """
        if is_error(answer)[0]:
            if len(answer) > 1:
                type = answer[1]
                value = OUTPUT_CONVERTER[type](answer[2:], gateway_client)
                if answer[1] == REFERENCE_TYPE:
                    raise Py4JJavaError(
                        "An error occurred while calling {0}{1}{2}.\n".
>                       format(target_id, ".", name), value)
E                   Py4JJavaError: An error occurred while calling o2114.loadAlignments.
E                   : java.lang.NoClassDefFoundError: Could not initialize class org.apache.spark.rdd.RDDOperationScope$
E                   	at org.apache.spark.SparkContext.withScope(SparkContext.scala:699)
E                   	at org.apache.spark.SparkContext.newAPIHadoopFile(SparkContext.scala:1146)
E                   	at org.bdgenomics.adam.rdd.ADAMContext.$anonfun$loadBam$1(ADAMContext.scala:2059)
E                   	at scala.Option.fold(Option.scala:175)
E                   	at org.apache.spark.rdd.Timer.time(Timer.scala:48)
E                   	at org.bdgenomics.adam.rdd.ADAMContext.loadBam(ADAMContext.scala:1999)
E                   	at org.bdgenomics.adam.rdd.ADAMContext.$anonfun$loadAlignments$1(ADAMContext.scala:3646)
E                   	at scala.Option.fold(Option.scala:175)
E                   	at org.apache.spark.rdd.Timer.time(Timer.scala:48)
E                   	at org.bdgenomics.adam.rdd.ADAMContext.loadAlignments(ADAMContext.scala:3637)
E                   	at org.bdgenomics.adam.api.java.JavaADAMContext.loadAlignments(JavaADAMContext.scala:110)
E                   	at sun.reflect.GeneratedMethodAccessor40.invoke(Unknown Source)
E                   	at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
E                   	at java.lang.reflect.Method.invoke(Method.java:498)
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:282)
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:238)
E                   	at java.lang.Thread.run(Thread.java:748)

/tmp/adamTest1UPduEN/deleteMePleaseThisIsNoLongerNeeded/spark-2.4.4-bin-without-hadoop-scala-2.12/python/lib/py4j-0.10.7-src.zip/py4j/protocol.py:328: Py4JJavaError
____________________ AlignmentDatasetTest.test_to_fragments ____________________

self = <bdgenomics.adam.test.alignmentDataset_test.AlignmentDatasetTest testMethod=test_to_fragments>

    def test_to_fragments(self):
    
        readsPath = self.resourceFile("unsorted.sam")
        ac = ADAMContext(self.ss)
    
>       reads = ac.loadAlignments(readsPath)

bdgenomics/adam/test/alignmentDataset_test.py:167: 
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 
bdgenomics/adam/adamContext.py:84: in loadAlignments
    _toJava(stringency, self._jvm))
/tmp/adamTest1UPduEN/deleteMePleaseThisIsNoLongerNeeded/spark-2.4.4-bin-without-hadoop-scala-2.12/python/lib/py4j-0.10.7-src.zip/py4j/java_gateway.py:1257: in __call__
    answer, self.gateway_client, self.target_id, self.name)
../spark-2.4.4-bin-without-hadoop-scala-2.12/python/pyspark/sql/utils.py:63: in deco
    return f(*a, **kw)
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 

answer = 'xro2182'
gateway_client = <py4j.java_gateway.GatewayClient object at 0x7f2f8c6ecbd0>
target_id = 'o2180', name = 'loadAlignments'

    def get_return_value(answer, gateway_client, target_id=None, name=None):
        """Converts an answer received from the Java gateway into a Python object.
    
        For example, string representation of integers are converted to Python
        integer, string representation of objects are converted to JavaObject
        instances, etc.
    
        :param answer: the string returned by the Java gateway
        :param gateway_client: the gateway client used to communicate with the Java
            Gateway. Only necessary if the answer is a reference (e.g., object,
            list, map)
        :param target_id: the name of the object from which the answer comes from
            (e.g., *object1* in `object1.hello()`). Optional.
        :param name: the name of the member from which the answer comes from
            (e.g., *hello* in `object1.hello()`). Optional.
        """
        if is_error(answer)[0]:
            if len(answer) > 1:
                type = answer[1]
                value = OUTPUT_CONVERTER[type](answer[2:], gateway_client)
                if answer[1] == REFERENCE_TYPE:
                    raise Py4JJavaError(
                        "An error occurred while calling {0}{1}{2}.\n".
>                       format(target_id, ".", name), value)
E                   Py4JJavaError: An error occurred while calling o2180.loadAlignments.
E                   : java.lang.NoClassDefFoundError: Could not initialize class org.apache.spark.rdd.RDDOperationScope$
E                   	at org.apache.spark.SparkContext.withScope(SparkContext.scala:699)
E                   	at org.apache.spark.SparkContext.newAPIHadoopFile(SparkContext.scala:1146)
E                   	at org.bdgenomics.adam.rdd.ADAMContext.$anonfun$loadBam$1(ADAMContext.scala:2059)
E                   	at scala.Option.fold(Option.scala:175)
E                   	at org.apache.spark.rdd.Timer.time(Timer.scala:48)
E                   	at org.bdgenomics.adam.rdd.ADAMContext.loadBam(ADAMContext.scala:1999)
E                   	at org.bdgenomics.adam.rdd.ADAMContext.$anonfun$loadAlignments$1(ADAMContext.scala:3646)
E                   	at scala.Option.fold(Option.scala:175)
E                   	at org.apache.spark.rdd.Timer.time(Timer.scala:48)
E                   	at org.bdgenomics.adam.rdd.ADAMContext.loadAlignments(ADAMContext.scala:3637)
E                   	at org.bdgenomics.adam.api.java.JavaADAMContext.loadAlignments(JavaADAMContext.scala:110)
E                   	at sun.reflect.GeneratedMethodAccessor40.invoke(Unknown Source)
E                   	at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
E                   	at java.lang.reflect.Method.invoke(Method.java:498)
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:282)
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:238)
E                   	at java.lang.Thread.run(Thread.java:748)

/tmp/adamTest1UPduEN/deleteMePleaseThisIsNoLongerNeeded/spark-2.4.4-bin-without-hadoop-scala-2.12/python/lib/py4j-0.10.7-src.zip/py4j/protocol.py:328: Py4JJavaError
_____________________ AlignmentDatasetTest.test_transform ______________________

self = <bdgenomics.adam.test.alignmentDataset_test.AlignmentDatasetTest testMethod=test_transform>

    def test_transform(self):
    
        readsPath = self.resourceFile("unsorted.sam")
        ac = ADAMContext(self.ss)
    
>       reads = ac.loadAlignments(readsPath)

bdgenomics/adam/test/alignmentDataset_test.py:121: 
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 
bdgenomics/adam/adamContext.py:84: in loadAlignments
    _toJava(stringency, self._jvm))
/tmp/adamTest1UPduEN/deleteMePleaseThisIsNoLongerNeeded/spark-2.4.4-bin-without-hadoop-scala-2.12/python/lib/py4j-0.10.7-src.zip/py4j/java_gateway.py:1257: in __call__
    answer, self.gateway_client, self.target_id, self.name)
../spark-2.4.4-bin-without-hadoop-scala-2.12/python/pyspark/sql/utils.py:63: in deco
    return f(*a, **kw)
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 

answer = 'xro2248'
gateway_client = <py4j.java_gateway.GatewayClient object at 0x7f2f8c6ecbd0>
target_id = 'o2246', name = 'loadAlignments'

    def get_return_value(answer, gateway_client, target_id=None, name=None):
        """Converts an answer received from the Java gateway into a Python object.
    
        For example, string representation of integers are converted to Python
        integer, string representation of objects are converted to JavaObject
        instances, etc.
    
        :param answer: the string returned by the Java gateway
        :param gateway_client: the gateway client used to communicate with the Java
            Gateway. Only necessary if the answer is a reference (e.g., object,
            list, map)
        :param target_id: the name of the object from which the answer comes from
            (e.g., *object1* in `object1.hello()`). Optional.
        :param name: the name of the member from which the answer comes from
            (e.g., *hello* in `object1.hello()`). Optional.
        """
        if is_error(answer)[0]:
            if len(answer) > 1:
                type = answer[1]
                value = OUTPUT_CONVERTER[type](answer[2:], gateway_client)
                if answer[1] == REFERENCE_TYPE:
                    raise Py4JJavaError(
                        "An error occurred while calling {0}{1}{2}.\n".
>                       format(target_id, ".", name), value)
E                   Py4JJavaError: An error occurred while calling o2246.loadAlignments.
E                   : java.lang.NoClassDefFoundError: Could not initialize class org.apache.spark.rdd.RDDOperationScope$
E                   	at org.apache.spark.SparkContext.withScope(SparkContext.scala:699)
E                   	at org.apache.spark.SparkContext.newAPIHadoopFile(SparkContext.scala:1146)
E                   	at org.bdgenomics.adam.rdd.ADAMContext.$anonfun$loadBam$1(ADAMContext.scala:2059)
E                   	at scala.Option.fold(Option.scala:175)
E                   	at org.apache.spark.rdd.Timer.time(Timer.scala:48)
E                   	at org.bdgenomics.adam.rdd.ADAMContext.loadBam(ADAMContext.scala:1999)
E                   	at org.bdgenomics.adam.rdd.ADAMContext.$anonfun$loadAlignments$1(ADAMContext.scala:3646)
E                   	at scala.Option.fold(Option.scala:175)
E                   	at org.apache.spark.rdd.Timer.time(Timer.scala:48)
E                   	at org.bdgenomics.adam.rdd.ADAMContext.loadAlignments(ADAMContext.scala:3637)
E                   	at org.bdgenomics.adam.api.java.JavaADAMContext.loadAlignments(JavaADAMContext.scala:110)
E                   	at sun.reflect.GeneratedMethodAccessor40.invoke(Unknown Source)
E                   	at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
E                   	at java.lang.reflect.Method.invoke(Method.java:498)
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:282)
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:238)
E                   	at java.lang.Thread.run(Thread.java:748)

/tmp/adamTest1UPduEN/deleteMePleaseThisIsNoLongerNeeded/spark-2.4.4-bin-without-hadoop-scala-2.12/python/lib/py4j-0.10.7-src.zip/py4j/protocol.py:328: Py4JJavaError
_______________ AlignmentDatasetTest.test_transmute_to_coverage ________________

self = <bdgenomics.adam.test.alignmentDataset_test.AlignmentDatasetTest testMethod=test_transmute_to_coverage>

    def test_transmute_to_coverage(self):
    
        readsPath = self.resourceFile("unsorted.sam")
        ac = ADAMContext(self.ss)
    
>       reads = ac.loadAlignments(readsPath)

bdgenomics/adam/test/alignmentDataset_test.py:133: 
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 
bdgenomics/adam/adamContext.py:84: in loadAlignments
    _toJava(stringency, self._jvm))
/tmp/adamTest1UPduEN/deleteMePleaseThisIsNoLongerNeeded/spark-2.4.4-bin-without-hadoop-scala-2.12/python/lib/py4j-0.10.7-src.zip/py4j/java_gateway.py:1257: in __call__
    answer, self.gateway_client, self.target_id, self.name)
../spark-2.4.4-bin-without-hadoop-scala-2.12/python/pyspark/sql/utils.py:63: in deco
    return f(*a, **kw)
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 

answer = 'xro2314'
gateway_client = <py4j.java_gateway.GatewayClient object at 0x7f2f8c6ecbd0>
target_id = 'o2312', name = 'loadAlignments'

    def get_return_value(answer, gateway_client, target_id=None, name=None):
        """Converts an answer received from the Java gateway into a Python object.
    
        For example, string representation of integers are converted to Python
        integer, string representation of objects are converted to JavaObject
        instances, etc.
    
        :param answer: the string returned by the Java gateway
        :param gateway_client: the gateway client used to communicate with the Java
            Gateway. Only necessary if the answer is a reference (e.g., object,
            list, map)
        :param target_id: the name of the object from which the answer comes from
            (e.g., *object1* in `object1.hello()`). Optional.
        :param name: the name of the member from which the answer comes from
            (e.g., *hello* in `object1.hello()`). Optional.
        """
        if is_error(answer)[0]:
            if len(answer) > 1:
                type = answer[1]
                value = OUTPUT_CONVERTER[type](answer[2:], gateway_client)
                if answer[1] == REFERENCE_TYPE:
                    raise Py4JJavaError(
                        "An error occurred while calling {0}{1}{2}.\n".
>                       format(target_id, ".", name), value)
E                   Py4JJavaError: An error occurred while calling o2312.loadAlignments.
E                   : java.lang.NoClassDefFoundError: Could not initialize class org.apache.spark.rdd.RDDOperationScope$
E                   	at org.apache.spark.SparkContext.withScope(SparkContext.scala:699)
E                   	at org.apache.spark.SparkContext.newAPIHadoopFile(SparkContext.scala:1146)
E                   	at org.bdgenomics.adam.rdd.ADAMContext.$anonfun$loadBam$1(ADAMContext.scala:2059)
E                   	at scala.Option.fold(Option.scala:175)
E                   	at org.apache.spark.rdd.Timer.time(Timer.scala:48)
E                   	at org.bdgenomics.adam.rdd.ADAMContext.loadBam(ADAMContext.scala:1999)
E                   	at org.bdgenomics.adam.rdd.ADAMContext.$anonfun$loadAlignments$1(ADAMContext.scala:3646)
E                   	at scala.Option.fold(Option.scala:175)
E                   	at org.apache.spark.rdd.Timer.time(Timer.scala:48)
E                   	at org.bdgenomics.adam.rdd.ADAMContext.loadAlignments(ADAMContext.scala:3637)
E                   	at org.bdgenomics.adam.api.java.JavaADAMContext.loadAlignments(JavaADAMContext.scala:110)
E                   	at sun.reflect.GeneratedMethodAccessor40.invoke(Unknown Source)
E                   	at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
E                   	at java.lang.reflect.Method.invoke(Method.java:498)
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:282)
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:238)
E                   	at java.lang.Thread.run(Thread.java:748)

/tmp/adamTest1UPduEN/deleteMePleaseThisIsNoLongerNeeded/spark-2.4.4-bin-without-hadoop-scala-2.12/python/lib/py4j-0.10.7-src.zip/py4j/protocol.py:328: Py4JJavaError
_______________________ AlignmentDatasetTest.test_union ________________________

self = <bdgenomics.adam.test.alignmentDataset_test.AlignmentDatasetTest testMethod=test_union>

    def test_union(self):
    
        testFile1 = self.resourceFile("sorted.sam")
        testFile2 = self.resourceFile("unordered.sam")
        ac = ADAMContext(self.ss)
    
>       reads1 = ac.loadAlignments(testFile1)

bdgenomics/adam/test/alignmentDataset_test.py:65: 
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 
bdgenomics/adam/adamContext.py:84: in loadAlignments
    _toJava(stringency, self._jvm))
/tmp/adamTest1UPduEN/deleteMePleaseThisIsNoLongerNeeded/spark-2.4.4-bin-without-hadoop-scala-2.12/python/lib/py4j-0.10.7-src.zip/py4j/java_gateway.py:1257: in __call__
    answer, self.gateway_client, self.target_id, self.name)
../spark-2.4.4-bin-without-hadoop-scala-2.12/python/pyspark/sql/utils.py:63: in deco
    return f(*a, **kw)
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 

answer = 'xro2380'
gateway_client = <py4j.java_gateway.GatewayClient object at 0x7f2f8c6ecbd0>
target_id = 'o2378', name = 'loadAlignments'

    def get_return_value(answer, gateway_client, target_id=None, name=None):
        """Converts an answer received from the Java gateway into a Python object.
    
        For example, string representation of integers are converted to Python
        integer, string representation of objects are converted to JavaObject
        instances, etc.
    
        :param answer: the string returned by the Java gateway
        :param gateway_client: the gateway client used to communicate with the Java
            Gateway. Only necessary if the answer is a reference (e.g., object,
            list, map)
        :param target_id: the name of the object from which the answer comes from
            (e.g., *object1* in `object1.hello()`). Optional.
        :param name: the name of the member from which the answer comes from
            (e.g., *hello* in `object1.hello()`). Optional.
        """
        if is_error(answer)[0]:
            if len(answer) > 1:
                type = answer[1]
                value = OUTPUT_CONVERTER[type](answer[2:], gateway_client)
                if answer[1] == REFERENCE_TYPE:
                    raise Py4JJavaError(
                        "An error occurred while calling {0}{1}{2}.\n".
>                       format(target_id, ".", name), value)
E                   Py4JJavaError: An error occurred while calling o2378.loadAlignments.
E                   : java.lang.NoClassDefFoundError: Could not initialize class org.apache.spark.rdd.RDDOperationScope$
E                   	at org.apache.spark.SparkContext.withScope(SparkContext.scala:699)
E                   	at org.apache.spark.SparkContext.newAPIHadoopFile(SparkContext.scala:1146)
E                   	at org.bdgenomics.adam.rdd.ADAMContext.$anonfun$loadBam$1(ADAMContext.scala:2059)
E                   	at scala.Option.fold(Option.scala:175)
E                   	at org.apache.spark.rdd.Timer.time(Timer.scala:48)
E                   	at org.bdgenomics.adam.rdd.ADAMContext.loadBam(ADAMContext.scala:1999)
E                   	at org.bdgenomics.adam.rdd.ADAMContext.$anonfun$loadAlignments$1(ADAMContext.scala:3646)
E                   	at scala.Option.fold(Option.scala:175)
E                   	at org.apache.spark.rdd.Timer.time(Timer.scala:48)
E                   	at org.bdgenomics.adam.rdd.ADAMContext.loadAlignments(ADAMContext.scala:3637)
E                   	at org.bdgenomics.adam.api.java.JavaADAMContext.loadAlignments(JavaADAMContext.scala:110)
E                   	at sun.reflect.GeneratedMethodAccessor40.invoke(Unknown Source)
E                   	at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
E                   	at java.lang.reflect.Method.invoke(Method.java:498)
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:282)
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:238)
E                   	at java.lang.Thread.run(Thread.java:748)

/tmp/adamTest1UPduEN/deleteMePleaseThisIsNoLongerNeeded/spark-2.4.4-bin-without-hadoop-scala-2.12/python/lib/py4j-0.10.7-src.zip/py4j/protocol.py:328: Py4JJavaError
_________________ CoverageDatasetTest.test_aggregatedCoverage __________________

self = <bdgenomics.adam.test.coverageDataset_test.CoverageDatasetTest testMethod=test_aggregatedCoverage>

    def test_aggregatedCoverage(self):
        testFile = self.resourceFile("small.sam")
        ac = ADAMContext(self.ss)
    
>       reads = ac.loadAlignments(testFile)

bdgenomics/adam/test/coverageDataset_test.py:65: 
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 
bdgenomics/adam/adamContext.py:84: in loadAlignments
    _toJava(stringency, self._jvm))
/tmp/adamTest1UPduEN/deleteMePleaseThisIsNoLongerNeeded/spark-2.4.4-bin-without-hadoop-scala-2.12/python/lib/py4j-0.10.7-src.zip/py4j/java_gateway.py:1257: in __call__
    answer, self.gateway_client, self.target_id, self.name)
../spark-2.4.4-bin-without-hadoop-scala-2.12/python/pyspark/sql/utils.py:63: in deco
    return f(*a, **kw)
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 

answer = 'xro2446'
gateway_client = <py4j.java_gateway.GatewayClient object at 0x7f2f8c6ecbd0>
target_id = 'o2444', name = 'loadAlignments'

    def get_return_value(answer, gateway_client, target_id=None, name=None):
        """Converts an answer received from the Java gateway into a Python object.
    
        For example, string representation of integers are converted to Python
        integer, string representation of objects are converted to JavaObject
        instances, etc.
    
        :param answer: the string returned by the Java gateway
        :param gateway_client: the gateway client used to communicate with the Java
            Gateway. Only necessary if the answer is a reference (e.g., object,
            list, map)
        :param target_id: the name of the object from which the answer comes from
            (e.g., *object1* in `object1.hello()`). Optional.
        :param name: the name of the member from which the answer comes from
            (e.g., *hello* in `object1.hello()`). Optional.
        """
        if is_error(answer)[0]:
            if len(answer) > 1:
                type = answer[1]
                value = OUTPUT_CONVERTER[type](answer[2:], gateway_client)
                if answer[1] == REFERENCE_TYPE:
                    raise Py4JJavaError(
                        "An error occurred while calling {0}{1}{2}.\n".
>                       format(target_id, ".", name), value)
E                   Py4JJavaError: An error occurred while calling o2444.loadAlignments.
E                   : java.lang.NoClassDefFoundError: Could not initialize class org.apache.spark.rdd.RDDOperationScope$
E                   	at org.apache.spark.SparkContext.withScope(SparkContext.scala:699)
E                   	at org.apache.spark.SparkContext.newAPIHadoopFile(SparkContext.scala:1146)
E                   	at org.bdgenomics.adam.rdd.ADAMContext.$anonfun$loadBam$1(ADAMContext.scala:2059)
E                   	at scala.Option.fold(Option.scala:175)
E                   	at org.apache.spark.rdd.Timer.time(Timer.scala:48)
E                   	at org.bdgenomics.adam.rdd.ADAMContext.loadBam(ADAMContext.scala:1999)
E                   	at org.bdgenomics.adam.rdd.ADAMContext.$anonfun$loadAlignments$1(ADAMContext.scala:3646)
E                   	at scala.Option.fold(Option.scala:175)
E                   	at org.apache.spark.rdd.Timer.time(Timer.scala:48)
E                   	at org.bdgenomics.adam.rdd.ADAMContext.loadAlignments(ADAMContext.scala:3637)
E                   	at org.bdgenomics.adam.api.java.JavaADAMContext.loadAlignments(JavaADAMContext.scala:110)
E                   	at sun.reflect.GeneratedMethodAccessor40.invoke(Unknown Source)
E                   	at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
E                   	at java.lang.reflect.Method.invoke(Method.java:498)
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:282)
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:238)
E                   	at java.lang.Thread.run(Thread.java:748)

/tmp/adamTest1UPduEN/deleteMePleaseThisIsNoLongerNeeded/spark-2.4.4-bin-without-hadoop-scala-2.12/python/lib/py4j-0.10.7-src.zip/py4j/protocol.py:328: Py4JJavaError
______________________ CoverageDatasetTest.test_collapse _______________________

self = <bdgenomics.adam.test.coverageDataset_test.CoverageDatasetTest testMethod=test_collapse>

    def test_collapse(self):
        testFile = self.resourceFile("sorted.sam")
        ac = ADAMContext(self.ss)
    
>       reads = ac.loadAlignments(testFile)

bdgenomics/adam/test/coverageDataset_test.py:45: 
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 
bdgenomics/adam/adamContext.py:84: in loadAlignments
    _toJava(stringency, self._jvm))
/tmp/adamTest1UPduEN/deleteMePleaseThisIsNoLongerNeeded/spark-2.4.4-bin-without-hadoop-scala-2.12/python/lib/py4j-0.10.7-src.zip/py4j/java_gateway.py:1257: in __call__
    answer, self.gateway_client, self.target_id, self.name)
../spark-2.4.4-bin-without-hadoop-scala-2.12/python/pyspark/sql/utils.py:63: in deco
    return f(*a, **kw)
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 

answer = 'xro2512'
gateway_client = <py4j.java_gateway.GatewayClient object at 0x7f2f8c6ecbd0>
target_id = 'o2510', name = 'loadAlignments'

    def get_return_value(answer, gateway_client, target_id=None, name=None):
        """Converts an answer received from the Java gateway into a Python object.
    
        For example, string representation of integers are converted to Python
        integer, string representation of objects are converted to JavaObject
        instances, etc.
    
        :param answer: the string returned by the Java gateway
        :param gateway_client: the gateway client used to communicate with the Java
            Gateway. Only necessary if the answer is a reference (e.g., object,
            list, map)
        :param target_id: the name of the object from which the answer comes from
            (e.g., *object1* in `object1.hello()`). Optional.
        :param name: the name of the member from which the answer comes from
            (e.g., *hello* in `object1.hello()`). Optional.
        """
        if is_error(answer)[0]:
            if len(answer) > 1:
                type = answer[1]
                value = OUTPUT_CONVERTER[type](answer[2:], gateway_client)
                if answer[1] == REFERENCE_TYPE:
                    raise Py4JJavaError(
                        "An error occurred while calling {0}{1}{2}.\n".
>                       format(target_id, ".", name), value)
E                   Py4JJavaError: An error occurred while calling o2510.loadAlignments.
E                   : java.lang.NoClassDefFoundError: Could not initialize class org.apache.spark.rdd.RDDOperationScope$
E                   	at org.apache.spark.SparkContext.withScope(SparkContext.scala:699)
E                   	at org.apache.spark.SparkContext.newAPIHadoopFile(SparkContext.scala:1146)
E                   	at org.bdgenomics.adam.rdd.ADAMContext.$anonfun$loadBam$1(ADAMContext.scala:2059)
E                   	at scala.Option.fold(Option.scala:175)
E                   	at org.apache.spark.rdd.Timer.time(Timer.scala:48)
E                   	at org.bdgenomics.adam.rdd.ADAMContext.loadBam(ADAMContext.scala:1999)
E                   	at org.bdgenomics.adam.rdd.ADAMContext.$anonfun$loadAlignments$1(ADAMContext.scala:3646)
E                   	at scala.Option.fold(Option.scala:175)
E                   	at org.apache.spark.rdd.Timer.time(Timer.scala:48)
E                   	at org.bdgenomics.adam.rdd.ADAMContext.loadAlignments(ADAMContext.scala:3637)
E                   	at org.bdgenomics.adam.api.java.JavaADAMContext.loadAlignments(JavaADAMContext.scala:110)
E                   	at sun.reflect.GeneratedMethodAccessor40.invoke(Unknown Source)
E                   	at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
E                   	at java.lang.reflect.Method.invoke(Method.java:498)
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:282)
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:238)
E                   	at java.lang.Thread.run(Thread.java:748)

/tmp/adamTest1UPduEN/deleteMePleaseThisIsNoLongerNeeded/spark-2.4.4-bin-without-hadoop-scala-2.12/python/lib/py4j-0.10.7-src.zip/py4j/protocol.py:328: Py4JJavaError
_______________________ CoverageDatasetTest.test_flatten _______________________

self = <bdgenomics.adam.test.coverageDataset_test.CoverageDatasetTest testMethod=test_flatten>

    def test_flatten(self):
        testFile = self.resourceFile("small.sam")
        ac = ADAMContext(self.ss)
    
>       reads = ac.loadAlignments(testFile)

bdgenomics/adam/test/coverageDataset_test.py:74: 
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 
bdgenomics/adam/adamContext.py:84: in loadAlignments
    _toJava(stringency, self._jvm))
/tmp/adamTest1UPduEN/deleteMePleaseThisIsNoLongerNeeded/spark-2.4.4-bin-without-hadoop-scala-2.12/python/lib/py4j-0.10.7-src.zip/py4j/java_gateway.py:1257: in __call__
    answer, self.gateway_client, self.target_id, self.name)
../spark-2.4.4-bin-without-hadoop-scala-2.12/python/pyspark/sql/utils.py:63: in deco
    return f(*a, **kw)
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 

answer = 'xro2578'
gateway_client = <py4j.java_gateway.GatewayClient object at 0x7f2f8c6ecbd0>
target_id = 'o2576', name = 'loadAlignments'

    def get_return_value(answer, gateway_client, target_id=None, name=None):
        """Converts an answer received from the Java gateway into a Python object.
    
        For example, string representation of integers are converted to Python
        integer, string representation of objects are converted to JavaObject
        instances, etc.
    
        :param answer: the string returned by the Java gateway
        :param gateway_client: the gateway client used to communicate with the Java
            Gateway. Only necessary if the answer is a reference (e.g., object,
            list, map)
        :param target_id: the name of the object from which the answer comes from
            (e.g., *object1* in `object1.hello()`). Optional.
        :param name: the name of the member from which the answer comes from
            (e.g., *hello* in `object1.hello()`). Optional.
        """
        if is_error(answer)[0]:
            if len(answer) > 1:
                type = answer[1]
                value = OUTPUT_CONVERTER[type](answer[2:], gateway_client)
                if answer[1] == REFERENCE_TYPE:
                    raise Py4JJavaError(
                        "An error occurred while calling {0}{1}{2}.\n".
>                       format(target_id, ".", name), value)
E                   Py4JJavaError: An error occurred while calling o2576.loadAlignments.
E                   : java.lang.NoClassDefFoundError: Could not initialize class org.apache.spark.rdd.RDDOperationScope$
E                   	at org.apache.spark.SparkContext.withScope(SparkContext.scala:699)
E                   	at org.apache.spark.SparkContext.newAPIHadoopFile(SparkContext.scala:1146)
E                   	at org.bdgenomics.adam.rdd.ADAMContext.$anonfun$loadBam$1(ADAMContext.scala:2059)
E                   	at scala.Option.fold(Option.scala:175)
E                   	at org.apache.spark.rdd.Timer.time(Timer.scala:48)
E                   	at org.bdgenomics.adam.rdd.ADAMContext.loadBam(ADAMContext.scala:1999)
E                   	at org.bdgenomics.adam.rdd.ADAMContext.$anonfun$loadAlignments$1(ADAMContext.scala:3646)
E                   	at scala.Option.fold(Option.scala:175)
E                   	at org.apache.spark.rdd.Timer.time(Timer.scala:48)
E                   	at org.bdgenomics.adam.rdd.ADAMContext.loadAlignments(ADAMContext.scala:3637)
E                   	at org.bdgenomics.adam.api.java.JavaADAMContext.loadAlignments(JavaADAMContext.scala:110)
E                   	at sun.reflect.GeneratedMethodAccessor40.invoke(Unknown Source)
E                   	at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
E                   	at java.lang.reflect.Method.invoke(Method.java:498)
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:282)
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:238)
E                   	at java.lang.Thread.run(Thread.java:748)

/tmp/adamTest1UPduEN/deleteMePleaseThisIsNoLongerNeeded/spark-2.4.4-bin-without-hadoop-scala-2.12/python/lib/py4j-0.10.7-src.zip/py4j/protocol.py:328: Py4JJavaError
________________________ CoverageDatasetTest.test_save _________________________

self = <bdgenomics.adam.test.coverageDataset_test.CoverageDatasetTest testMethod=test_save>

    def test_save(self):
    
        testFile = self.resourceFile("sorted.sam")
        ac = ADAMContext(self.ss)
    
>       reads = ac.loadAlignments(testFile)

bdgenomics/adam/test/coverageDataset_test.py:32: 
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 
bdgenomics/adam/adamContext.py:84: in loadAlignments
    _toJava(stringency, self._jvm))
/tmp/adamTest1UPduEN/deleteMePleaseThisIsNoLongerNeeded/spark-2.4.4-bin-without-hadoop-scala-2.12/python/lib/py4j-0.10.7-src.zip/py4j/java_gateway.py:1257: in __call__
    answer, self.gateway_client, self.target_id, self.name)
../spark-2.4.4-bin-without-hadoop-scala-2.12/python/pyspark/sql/utils.py:63: in deco
    return f(*a, **kw)
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 

answer = 'xro2644'
gateway_client = <py4j.java_gateway.GatewayClient object at 0x7f2f8c6ecbd0>
target_id = 'o2642', name = 'loadAlignments'

    def get_return_value(answer, gateway_client, target_id=None, name=None):
        """Converts an answer received from the Java gateway into a Python object.
    
        For example, string representation of integers are converted to Python
        integer, string representation of objects are converted to JavaObject
        instances, etc.
    
        :param answer: the string returned by the Java gateway
        :param gateway_client: the gateway client used to communicate with the Java
            Gateway. Only necessary if the answer is a reference (e.g., object,
            list, map)
        :param target_id: the name of the object from which the answer comes from
            (e.g., *object1* in `object1.hello()`). Optional.
        :param name: the name of the member from which the answer comes from
            (e.g., *hello* in `object1.hello()`). Optional.
        """
        if is_error(answer)[0]:
            if len(answer) > 1:
                type = answer[1]
                value = OUTPUT_CONVERTER[type](answer[2:], gateway_client)
                if answer[1] == REFERENCE_TYPE:
                    raise Py4JJavaError(
                        "An error occurred while calling {0}{1}{2}.\n".
>                       format(target_id, ".", name), value)
E                   Py4JJavaError: An error occurred while calling o2642.loadAlignments.
E                   : java.lang.NoClassDefFoundError: Could not initialize class org.apache.spark.rdd.RDDOperationScope$
E                   	at org.apache.spark.SparkContext.withScope(SparkContext.scala:699)
E                   	at org.apache.spark.SparkContext.newAPIHadoopFile(SparkContext.scala:1146)
E                   	at org.bdgenomics.adam.rdd.ADAMContext.$anonfun$loadBam$1(ADAMContext.scala:2059)
E                   	at scala.Option.fold(Option.scala:175)
E                   	at org.apache.spark.rdd.Timer.time(Timer.scala:48)
E                   	at org.bdgenomics.adam.rdd.ADAMContext.loadBam(ADAMContext.scala:1999)
E                   	at org.bdgenomics.adam.rdd.ADAMContext.$anonfun$loadAlignments$1(ADAMContext.scala:3646)
E                   	at scala.Option.fold(Option.scala:175)
E                   	at org.apache.spark.rdd.Timer.time(Timer.scala:48)
E                   	at org.bdgenomics.adam.rdd.ADAMContext.loadAlignments(ADAMContext.scala:3637)
E                   	at org.bdgenomics.adam.api.java.JavaADAMContext.loadAlignments(JavaADAMContext.scala:110)
E                   	at sun.reflect.GeneratedMethodAccessor40.invoke(Unknown Source)
E                   	at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
E                   	at java.lang.reflect.Method.invoke(Method.java:498)
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:282)
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:238)
E                   	at java.lang.Thread.run(Thread.java:748)

/tmp/adamTest1UPduEN/deleteMePleaseThisIsNoLongerNeeded/spark-2.4.4-bin-without-hadoop-scala-2.12/python/lib/py4j-0.10.7-src.zip/py4j/protocol.py:328: Py4JJavaError
_____________________ CoverageDatasetTest.test_toFeatures ______________________

self = <bdgenomics.adam.test.coverageDataset_test.CoverageDatasetTest testMethod=test_toFeatures>

    def test_toFeatures(self):
        testFile = self.resourceFile("sorted.sam")
        ac = ADAMContext(self.ss)
    
>       reads = ac.loadAlignments(testFile)

bdgenomics/adam/test/coverageDataset_test.py:54: 
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 
bdgenomics/adam/adamContext.py:84: in loadAlignments
    _toJava(stringency, self._jvm))
/tmp/adamTest1UPduEN/deleteMePleaseThisIsNoLongerNeeded/spark-2.4.4-bin-without-hadoop-scala-2.12/python/lib/py4j-0.10.7-src.zip/py4j/java_gateway.py:1257: in __call__
    answer, self.gateway_client, self.target_id, self.name)
../spark-2.4.4-bin-without-hadoop-scala-2.12/python/pyspark/sql/utils.py:63: in deco
    return f(*a, **kw)
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 

answer = 'xro2710'
gateway_client = <py4j.java_gateway.GatewayClient object at 0x7f2f8c6ecbd0>
target_id = 'o2708', name = 'loadAlignments'

    def get_return_value(answer, gateway_client, target_id=None, name=None):
        """Converts an answer received from the Java gateway into a Python object.
    
        For example, string representation of integers are converted to Python
        integer, string representation of objects are converted to JavaObject
        instances, etc.
    
        :param answer: the string returned by the Java gateway
        :param gateway_client: the gateway client used to communicate with the Java
            Gateway. Only necessary if the answer is a reference (e.g., object,
            list, map)
        :param target_id: the name of the object from which the answer comes from
            (e.g., *object1* in `object1.hello()`). Optional.
        :param name: the name of the member from which the answer comes from
            (e.g., *hello* in `object1.hello()`). Optional.
        """
        if is_error(answer)[0]:
            if len(answer) > 1:
                type = answer[1]
                value = OUTPUT_CONVERTER[type](answer[2:], gateway_client)
                if answer[1] == REFERENCE_TYPE:
                    raise Py4JJavaError(
                        "An error occurred while calling {0}{1}{2}.\n".
>                       format(target_id, ".", name), value)
E                   Py4JJavaError: An error occurred while calling o2708.loadAlignments.
E                   : java.lang.NoClassDefFoundError: Could not initialize class org.apache.spark.rdd.RDDOperationScope$
E                   	at org.apache.spark.SparkContext.withScope(SparkContext.scala:699)
E                   	at org.apache.spark.SparkContext.newAPIHadoopFile(SparkContext.scala:1146)
E                   	at org.bdgenomics.adam.rdd.ADAMContext.$anonfun$loadBam$1(ADAMContext.scala:2059)
E                   	at scala.Option.fold(Option.scala:175)
E                   	at org.apache.spark.rdd.Timer.time(Timer.scala:48)
E                   	at org.bdgenomics.adam.rdd.ADAMContext.loadBam(ADAMContext.scala:1999)
E                   	at org.bdgenomics.adam.rdd.ADAMContext.$anonfun$loadAlignments$1(ADAMContext.scala:3646)
E                   	at scala.Option.fold(Option.scala:175)
E                   	at org.apache.spark.rdd.Timer.time(Timer.scala:48)
E                   	at org.bdgenomics.adam.rdd.ADAMContext.loadAlignments(ADAMContext.scala:3637)
E                   	at org.bdgenomics.adam.api.java.JavaADAMContext.loadAlignments(JavaADAMContext.scala:110)
E                   	at sun.reflect.GeneratedMethodAccessor40.invoke(Unknown Source)
E                   	at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
E                   	at java.lang.reflect.Method.invoke(Method.java:498)
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:282)
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:238)
E                   	at java.lang.Thread.run(Thread.java:748)

/tmp/adamTest1UPduEN/deleteMePleaseThisIsNoLongerNeeded/spark-2.4.4-bin-without-hadoop-scala-2.12/python/lib/py4j-0.10.7-src.zip/py4j/protocol.py:328: Py4JJavaError
____________________ FeatureDatasetTest.test_round_trip_bed ____________________

self = <bdgenomics.adam.test.featureDataset_test.FeatureDatasetTest testMethod=test_round_trip_bed>

    def test_round_trip_bed(self):
    
        testFile = self.resourceFile("gencode.v7.annotation.trunc10.bed")
        ac = ADAMContext(self.ss)
    
>       features = ac.loadFeatures(testFile)

bdgenomics/adam/test/featureDataset_test.py:48: 
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 
bdgenomics/adam/adamContext.py:199: in loadFeatures
    _toJava(stringency, self._jvm))
/tmp/adamTest1UPduEN/deleteMePleaseThisIsNoLongerNeeded/spark-2.4.4-bin-without-hadoop-scala-2.12/python/lib/py4j-0.10.7-src.zip/py4j/java_gateway.py:1257: in __call__
    answer, self.gateway_client, self.target_id, self.name)
../spark-2.4.4-bin-without-hadoop-scala-2.12/python/pyspark/sql/utils.py:63: in deco
    return f(*a, **kw)
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 

answer = 'xro2776'
gateway_client = <py4j.java_gateway.GatewayClient object at 0x7f2f8c6ecbd0>
target_id = 'o2774', name = 'loadFeatures'

    def get_return_value(answer, gateway_client, target_id=None, name=None):
        """Converts an answer received from the Java gateway into a Python object.
    
        For example, string representation of integers are converted to Python
        integer, string representation of objects are converted to JavaObject
        instances, etc.
    
        :param answer: the string returned by the Java gateway
        :param gateway_client: the gateway client used to communicate with the Java
            Gateway. Only necessary if the answer is a reference (e.g., object,
            list, map)
        :param target_id: the name of the object from which the answer comes from
            (e.g., *object1* in `object1.hello()`). Optional.
        :param name: the name of the member from which the answer comes from
            (e.g., *hello* in `object1.hello()`). Optional.
        """
        if is_error(answer)[0]:
            if len(answer) > 1:
                type = answer[1]
                value = OUTPUT_CONVERTER[type](answer[2:], gateway_client)
                if answer[1] == REFERENCE_TYPE:
                    raise Py4JJavaError(
                        "An error occurred while calling {0}{1}{2}.\n".
>                       format(target_id, ".", name), value)
E                   Py4JJavaError: An error occurred while calling o2774.loadFeatures.
E                   : java.lang.NoClassDefFoundError: Could not initialize class org.apache.spark.rdd.RDDOperationScope$
E                   	at org.apache.spark.SparkContext.withScope(SparkContext.scala:699)
E                   	at org.apache.spark.SparkContext.textFile(SparkContext.scala:828)
E                   	at org.bdgenomics.adam.rdd.ADAMContext.$anonfun$loadBed$1(ADAMContext.scala:3222)
E                   	at scala.Option.fold(Option.scala:175)
E                   	at org.apache.spark.rdd.Timer.time(Timer.scala:48)
E                   	at org.bdgenomics.adam.rdd.ADAMContext.loadBed(ADAMContext.scala:3220)
E                   	at org.bdgenomics.adam.rdd.ADAMContext.$anonfun$loadFeatures$1(ADAMContext.scala:3434)
E                   	at scala.Option.fold(Option.scala:175)
E                   	at org.apache.spark.rdd.Timer.time(Timer.scala:48)
E                   	at org.bdgenomics.adam.rdd.ADAMContext.loadFeatures(ADAMContext.scala:3426)
E                   	at org.bdgenomics.adam.api.java.JavaADAMContext.loadFeatures(JavaADAMContext.scala:236)
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:498)
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:282)
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:238)
E                   	at java.lang.Thread.run(Thread.java:748)

/tmp/adamTest1UPduEN/deleteMePleaseThisIsNoLongerNeeded/spark-2.4.4-bin-without-hadoop-scala-2.12/python/lib/py4j-0.10.7-src.zip/py4j/protocol.py:328: Py4JJavaError
____________________ FeatureDatasetTest.test_round_trip_gtf ____________________

self = <bdgenomics.adam.test.featureDataset_test.FeatureDatasetTest testMethod=test_round_trip_gtf>

    def test_round_trip_gtf(self):
    
        testFile = self.resourceFile("Homo_sapiens.GRCh37.75.trun20.gtf")
        ac = ADAMContext(self.ss)
    
>       features = ac.loadFeatures(testFile)

bdgenomics/adam/test/featureDataset_test.py:32: 
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 
bdgenomics/adam/adamContext.py:199: in loadFeatures
    _toJava(stringency, self._jvm))
/tmp/adamTest1UPduEN/deleteMePleaseThisIsNoLongerNeeded/spark-2.4.4-bin-without-hadoop-scala-2.12/python/lib/py4j-0.10.7-src.zip/py4j/java_gateway.py:1257: in __call__
    answer, self.gateway_client, self.target_id, self.name)
../spark-2.4.4-bin-without-hadoop-scala-2.12/python/pyspark/sql/utils.py:63: in deco
    return f(*a, **kw)
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 

answer = 'xro2843'
gateway_client = <py4j.java_gateway.GatewayClient object at 0x7f2f8c6ecbd0>
target_id = 'o2841', name = 'loadFeatures'

    def get_return_value(answer, gateway_client, target_id=None, name=None):
        """Converts an answer received from the Java gateway into a Python object.
    
        For example, string representation of integers are converted to Python
        integer, string representation of objects are converted to JavaObject
        instances, etc.
    
        :param answer: the string returned by the Java gateway
        :param gateway_client: the gateway client used to communicate with the Java
            Gateway. Only necessary if the answer is a reference (e.g., object,
            list, map)
        :param target_id: the name of the object from which the answer comes from
            (e.g., *object1* in `object1.hello()`). Optional.
        :param name: the name of the member from which the answer comes from
            (e.g., *hello* in `object1.hello()`). Optional.
        """
        if is_error(answer)[0]:
            if len(answer) > 1:
                type = answer[1]
                value = OUTPUT_CONVERTER[type](answer[2:], gateway_client)
                if answer[1] == REFERENCE_TYPE:
                    raise Py4JJavaError(
                        "An error occurred while calling {0}{1}{2}.\n".
>                       format(target_id, ".", name), value)
E                   Py4JJavaError: An error occurred while calling o2841.loadFeatures.
E                   : java.lang.NoClassDefFoundError: Could not initialize class org.apache.spark.rdd.RDDOperationScope$
E                   	at org.apache.spark.SparkContext.withScope(SparkContext.scala:699)
E                   	at org.apache.spark.SparkContext.textFile(SparkContext.scala:828)
E                   	at org.bdgenomics.adam.rdd.ADAMContext.$anonfun$loadGtf$1(ADAMContext.scala:3196)
E                   	at scala.Option.fold(Option.scala:175)
E                   	at org.apache.spark.rdd.Timer.time(Timer.scala:48)
E                   	at org.bdgenomics.adam.rdd.ADAMContext.loadGtf(ADAMContext.scala:3194)
E                   	at org.bdgenomics.adam.rdd.ADAMContext.$anonfun$loadFeatures$1(ADAMContext.scala:3446)
E                   	at scala.Option.fold(Option.scala:175)
E                   	at org.apache.spark.rdd.Timer.time(Timer.scala:48)
E                   	at org.bdgenomics.adam.rdd.ADAMContext.loadFeatures(ADAMContext.scala:3426)
E                   	at org.bdgenomics.adam.api.java.JavaADAMContext.loadFeatures(JavaADAMContext.scala:236)
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:498)
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:282)
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:238)
E                   	at java.lang.Thread.run(Thread.java:748)

/tmp/adamTest1UPduEN/deleteMePleaseThisIsNoLongerNeeded/spark-2.4.4-bin-without-hadoop-scala-2.12/python/lib/py4j-0.10.7-src.zip/py4j/protocol.py:328: Py4JJavaError
_______________ FeatureDatasetTest.test_round_trip_interval_list _______________

self = <bdgenomics.adam.test.featureDataset_test.FeatureDatasetTest testMethod=test_round_trip_interval_list>

    def test_round_trip_interval_list(self):
    
        testFile = self.resourceFile("SeqCap_EZ_Exome_v3.hg19.interval_list")
        ac = ADAMContext(self.ss)
    
>       features = ac.loadFeatures(testFile)

bdgenomics/adam/test/featureDataset_test.py:80: 
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 
bdgenomics/adam/adamContext.py:199: in loadFeatures
    _toJava(stringency, self._jvm))
/tmp/adamTest1UPduEN/deleteMePleaseThisIsNoLongerNeeded/spark-2.4.4-bin-without-hadoop-scala-2.12/python/lib/py4j-0.10.7-src.zip/py4j/java_gateway.py:1257: in __call__
    answer, self.gateway_client, self.target_id, self.name)
../spark-2.4.4-bin-without-hadoop-scala-2.12/python/pyspark/sql/utils.py:63: in deco
    return f(*a, **kw)
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 

answer = 'xro2910'
gateway_client = <py4j.java_gateway.GatewayClient object at 0x7f2f8c6ecbd0>
target_id = 'o2908', name = 'loadFeatures'

    def get_return_value(answer, gateway_client, target_id=None, name=None):
        """Converts an answer received from the Java gateway into a Python object.
    
        For example, string representation of integers are converted to Python
        integer, string representation of objects are converted to JavaObject
        instances, etc.
    
        :param answer: the string returned by the Java gateway
        :param gateway_client: the gateway client used to communicate with the Java
            Gateway. Only necessary if the answer is a reference (e.g., object,
            list, map)
        :param target_id: the name of the object from which the answer comes from
            (e.g., *object1* in `object1.hello()`). Optional.
        :param name: the name of the member from which the answer comes from
            (e.g., *hello* in `object1.hello()`). Optional.
        """
        if is_error(answer)[0]:
            if len(answer) > 1:
                type = answer[1]
                value = OUTPUT_CONVERTER[type](answer[2:], gateway_client)
                if answer[1] == REFERENCE_TYPE:
                    raise Py4JJavaError(
                        "An error occurred while calling {0}{1}{2}.\n".
>                       format(target_id, ".", name), value)
E                   Py4JJavaError: An error occurred while calling o2908.loadFeatures.
E                   : java.lang.NoClassDefFoundError: Could not initialize class org.apache.spark.rdd.RDDOperationScope$
E                   	at org.apache.spark.SparkContext.withScope(SparkContext.scala:699)
E                   	at org.apache.spark.SparkContext.textFile(SparkContext.scala:828)
E                   	at org.bdgenomics.adam.rdd.ADAMContext.$anonfun$loadIntervalList$1(ADAMContext.scala:3272)
E                   	at scala.Option.fold(Option.scala:175)
E                   	at org.apache.spark.rdd.Timer.time(Timer.scala:48)
E                   	at org.bdgenomics.adam.rdd.ADAMContext.loadIntervalList(ADAMContext.scala:3270)
E                   	at org.bdgenomics.adam.rdd.ADAMContext.$anonfun$loadFeatures$1(ADAMContext.scala:3457)
E                   	at scala.Option.fold(Option.scala:175)
E                   	at org.apache.spark.rdd.Timer.time(Timer.scala:48)
E                   	at org.bdgenomics.adam.rdd.ADAMContext.loadFeatures(ADAMContext.scala:3426)
E                   	at org.bdgenomics.adam.api.java.JavaADAMContext.loadFeatures(JavaADAMContext.scala:236)
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:498)
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:282)
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:238)
E                   	at java.lang.Thread.run(Thread.java:748)

/tmp/adamTest1UPduEN/deleteMePleaseThisIsNoLongerNeeded/spark-2.4.4-bin-without-hadoop-scala-2.12/python/lib/py4j-0.10.7-src.zip/py4j/protocol.py:328: Py4JJavaError
________________ FeatureDatasetTest.test_round_trip_narrowPeak _________________

self = <bdgenomics.adam.test.featureDataset_test.FeatureDatasetTest testMethod=test_round_trip_narrowPeak>

    def test_round_trip_narrowPeak(self):
    
        testFile = self.resourceFile("wgEncodeOpenChromDnaseGm19238Pk.trunc10.narrowPeak")
        ac = ADAMContext(self.ss)
    
>       features = ac.loadFeatures(testFile)

bdgenomics/adam/test/featureDataset_test.py:64: 
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 
bdgenomics/adam/adamContext.py:199: in loadFeatures
    _toJava(stringency, self._jvm))
/tmp/adamTest1UPduEN/deleteMePleaseThisIsNoLongerNeeded/spark-2.4.4-bin-without-hadoop-scala-2.12/python/lib/py4j-0.10.7-src.zip/py4j/java_gateway.py:1257: in __call__
    answer, self.gateway_client, self.target_id, self.name)
../spark-2.4.4-bin-without-hadoop-scala-2.12/python/pyspark/sql/utils.py:63: in deco
    return f(*a, **kw)
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 

answer = 'xro2977'
gateway_client = <py4j.java_gateway.GatewayClient object at 0x7f2f8c6ecbd0>
target_id = 'o2975', name = 'loadFeatures'

    def get_return_value(answer, gateway_client, target_id=None, name=None):
        """Converts an answer received from the Java gateway into a Python object.
    
        For example, string representation of integers are converted to Python
        integer, string representation of objects are converted to JavaObject
        instances, etc.
    
        :param answer: the string returned by the Java gateway
        :param gateway_client: the gateway client used to communicate with the Java
            Gateway. Only necessary if the answer is a reference (e.g., object,
            list, map)
        :param target_id: the name of the object from which the answer comes from
            (e.g., *object1* in `object1.hello()`). Optional.
        :param name: the name of the member from which the answer comes from
            (e.g., *hello* in `object1.hello()`). Optional.
        """
        if is_error(answer)[0]:
            if len(answer) > 1:
                type = answer[1]
                value = OUTPUT_CONVERTER[type](answer[2:], gateway_client)
                if answer[1] == REFERENCE_TYPE:
                    raise Py4JJavaError(
                        "An error occurred while calling {0}{1}{2}.\n".
>                       format(target_id, ".", name), value)
E                   Py4JJavaError: An error occurred while calling o2975.loadFeatures.
E                   : java.lang.NoClassDefFoundError: Could not initialize class org.apache.spark.rdd.RDDOperationScope$
E                   	at org.apache.spark.SparkContext.withScope(SparkContext.scala:699)
E                   	at org.apache.spark.SparkContext.textFile(SparkContext.scala:828)
E                   	at org.bdgenomics.adam.rdd.ADAMContext.$anonfun$loadNarrowPeak$1(ADAMContext.scala:3248)
E                   	at scala.Option.fold(Option.scala:175)
E                   	at org.apache.spark.rdd.Timer.time(Timer.scala:48)
E                   	at org.bdgenomics.adam.rdd.ADAMContext.loadNarrowPeak(ADAMContext.scala:3246)
E                   	at org.bdgenomics.adam.rdd.ADAMContext.$anonfun$loadFeatures$1(ADAMContext.scala:3452)
E                   	at scala.Option.fold(Option.scala:175)
E                   	at org.apache.spark.rdd.Timer.time(Timer.scala:48)
E                   	at org.bdgenomics.adam.rdd.ADAMContext.loadFeatures(ADAMContext.scala:3426)
E                   	at org.bdgenomics.adam.api.java.JavaADAMContext.loadFeatures(JavaADAMContext.scala:236)
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:498)
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:282)
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:238)
E                   	at java.lang.Thread.run(Thread.java:748)

/tmp/adamTest1UPduEN/deleteMePleaseThisIsNoLongerNeeded/spark-2.4.4-bin-without-hadoop-scala-2.12/python/lib/py4j-0.10.7-src.zip/py4j/protocol.py:328: Py4JJavaError
______________________ FeatureDatasetTest.test_transform _______________________

self = <bdgenomics.adam.test.featureDataset_test.FeatureDatasetTest testMethod=test_transform>

    def test_transform(self):
    
        featurePath = self.resourceFile("gencode.v7.annotation.trunc10.bed")
        ac = ADAMContext(self.ss)
    
>       features = ac.loadFeatures(featurePath)

bdgenomics/adam/test/featureDataset_test.py:96: 
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 
bdgenomics/adam/adamContext.py:199: in loadFeatures
    _toJava(stringency, self._jvm))
/tmp/adamTest1UPduEN/deleteMePleaseThisIsNoLongerNeeded/spark-2.4.4-bin-without-hadoop-scala-2.12/python/lib/py4j-0.10.7-src.zip/py4j/java_gateway.py:1257: in __call__
    answer, self.gateway_client, self.target_id, self.name)
../spark-2.4.4-bin-without-hadoop-scala-2.12/python/pyspark/sql/utils.py:63: in deco
    return f(*a, **kw)
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 

answer = 'xro3044'
gateway_client = <py4j.java_gateway.GatewayClient object at 0x7f2f8c6ecbd0>
target_id = 'o3042', name = 'loadFeatures'

    def get_return_value(answer, gateway_client, target_id=None, name=None):
        """Converts an answer received from the Java gateway into a Python object.
    
        For example, string representation of integers are converted to Python
        integer, string representation of objects are converted to JavaObject
        instances, etc.
    
        :param answer: the string returned by the Java gateway
        :param gateway_client: the gateway client used to communicate with the Java
            Gateway. Only necessary if the answer is a reference (e.g., object,
            list, map)
        :param target_id: the name of the object from which the answer comes from
            (e.g., *object1* in `object1.hello()`). Optional.
        :param name: the name of the member from which the answer comes from
            (e.g., *hello* in `object1.hello()`). Optional.
        """
        if is_error(answer)[0]:
            if len(answer) > 1:
                type = answer[1]
                value = OUTPUT_CONVERTER[type](answer[2:], gateway_client)
                if answer[1] == REFERENCE_TYPE:
                    raise Py4JJavaError(
                        "An error occurred while calling {0}{1}{2}.\n".
>                       format(target_id, ".", name), value)
E                   Py4JJavaError: An error occurred while calling o3042.loadFeatures.
E                   : java.lang.NoClassDefFoundError: Could not initialize class org.apache.spark.rdd.RDDOperationScope$
E                   	at org.apache.spark.SparkContext.withScope(SparkContext.scala:699)
E                   	at org.apache.spark.SparkContext.textFile(SparkContext.scala:828)
E                   	at org.bdgenomics.adam.rdd.ADAMContext.$anonfun$loadBed$1(ADAMContext.scala:3222)
E                   	at scala.Option.fold(Option.scala:175)
E                   	at org.apache.spark.rdd.Timer.time(Timer.scala:48)
E                   	at org.bdgenomics.adam.rdd.ADAMContext.loadBed(ADAMContext.scala:3220)
E                   	at org.bdgenomics.adam.rdd.ADAMContext.$anonfun$loadFeatures$1(ADAMContext.scala:3434)
E                   	at scala.Option.fold(Option.scala:175)
E                   	at org.apache.spark.rdd.Timer.time(Timer.scala:48)
E                   	at org.bdgenomics.adam.rdd.ADAMContext.loadFeatures(ADAMContext.scala:3426)
E                   	at org.bdgenomics.adam.api.java.JavaADAMContext.loadFeatures(JavaADAMContext.scala:236)
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:498)
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:282)
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:238)
E                   	at java.lang.Thread.run(Thread.java:748)

/tmp/adamTest1UPduEN/deleteMePleaseThisIsNoLongerNeeded/spark-2.4.4-bin-without-hadoop-scala-2.12/python/lib/py4j-0.10.7-src.zip/py4j/protocol.py:328: Py4JJavaError
_____________________ GenotypeDatasetTest.test_to_variants _____________________

self = <bdgenomics.adam.test.genotypeDataset_test.GenotypeDatasetTest testMethod=test_to_variants>

    def test_to_variants(self):
        testFile = self.resourceFile("small.vcf")
        ac = ADAMContext(self.ss)
    
>       genotypes = ac.loadGenotypes(testFile)

bdgenomics/adam/test/genotypeDataset_test.py:261: 
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 
bdgenomics/adam/adamContext.py:218: in loadGenotypes
    _toJava(stringency, self._jvm))
/tmp/adamTest1UPduEN/deleteMePleaseThisIsNoLongerNeeded/spark-2.4.4-bin-without-hadoop-scala-2.12/python/lib/py4j-0.10.7-src.zip/py4j/java_gateway.py:1257: in __call__
    answer, self.gateway_client, self.target_id, self.name)
../spark-2.4.4-bin-without-hadoop-scala-2.12/python/pyspark/sql/utils.py:63: in deco
    return f(*a, **kw)
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 

answer = 'xro3111'
gateway_client = <py4j.java_gateway.GatewayClient object at 0x7f2f8c6ecbd0>
target_id = 'o3109', name = 'loadGenotypes'

    def get_return_value(answer, gateway_client, target_id=None, name=None):
        """Converts an answer received from the Java gateway into a Python object.
    
        For example, string representation of integers are converted to Python
        integer, string representation of objects are converted to JavaObject
        instances, etc.
    
        :param answer: the string returned by the Java gateway
        :param gateway_client: the gateway client used to communicate with the Java
            Gateway. Only necessary if the answer is a reference (e.g., object,
            list, map)
        :param target_id: the name of the object from which the answer comes from
            (e.g., *object1* in `object1.hello()`). Optional.
        :param name: the name of the member from which the answer comes from
            (e.g., *hello* in `object1.hello()`). Optional.
        """
        if is_error(answer)[0]:
            if len(answer) > 1:
                type = answer[1]
                value = OUTPUT_CONVERTER[type](answer[2:], gateway_client)
                if answer[1] == REFERENCE_TYPE:
                    raise Py4JJavaError(
                        "An error occurred while calling {0}{1}{2}.\n".
>                       format(target_id, ".", name), value)
E                   Py4JJavaError: An error occurred while calling o3109.loadGenotypes.
E                   : java.lang.NoClassDefFoundError: Could not initialize class org.apache.spark.rdd.RDDOperationScope$
E                   	at org.apache.spark.SparkContext.withScope(SparkContext.scala:699)
E                   	at org.apache.spark.SparkContext.newAPIHadoopFile(SparkContext.scala:1146)
E                   	at org.bdgenomics.adam.rdd.ADAMContext.readVcfRecords(ADAMContext.scala:2627)
E                   	at org.bdgenomics.adam.rdd.ADAMContext.$anonfun$loadVcf$1(ADAMContext.scala:2645)
E                   	at scala.Option.fold(Option.scala:175)
E                   	at org.apache.spark.rdd.Timer.time(Timer.scala:48)
E                   	at org.bdgenomics.adam.rdd.ADAMContext.loadVcf(ADAMContext.scala:2642)
E                   	at org.bdgenomics.adam.rdd.ADAMContext.$anonfun$loadGenotypes$1(ADAMContext.scala:3551)
E                   	at scala.Option.fold(Option.scala:175)
E                   	at org.apache.spark.rdd.Timer.time(Timer.scala:48)
E                   	at org.bdgenomics.adam.rdd.ADAMContext.loadGenotypes(ADAMContext.scala:3549)
E                   	at org.bdgenomics.adam.api.java.JavaADAMContext.loadGenotypes(JavaADAMContext.scala:333)
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:498)
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:282)
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:238)
E                   	at java.lang.Thread.run(Thread.java:748)

/tmp/adamTest1UPduEN/deleteMePleaseThisIsNoLongerNeeded/spark-2.4.4-bin-without-hadoop-scala-2.12/python/lib/py4j-0.10.7-src.zip/py4j/protocol.py:328: Py4JJavaError
______________________ GenotypeDatasetTest.test_transform ______________________

self = <bdgenomics.adam.test.genotypeDataset_test.GenotypeDatasetTest testMethod=test_transform>

    def test_transform(self):
        testFile = self.resourceFile("random.vcf")
        ac = ADAMContext(self.ss)
    
>       genotypes = ac.loadGenotypes(testFile)

bdgenomics/adam/test/genotypeDataset_test.py:249: 
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 
bdgenomics/adam/adamContext.py:218: in loadGenotypes
    _toJava(stringency, self._jvm))
/tmp/adamTest1UPduEN/deleteMePleaseThisIsNoLongerNeeded/spark-2.4.4-bin-without-hadoop-scala-2.12/python/lib/py4j-0.10.7-src.zip/py4j/java_gateway.py:1257: in __call__
    answer, self.gateway_client, self.target_id, self.name)
../spark-2.4.4-bin-without-hadoop-scala-2.12/python/pyspark/sql/utils.py:63: in deco
    return f(*a, **kw)
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 

answer = 'xro3179'
gateway_client = <py4j.java_gateway.GatewayClient object at 0x7f2f8c6ecbd0>
target_id = 'o3177', name = 'loadGenotypes'

    def get_return_value(answer, gateway_client, target_id=None, name=None):
        """Converts an answer received from the Java gateway into a Python object.
    
        For example, string representation of integers are converted to Python
        integer, string representation of objects are converted to JavaObject
        instances, etc.
    
        :param answer: the string returned by the Java gateway
        :param gateway_client: the gateway client used to communicate with the Java
            Gateway. Only necessary if the answer is a reference (e.g., object,
            list, map)
        :param target_id: the name of the object from which the answer comes from
            (e.g., *object1* in `object1.hello()`). Optional.
        :param name: the name of the member from which the answer comes from
            (e.g., *hello* in `object1.hello()`). Optional.
        """
        if is_error(answer)[0]:
            if len(answer) > 1:
                type = answer[1]
                value = OUTPUT_CONVERTER[type](answer[2:], gateway_client)
                if answer[1] == REFERENCE_TYPE:
                    raise Py4JJavaError(
                        "An error occurred while calling {0}{1}{2}.\n".
>                       format(target_id, ".", name), value)
E                   Py4JJavaError: An error occurred while calling o3177.loadGenotypes.
E                   : java.lang.NoClassDefFoundError: Could not initialize class org.apache.spark.rdd.RDDOperationScope$
E                   	at org.apache.spark.SparkContext.withScope(SparkContext.scala:699)
E                   	at org.apache.spark.SparkContext.newAPIHadoopFile(SparkContext.scala:1146)
E                   	at org.bdgenomics.adam.rdd.ADAMContext.readVcfRecords(ADAMContext.scala:2627)
E                   	at org.bdgenomics.adam.rdd.ADAMContext.$anonfun$loadVcf$1(ADAMContext.scala:2645)
E                   	at scala.Option.fold(Option.scala:175)
E                   	at org.apache.spark.rdd.Timer.time(Timer.scala:48)
E                   	at org.bdgenomics.adam.rdd.ADAMContext.loadVcf(ADAMContext.scala:2642)
E                   	at org.bdgenomics.adam.rdd.ADAMContext.$anonfun$loadGenotypes$1(ADAMContext.scala:3551)
E                   	at scala.Option.fold(Option.scala:175)
E                   	at org.apache.spark.rdd.Timer.time(Timer.scala:48)
E                   	at org.bdgenomics.adam.rdd.ADAMContext.loadGenotypes(ADAMContext.scala:3549)
E                   	at org.bdgenomics.adam.api.java.JavaADAMContext.loadGenotypes(JavaADAMContext.scala:333)
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:498)
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:282)
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:238)
E                   	at java.lang.Thread.run(Thread.java:748)

/tmp/adamTest1UPduEN/deleteMePleaseThisIsNoLongerNeeded/spark-2.4.4-bin-without-hadoop-scala-2.12/python/lib/py4j-0.10.7-src.zip/py4j/protocol.py:328: Py4JJavaError
___________________ GenotypeDatasetTest.test_vcf_add_filter ____________________

self = <bdgenomics.adam.test.genotypeDataset_test.GenotypeDatasetTest testMethod=test_vcf_add_filter>

    def test_vcf_add_filter(self):
    
        testFile = self.resourceFile("small.vcf")
        ac = ADAMContext(self.ss)
    
>       genotypes = ac.loadGenotypes(testFile)

bdgenomics/adam/test/genotypeDataset_test.py:63: 
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 
bdgenomics/adam/adamContext.py:218: in loadGenotypes
    _toJava(stringency, self._jvm))
/tmp/adamTest1UPduEN/deleteMePleaseThisIsNoLongerNeeded/spark-2.4.4-bin-without-hadoop-scala-2.12/python/lib/py4j-0.10.7-src.zip/py4j/java_gateway.py:1257: in __call__
    answer, self.gateway_client, self.target_id, self.name)
../spark-2.4.4-bin-without-hadoop-scala-2.12/python/pyspark/sql/utils.py:63: in deco
    return f(*a, **kw)
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 

answer = 'xro3247'
gateway_client = <py4j.java_gateway.GatewayClient object at 0x7f2f8c6ecbd0>
target_id = 'o3245', name = 'loadGenotypes'

    def get_return_value(answer, gateway_client, target_id=None, name=None):
        """Converts an answer received from the Java gateway into a Python object.
    
        For example, string representation of integers are converted to Python
        integer, string representation of objects are converted to JavaObject
        instances, etc.
    
        :param answer: the string returned by the Java gateway
        :param gateway_client: the gateway client used to communicate with the Java
            Gateway. Only necessary if the answer is a reference (e.g., object,
            list, map)
        :param target_id: the name of the object from which the answer comes from
            (e.g., *object1* in `object1.hello()`). Optional.
        :param name: the name of the member from which the answer comes from
            (e.g., *hello* in `object1.hello()`). Optional.
        """
        if is_error(answer)[0]:
            if len(answer) > 1:
                type = answer[1]
                value = OUTPUT_CONVERTER[type](answer[2:], gateway_client)
                if answer[1] == REFERENCE_TYPE:
                    raise Py4JJavaError(
                        "An error occurred while calling {0}{1}{2}.\n".
>                       format(target_id, ".", name), value)
E                   Py4JJavaError: An error occurred while calling o3245.loadGenotypes.
E                   : java.lang.NoClassDefFoundError: Could not initialize class org.apache.spark.rdd.RDDOperationScope$
E                   	at org.apache.spark.SparkContext.withScope(SparkContext.scala:699)
E                   	at org.apache.spark.SparkContext.newAPIHadoopFile(SparkContext.scala:1146)
E                   	at org.bdgenomics.adam.rdd.ADAMContext.readVcfRecords(ADAMContext.scala:2627)
E                   	at org.bdgenomics.adam.rdd.ADAMContext.$anonfun$loadVcf$1(ADAMContext.scala:2645)
E                   	at scala.Option.fold(Option.scala:175)
E                   	at org.apache.spark.rdd.Timer.time(Timer.scala:48)
E                   	at org.bdgenomics.adam.rdd.ADAMContext.loadVcf(ADAMContext.scala:2642)
E                   	at org.bdgenomics.adam.rdd.ADAMContext.$anonfun$loadGenotypes$1(ADAMContext.scala:3551)
E                   	at scala.Option.fold(Option.scala:175)
E                   	at org.apache.spark.rdd.Timer.time(Timer.scala:48)
E                   	at org.bdgenomics.adam.rdd.ADAMContext.loadGenotypes(ADAMContext.scala:3549)
E                   	at org.bdgenomics.adam.api.java.JavaADAMContext.loadGenotypes(JavaADAMContext.scala:333)
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:498)
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:282)
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:238)
E                   	at java.lang.Thread.run(Thread.java:748)

/tmp/adamTest1UPduEN/deleteMePleaseThisIsNoLongerNeeded/spark-2.4.4-bin-without-hadoop-scala-2.12/python/lib/py4j-0.10.7-src.zip/py4j/protocol.py:328: Py4JJavaError
______________ GenotypeDatasetTest.test_vcf_add_format_all_array _______________

self = <bdgenomics.adam.test.genotypeDataset_test.GenotypeDatasetTest testMethod=test_vcf_add_format_all_array>

    def test_vcf_add_format_all_array(self):
    
        testFile = self.resourceFile("small.vcf")
        ac = ADAMContext(self.ss)
    
>       genotypes = ac.loadGenotypes(testFile)

bdgenomics/adam/test/genotypeDataset_test.py:141: 
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 
bdgenomics/adam/adamContext.py:218: in loadGenotypes
    _toJava(stringency, self._jvm))
/tmp/adamTest1UPduEN/deleteMePleaseThisIsNoLongerNeeded/spark-2.4.4-bin-without-hadoop-scala-2.12/python/lib/py4j-0.10.7-src.zip/py4j/java_gateway.py:1257: in __call__
    answer, self.gateway_client, self.target_id, self.name)
../spark-2.4.4-bin-without-hadoop-scala-2.12/python/pyspark/sql/utils.py:63: in deco
    return f(*a, **kw)
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 

answer = 'xro3315'
gateway_client = <py4j.java_gateway.GatewayClient object at 0x7f2f8c6ecbd0>
target_id = 'o3313', name = 'loadGenotypes'

    def get_return_value(answer, gateway_client, target_id=None, name=None):
        """Converts an answer received from the Java gateway into a Python object.
    
        For example, string representation of integers are converted to Python
        integer, string representation of objects are converted to JavaObject
        instances, etc.
    
        :param answer: the string returned by the Java gateway
        :param gateway_client: the gateway client used to communicate with the Java
            Gateway. Only necessary if the answer is a reference (e.g., object,
            list, map)
        :param target_id: the name of the object from which the answer comes from
            (e.g., *object1* in `object1.hello()`). Optional.
        :param name: the name of the member from which the answer comes from
            (e.g., *hello* in `object1.hello()`). Optional.
        """
        if is_error(answer)[0]:
            if len(answer) > 1:
                type = answer[1]
                value = OUTPUT_CONVERTER[type](answer[2:], gateway_client)
                if answer[1] == REFERENCE_TYPE:
                    raise Py4JJavaError(
                        "An error occurred while calling {0}{1}{2}.\n".
>                       format(target_id, ".", name), value)
E                   Py4JJavaError: An error occurred while calling o3313.loadGenotypes.
E                   : java.lang.NoClassDefFoundError: Could not initialize class org.apache.spark.rdd.RDDOperationScope$
E                   	at org.apache.spark.SparkContext.withScope(SparkContext.scala:699)
E                   	at org.apache.spark.SparkContext.newAPIHadoopFile(SparkContext.scala:1146)
E                   	at org.bdgenomics.adam.rdd.ADAMContext.readVcfRecords(ADAMContext.scala:2627)
E                   	at org.bdgenomics.adam.rdd.ADAMContext.$anonfun$loadVcf$1(ADAMContext.scala:2645)
E                   	at scala.Option.fold(Option.scala:175)
E                   	at org.apache.spark.rdd.Timer.time(Timer.scala:48)
E                   	at org.bdgenomics.adam.rdd.ADAMContext.loadVcf(ADAMContext.scala:2642)
E                   	at org.bdgenomics.adam.rdd.ADAMContext.$anonfun$loadGenotypes$1(ADAMContext.scala:3551)
E                   	at scala.Option.fold(Option.scala:175)
E                   	at org.apache.spark.rdd.Timer.time(Timer.scala:48)
E                   	at org.bdgenomics.adam.rdd.ADAMContext.loadGenotypes(ADAMContext.scala:3549)
E                   	at org.bdgenomics.adam.api.java.JavaADAMContext.loadGenotypes(JavaADAMContext.scala:333)
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:498)
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:282)
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:238)
E                   	at java.lang.Thread.run(Thread.java:748)

/tmp/adamTest1UPduEN/deleteMePleaseThisIsNoLongerNeeded/spark-2.4.4-bin-without-hadoop-scala-2.12/python/lib/py4j-0.10.7-src.zip/py4j/protocol.py:328: Py4JJavaError
______________ GenotypeDatasetTest.test_vcf_add_format_alts_array ______________

self = <bdgenomics.adam.test.genotypeDataset_test.GenotypeDatasetTest testMethod=test_vcf_add_format_alts_array>

    def test_vcf_add_format_alts_array(self):
    
        testFile = self.resourceFile("small.vcf")
        ac = ADAMContext(self.ss)
    
>       genotypes = ac.loadGenotypes(testFile)

bdgenomics/adam/test/genotypeDataset_test.py:125: 
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 
bdgenomics/adam/adamContext.py:218: in loadGenotypes
    _toJava(stringency, self._jvm))
/tmp/adamTest1UPduEN/deleteMePleaseThisIsNoLongerNeeded/spark-2.4.4-bin-without-hadoop-scala-2.12/python/lib/py4j-0.10.7-src.zip/py4j/java_gateway.py:1257: in __call__
    answer, self.gateway_client, self.target_id, self.name)
../spark-2.4.4-bin-without-hadoop-scala-2.12/python/pyspark/sql/utils.py:63: in deco
    return f(*a, **kw)
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 

answer = 'xro3383'
gateway_client = <py4j.java_gateway.GatewayClient object at 0x7f2f8c6ecbd0>
target_id = 'o3381', name = 'loadGenotypes'

    def get_return_value(answer, gateway_client, target_id=None, name=None):
        """Converts an answer received from the Java gateway into a Python object.
    
        For example, string representation of integers are converted to Python
        integer, string representation of objects are converted to JavaObject
        instances, etc.
    
        :param answer: the string returned by the Java gateway
        :param gateway_client: the gateway client used to communicate with the Java
            Gateway. Only necessary if the answer is a reference (e.g., object,
            list, map)
        :param target_id: the name of the object from which the answer comes from
            (e.g., *object1* in `object1.hello()`). Optional.
        :param name: the name of the member from which the answer comes from
            (e.g., *hello* in `object1.hello()`). Optional.
        """
        if is_error(answer)[0]:
            if len(answer) > 1:
                type = answer[1]
                value = OUTPUT_CONVERTER[type](answer[2:], gateway_client)
                if answer[1] == REFERENCE_TYPE:
                    raise Py4JJavaError(
                        "An error occurred while calling {0}{1}{2}.\n".
>                       format(target_id, ".", name), value)
E                   Py4JJavaError: An error occurred while calling o3381.loadGenotypes.
E                   : java.lang.NoClassDefFoundError: Could not initialize class org.apache.spark.rdd.RDDOperationScope$
E                   	at org.apache.spark.SparkContext.withScope(SparkContext.scala:699)
E                   	at org.apache.spark.SparkContext.newAPIHadoopFile(SparkContext.scala:1146)
E                   	at org.bdgenomics.adam.rdd.ADAMContext.readVcfRecords(ADAMContext.scala:2627)
E                   	at org.bdgenomics.adam.rdd.ADAMContext.$anonfun$loadVcf$1(ADAMContext.scala:2645)
E                   	at scala.Option.fold(Option.scala:175)
E                   	at org.apache.spark.rdd.Timer.time(Timer.scala:48)
E                   	at org.bdgenomics.adam.rdd.ADAMContext.loadVcf(ADAMContext.scala:2642)
E                   	at org.bdgenomics.adam.rdd.ADAMContext.$anonfun$loadGenotypes$1(ADAMContext.scala:3551)
E                   	at scala.Option.fold(Option.scala:175)
E                   	at org.apache.spark.rdd.Timer.time(Timer.scala:48)
E                   	at org.bdgenomics.adam.rdd.ADAMContext.loadGenotypes(ADAMContext.scala:3549)
E                   	at org.bdgenomics.adam.api.java.JavaADAMContext.loadGenotypes(JavaADAMContext.scala:333)
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:498)
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:282)
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:238)
E                   	at java.lang.Thread.run(Thread.java:748)

/tmp/adamTest1UPduEN/deleteMePleaseThisIsNoLongerNeeded/spark-2.4.4-bin-without-hadoop-scala-2.12/python/lib/py4j-0.10.7-src.zip/py4j/protocol.py:328: Py4JJavaError
________________ GenotypeDatasetTest.test_vcf_add_format_array _________________

self = <bdgenomics.adam.test.genotypeDataset_test.GenotypeDatasetTest testMethod=test_vcf_add_format_array>

    def test_vcf_add_format_array(self):
    
        testFile = self.resourceFile("small.vcf")
        ac = ADAMContext(self.ss)
    
>       genotypes = ac.loadGenotypes(testFile)

bdgenomics/adam/test/genotypeDataset_test.py:77: 
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 
bdgenomics/adam/adamContext.py:218: in loadGenotypes
    _toJava(stringency, self._jvm))
/tmp/adamTest1UPduEN/deleteMePleaseThisIsNoLongerNeeded/spark-2.4.4-bin-without-hadoop-scala-2.12/python/lib/py4j-0.10.7-src.zip/py4j/java_gateway.py:1257: in __call__
    answer, self.gateway_client, self.target_id, self.name)
../spark-2.4.4-bin-without-hadoop-scala-2.12/python/pyspark/sql/utils.py:63: in deco
    return f(*a, **kw)
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 

answer = 'xro3451'
gateway_client = <py4j.java_gateway.GatewayClient object at 0x7f2f8c6ecbd0>
target_id = 'o3449', name = 'loadGenotypes'

    def get_return_value(answer, gateway_client, target_id=None, name=None):
        """Converts an answer received from the Java gateway into a Python object.
    
        For example, string representation of integers are converted to Python
        integer, string representation of objects are converted to JavaObject
        instances, etc.
    
        :param answer: the string returned by the Java gateway
        :param gateway_client: the gateway client used to communicate with the Java
            Gateway. Only necessary if the answer is a reference (e.g., object,
            list, map)
        :param target_id: the name of the object from which the answer comes from
            (e.g., *object1* in `object1.hello()`). Optional.
        :param name: the name of the member from which the answer comes from
            (e.g., *hello* in `object1.hello()`). Optional.
        """
        if is_error(answer)[0]:
            if len(answer) > 1:
                type = answer[1]
                value = OUTPUT_CONVERTER[type](answer[2:], gateway_client)
                if answer[1] == REFERENCE_TYPE:
                    raise Py4JJavaError(
                        "An error occurred while calling {0}{1}{2}.\n".
>                       format(target_id, ".", name), value)
E                   Py4JJavaError: An error occurred while calling o3449.loadGenotypes.
E                   : java.lang.NoClassDefFoundError: Could not initialize class org.apache.spark.rdd.RDDOperationScope$
E                   	at org.apache.spark.SparkContext.withScope(SparkContext.scala:699)
E                   	at org.apache.spark.SparkContext.newAPIHadoopFile(SparkContext.scala:1146)
E                   	at org.bdgenomics.adam.rdd.ADAMContext.readVcfRecords(ADAMContext.scala:2627)
E                   	at org.bdgenomics.adam.rdd.ADAMContext.$anonfun$loadVcf$1(ADAMContext.scala:2645)
E                   	at scala.Option.fold(Option.scala:175)
E                   	at org.apache.spark.rdd.Timer.time(Timer.scala:48)
E                   	at org.bdgenomics.adam.rdd.ADAMContext.loadVcf(ADAMContext.scala:2642)
E                   	at org.bdgenomics.adam.rdd.ADAMContext.$anonfun$loadGenotypes$1(ADAMContext.scala:3551)
E                   	at scala.Option.fold(Option.scala:175)
E                   	at org.apache.spark.rdd.Timer.time(Timer.scala:48)
E                   	at org.bdgenomics.adam.rdd.ADAMContext.loadGenotypes(ADAMContext.scala:3549)
E                   	at org.bdgenomics.adam.api.java.JavaADAMContext.loadGenotypes(JavaADAMContext.scala:333)
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:498)
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:282)
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:238)
E                   	at java.lang.Thread.run(Thread.java:748)

/tmp/adamTest1UPduEN/deleteMePleaseThisIsNoLongerNeeded/spark-2.4.4-bin-without-hadoop-scala-2.12/python/lib/py4j-0.10.7-src.zip/py4j/protocol.py:328: Py4JJavaError
____________ GenotypeDatasetTest.test_vcf_add_format_genotype_array ____________

self = <bdgenomics.adam.test.genotypeDataset_test.GenotypeDatasetTest testMethod=test_vcf_add_format_genotype_array>

    def test_vcf_add_format_genotype_array(self):
    
        testFile = self.resourceFile("small.vcf")
        ac = ADAMContext(self.ss)
    
>       genotypes = ac.loadGenotypes(testFile)

bdgenomics/adam/test/genotypeDataset_test.py:110: 
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 
bdgenomics/adam/adamContext.py:218: in loadGenotypes
    _toJava(stringency, self._jvm))
/tmp/adamTest1UPduEN/deleteMePleaseThisIsNoLongerNeeded/spark-2.4.4-bin-without-hadoop-scala-2.12/python/lib/py4j-0.10.7-src.zip/py4j/java_gateway.py:1257: in __call__
    answer, self.gateway_client, self.target_id, self.name)
../spark-2.4.4-bin-without-hadoop-scala-2.12/python/pyspark/sql/utils.py:63: in deco
    return f(*a, **kw)
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 

answer = 'xro3519'
gateway_client = <py4j.java_gateway.GatewayClient object at 0x7f2f8c6ecbd0>
target_id = 'o3517', name = 'loadGenotypes'

    def get_return_value(answer, gateway_client, target_id=None, name=None):
        """Converts an answer received from the Java gateway into a Python object.
    
        For example, string representation of integers are converted to Python
        integer, string representation of objects are converted to JavaObject
        instances, etc.
    
        :param answer: the string returned by the Java gateway
        :param gateway_client: the gateway client used to communicate with the Java
            Gateway. Only necessary if the answer is a reference (e.g., object,
            list, map)
        :param target_id: the name of the object from which the answer comes from
            (e.g., *object1* in `object1.hello()`). Optional.
        :param name: the name of the member from which the answer comes from
            (e.g., *hello* in `object1.hello()`). Optional.
        """
        if is_error(answer)[0]:
            if len(answer) > 1:
                type = answer[1]
                value = OUTPUT_CONVERTER[type](answer[2:], gateway_client)
                if answer[1] == REFERENCE_TYPE:
                    raise Py4JJavaError(
                        "An error occurred while calling {0}{1}{2}.\n".
>                       format(target_id, ".", name), value)
E                   Py4JJavaError: An error occurred while calling o3517.loadGenotypes.
E                   : java.lang.NoClassDefFoundError: Could not initialize class org.apache.spark.rdd.RDDOperationScope$
E                   	at org.apache.spark.SparkContext.withScope(SparkContext.scala:699)
E                   	at org.apache.spark.SparkContext.newAPIHadoopFile(SparkContext.scala:1146)
E                   	at org.bdgenomics.adam.rdd.ADAMContext.readVcfRecords(ADAMContext.scala:2627)
E                   	at org.bdgenomics.adam.rdd.ADAMContext.$anonfun$loadVcf$1(ADAMContext.scala:2645)
E                   	at scala.Option.fold(Option.scala:175)
E                   	at org.apache.spark.rdd.Timer.time(Timer.scala:48)
E                   	at org.bdgenomics.adam.rdd.ADAMContext.loadVcf(ADAMContext.scala:2642)
E                   	at org.bdgenomics.adam.rdd.ADAMContext.$anonfun$loadGenotypes$1(ADAMContext.scala:3551)
E                   	at scala.Option.fold(Option.scala:175)
E                   	at org.apache.spark.rdd.Timer.time(Timer.scala:48)
E                   	at org.bdgenomics.adam.rdd.ADAMContext.loadGenotypes(ADAMContext.scala:3549)
E                   	at org.bdgenomics.adam.api.java.JavaADAMContext.loadGenotypes(JavaADAMContext.scala:333)
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:498)
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:282)
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:238)
E                   	at java.lang.Thread.run(Thread.java:748)

/tmp/adamTest1UPduEN/deleteMePleaseThisIsNoLongerNeeded/spark-2.4.4-bin-without-hadoop-scala-2.12/python/lib/py4j-0.10.7-src.zip/py4j/protocol.py:328: Py4JJavaError
________________ GenotypeDatasetTest.test_vcf_add_format_scalar ________________

self = <bdgenomics.adam.test.genotypeDataset_test.GenotypeDatasetTest testMethod=test_vcf_add_format_scalar>

    def test_vcf_add_format_scalar(self):
    
        testFile = self.resourceFile("small.vcf")
        ac = ADAMContext(self.ss)
    
>       genotypes = ac.loadGenotypes(testFile)

bdgenomics/adam/test/genotypeDataset_test.py:94: 
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 
bdgenomics/adam/adamContext.py:218: in loadGenotypes
    _toJava(stringency, self._jvm))
/tmp/adamTest1UPduEN/deleteMePleaseThisIsNoLongerNeeded/spark-2.4.4-bin-without-hadoop-scala-2.12/python/lib/py4j-0.10.7-src.zip/py4j/java_gateway.py:1257: in __call__
    answer, self.gateway_client, self.target_id, self.name)
../spark-2.4.4-bin-without-hadoop-scala-2.12/python/pyspark/sql/utils.py:63: in deco
    return f(*a, **kw)
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 

answer = 'xro3587'
gateway_client = <py4j.java_gateway.GatewayClient object at 0x7f2f8c6ecbd0>
target_id = 'o3585', name = 'loadGenotypes'

    def get_return_value(answer, gateway_client, target_id=None, name=None):
        """Converts an answer received from the Java gateway into a Python object.
    
        For example, string representation of integers are converted to Python
        integer, string representation of objects are converted to JavaObject
        instances, etc.
    
        :param answer: the string returned by the Java gateway
        :param gateway_client: the gateway client used to communicate with the Java
            Gateway. Only necessary if the answer is a reference (e.g., object,
            list, map)
        :param target_id: the name of the object from which the answer comes from
            (e.g., *object1* in `object1.hello()`). Optional.
        :param name: the name of the member from which the answer comes from
            (e.g., *hello* in `object1.hello()`). Optional.
        """
        if is_error(answer)[0]:
            if len(answer) > 1:
                type = answer[1]
                value = OUTPUT_CONVERTER[type](answer[2:], gateway_client)
                if answer[1] == REFERENCE_TYPE:
                    raise Py4JJavaError(
                        "An error occurred while calling {0}{1}{2}.\n".
>                       format(target_id, ".", name), value)
E                   Py4JJavaError: An error occurred while calling o3585.loadGenotypes.
E                   : java.lang.NoClassDefFoundError: Could not initialize class org.apache.spark.rdd.RDDOperationScope$
E                   	at org.apache.spark.SparkContext.withScope(SparkContext.scala:699)
E                   	at org.apache.spark.SparkContext.newAPIHadoopFile(SparkContext.scala:1146)
E                   	at org.bdgenomics.adam.rdd.ADAMContext.readVcfRecords(ADAMContext.scala:2627)
E                   	at org.bdgenomics.adam.rdd.ADAMContext.$anonfun$loadVcf$1(ADAMContext.scala:2645)
E                   	at scala.Option.fold(Option.scala:175)
E                   	at org.apache.spark.rdd.Timer.time(Timer.scala:48)
E                   	at org.bdgenomics.adam.rdd.ADAMContext.loadVcf(ADAMContext.scala:2642)
E                   	at org.bdgenomics.adam.rdd.ADAMContext.$anonfun$loadGenotypes$1(ADAMContext.scala:3551)
E                   	at scala.Option.fold(Option.scala:175)
E                   	at org.apache.spark.rdd.Timer.time(Timer.scala:48)
E                   	at org.bdgenomics.adam.rdd.ADAMContext.loadGenotypes(ADAMContext.scala:3549)
E                   	at org.bdgenomics.adam.api.java.JavaADAMContext.loadGenotypes(JavaADAMContext.scala:333)
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:498)
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:282)
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:238)
E                   	at java.lang.Thread.run(Thread.java:748)

/tmp/adamTest1UPduEN/deleteMePleaseThisIsNoLongerNeeded/spark-2.4.4-bin-without-hadoop-scala-2.12/python/lib/py4j-0.10.7-src.zip/py4j/protocol.py:328: Py4JJavaError
_______________ GenotypeDatasetTest.test_vcf_add_info_all_array ________________

self = <bdgenomics.adam.test.genotypeDataset_test.GenotypeDatasetTest testMethod=test_vcf_add_info_all_array>

    def test_vcf_add_info_all_array(self):
    
        testFile = self.resourceFile("small.vcf")
        ac = ADAMContext(self.ss)
    
>       genotypes = ac.loadGenotypes(testFile)

bdgenomics/adam/test/genotypeDataset_test.py:206: 
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 
bdgenomics/adam/adamContext.py:218: in loadGenotypes
    _toJava(stringency, self._jvm))
/tmp/adamTest1UPduEN/deleteMePleaseThisIsNoLongerNeeded/spark-2.4.4-bin-without-hadoop-scala-2.12/python/lib/py4j-0.10.7-src.zip/py4j/java_gateway.py:1257: in __call__
    answer, self.gateway_client, self.target_id, self.name)
../spark-2.4.4-bin-without-hadoop-scala-2.12/python/pyspark/sql/utils.py:63: in deco
    return f(*a, **kw)
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 

answer = 'xro3655'
gateway_client = <py4j.java_gateway.GatewayClient object at 0x7f2f8c6ecbd0>
target_id = 'o3653', name = 'loadGenotypes'

    def get_return_value(answer, gateway_client, target_id=None, name=None):
        """Converts an answer received from the Java gateway into a Python object.
    
        For example, string representation of integers are converted to Python
        integer, string representation of objects are converted to JavaObject
        instances, etc.
    
        :param answer: the string returned by the Java gateway
        :param gateway_client: the gateway client used to communicate with the Java
            Gateway. Only necessary if the answer is a reference (e.g., object,
            list, map)
        :param target_id: the name of the object from which the answer comes from
            (e.g., *object1* in `object1.hello()`). Optional.
        :param name: the name of the member from which the answer comes from
            (e.g., *hello* in `object1.hello()`). Optional.
        """
        if is_error(answer)[0]:
            if len(answer) > 1:
                type = answer[1]
                value = OUTPUT_CONVERTER[type](answer[2:], gateway_client)
                if answer[1] == REFERENCE_TYPE:
                    raise Py4JJavaError(
                        "An error occurred while calling {0}{1}{2}.\n".
>                       format(target_id, ".", name), value)
E                   Py4JJavaError: An error occurred while calling o3653.loadGenotypes.
E                   : java.lang.NoClassDefFoundError: Could not initialize class org.apache.spark.rdd.RDDOperationScope$
E                   	at org.apache.spark.SparkContext.withScope(SparkContext.scala:699)
E                   	at org.apache.spark.SparkContext.newAPIHadoopFile(SparkContext.scala:1146)
E                   	at org.bdgenomics.adam.rdd.ADAMContext.readVcfRecords(ADAMContext.scala:2627)
E                   	at org.bdgenomics.adam.rdd.ADAMContext.$anonfun$loadVcf$1(ADAMContext.scala:2645)
E                   	at scala.Option.fold(Option.scala:175)
E                   	at org.apache.spark.rdd.Timer.time(Timer.scala:48)
E                   	at org.bdgenomics.adam.rdd.ADAMContext.loadVcf(ADAMContext.scala:2642)
E                   	at org.bdgenomics.adam.rdd.ADAMContext.$anonfun$loadGenotypes$1(ADAMContext.scala:3551)
E                   	at scala.Option.fold(Option.scala:175)
E                   	at org.apache.spark.rdd.Timer.time(Timer.scala:48)
E                   	at org.bdgenomics.adam.rdd.ADAMContext.loadGenotypes(ADAMContext.scala:3549)
E                   	at org.bdgenomics.adam.api.java.JavaADAMContext.loadGenotypes(JavaADAMContext.scala:333)
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:498)
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:282)
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:238)
E                   	at java.lang.Thread.run(Thread.java:748)

/tmp/adamTest1UPduEN/deleteMePleaseThisIsNoLongerNeeded/spark-2.4.4-bin-without-hadoop-scala-2.12/python/lib/py4j-0.10.7-src.zip/py4j/protocol.py:328: Py4JJavaError
_______________ GenotypeDatasetTest.test_vcf_add_info_alts_array _______________

self = <bdgenomics.adam.test.genotypeDataset_test.GenotypeDatasetTest testMethod=test_vcf_add_info_alts_array>

    def test_vcf_add_info_alts_array(self):
    
        testFile = self.resourceFile("small.vcf")
        ac = ADAMContext(self.ss)
    
>       genotypes = ac.loadGenotypes(testFile)

bdgenomics/adam/test/genotypeDataset_test.py:190: 
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 
bdgenomics/adam/adamContext.py:218: in loadGenotypes
    _toJava(stringency, self._jvm))
/tmp/adamTest1UPduEN/deleteMePleaseThisIsNoLongerNeeded/spark-2.4.4-bin-without-hadoop-scala-2.12/python/lib/py4j-0.10.7-src.zip/py4j/java_gateway.py:1257: in __call__
    answer, self.gateway_client, self.target_id, self.name)
../spark-2.4.4-bin-without-hadoop-scala-2.12/python/pyspark/sql/utils.py:63: in deco
    return f(*a, **kw)
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 

answer = 'xro3723'
gateway_client = <py4j.java_gateway.GatewayClient object at 0x7f2f8c6ecbd0>
target_id = 'o3721', name = 'loadGenotypes'

    def get_return_value(answer, gateway_client, target_id=None, name=None):
        """Converts an answer received from the Java gateway into a Python object.
    
        For example, string representation of integers are converted to Python
        integer, string representation of objects are converted to JavaObject
        instances, etc.
    
        :param answer: the string returned by the Java gateway
        :param gateway_client: the gateway client used to communicate with the Java
            Gateway. Only necessary if the answer is a reference (e.g., object,
            list, map)
        :param target_id: the name of the object from which the answer comes from
            (e.g., *object1* in `object1.hello()`). Optional.
        :param name: the name of the member from which the answer comes from
            (e.g., *hello* in `object1.hello()`). Optional.
        """
        if is_error(answer)[0]:
            if len(answer) > 1:
                type = answer[1]
                value = OUTPUT_CONVERTER[type](answer[2:], gateway_client)
                if answer[1] == REFERENCE_TYPE:
                    raise Py4JJavaError(
                        "An error occurred while calling {0}{1}{2}.\n".
>                       format(target_id, ".", name), value)
E                   Py4JJavaError: An error occurred while calling o3721.loadGenotypes.
E                   : java.lang.NoClassDefFoundError: Could not initialize class org.apache.spark.rdd.RDDOperationScope$
E                   	at org.apache.spark.SparkContext.withScope(SparkContext.scala:699)
E                   	at org.apache.spark.SparkContext.newAPIHadoopFile(SparkContext.scala:1146)
E                   	at org.bdgenomics.adam.rdd.ADAMContext.readVcfRecords(ADAMContext.scala:2627)
E                   	at org.bdgenomics.adam.rdd.ADAMContext.$anonfun$loadVcf$1(ADAMContext.scala:2645)
E                   	at scala.Option.fold(Option.scala:175)
E                   	at org.apache.spark.rdd.Timer.time(Timer.scala:48)
E                   	at org.bdgenomics.adam.rdd.ADAMContext.loadVcf(ADAMContext.scala:2642)
E                   	at org.bdgenomics.adam.rdd.ADAMContext.$anonfun$loadGenotypes$1(ADAMContext.scala:3551)
E                   	at scala.Option.fold(Option.scala:175)
E                   	at org.apache.spark.rdd.Timer.time(Timer.scala:48)
E                   	at org.bdgenomics.adam.rdd.ADAMContext.loadGenotypes(ADAMContext.scala:3549)
E                   	at org.bdgenomics.adam.api.java.JavaADAMContext.loadGenotypes(JavaADAMContext.scala:333)
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:498)
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:282)
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:238)
E                   	at java.lang.Thread.run(Thread.java:748)

/tmp/adamTest1UPduEN/deleteMePleaseThisIsNoLongerNeeded/spark-2.4.4-bin-without-hadoop-scala-2.12/python/lib/py4j-0.10.7-src.zip/py4j/protocol.py:328: Py4JJavaError
_________________ GenotypeDatasetTest.test_vcf_add_info_array __________________

self = <bdgenomics.adam.test.genotypeDataset_test.GenotypeDatasetTest testMethod=test_vcf_add_info_array>

    def test_vcf_add_info_array(self):
    
        testFile = self.resourceFile("small.vcf")
        ac = ADAMContext(self.ss)
    
>       genotypes = ac.loadGenotypes(testFile)

bdgenomics/adam/test/genotypeDataset_test.py:157: 
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 
bdgenomics/adam/adamContext.py:218: in loadGenotypes
    _toJava(stringency, self._jvm))
/tmp/adamTest1UPduEN/deleteMePleaseThisIsNoLongerNeeded/spark-2.4.4-bin-without-hadoop-scala-2.12/python/lib/py4j-0.10.7-src.zip/py4j/java_gateway.py:1257: in __call__
    answer, self.gateway_client, self.target_id, self.name)
../spark-2.4.4-bin-without-hadoop-scala-2.12/python/pyspark/sql/utils.py:63: in deco
    return f(*a, **kw)
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 

answer = 'xro3791'
gateway_client = <py4j.java_gateway.GatewayClient object at 0x7f2f8c6ecbd0>
target_id = 'o3789', name = 'loadGenotypes'

    def get_return_value(answer, gateway_client, target_id=None, name=None):
        """Converts an answer received from the Java gateway into a Python object.
    
        For example, string representation of integers are converted to Python
        integer, string representation of objects are converted to JavaObject
        instances, etc.
    
        :param answer: the string returned by the Java gateway
        :param gateway_client: the gateway client used to communicate with the Java
            Gateway. Only necessary if the answer is a reference (e.g., object,
            list, map)
        :param target_id: the name of the object from which the answer comes from
            (e.g., *object1* in `object1.hello()`). Optional.
        :param name: the name of the member from which the answer comes from
            (e.g., *hello* in `object1.hello()`). Optional.
        """
        if is_error(answer)[0]:
            if len(answer) > 1:
                type = answer[1]
                value = OUTPUT_CONVERTER[type](answer[2:], gateway_client)
                if answer[1] == REFERENCE_TYPE:
                    raise Py4JJavaError(
                        "An error occurred while calling {0}{1}{2}.\n".
>                       format(target_id, ".", name), value)
E                   Py4JJavaError: An error occurred while calling o3789.loadGenotypes.
E                   : java.lang.NoClassDefFoundError: Could not initialize class org.apache.spark.rdd.RDDOperationScope$
E                   	at org.apache.spark.SparkContext.withScope(SparkContext.scala:699)
E                   	at org.apache.spark.SparkContext.newAPIHadoopFile(SparkContext.scala:1146)
E                   	at org.bdgenomics.adam.rdd.ADAMContext.readVcfRecords(ADAMContext.scala:2627)
E                   	at org.bdgenomics.adam.rdd.ADAMContext.$anonfun$loadVcf$1(ADAMContext.scala:2645)
E                   	at scala.Option.fold(Option.scala:175)
E                   	at org.apache.spark.rdd.Timer.time(Timer.scala:48)
E                   	at org.bdgenomics.adam.rdd.ADAMContext.loadVcf(ADAMContext.scala:2642)
E                   	at org.bdgenomics.adam.rdd.ADAMContext.$anonfun$loadGenotypes$1(ADAMContext.scala:3551)
E                   	at scala.Option.fold(Option.scala:175)
E                   	at org.apache.spark.rdd.Timer.time(Timer.scala:48)
E                   	at org.bdgenomics.adam.rdd.ADAMContext.loadGenotypes(ADAMContext.scala:3549)
E                   	at org.bdgenomics.adam.api.java.JavaADAMContext.loadGenotypes(JavaADAMContext.scala:333)
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:498)
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:282)
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:238)
E                   	at java.lang.Thread.run(Thread.java:748)

/tmp/adamTest1UPduEN/deleteMePleaseThisIsNoLongerNeeded/spark-2.4.4-bin-without-hadoop-scala-2.12/python/lib/py4j-0.10.7-src.zip/py4j/protocol.py:328: Py4JJavaError
_________________ GenotypeDatasetTest.test_vcf_add_info_scalar _________________

self = <bdgenomics.adam.test.genotypeDataset_test.GenotypeDatasetTest testMethod=test_vcf_add_info_scalar>

    def test_vcf_add_info_scalar(self):
    
        testFile = self.resourceFile("small.vcf")
        ac = ADAMContext(self.ss)
    
>       genotypes = ac.loadGenotypes(testFile)

bdgenomics/adam/test/genotypeDataset_test.py:174: 
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 
bdgenomics/adam/adamContext.py:218: in loadGenotypes
    _toJava(stringency, self._jvm))
/tmp/adamTest1UPduEN/deleteMePleaseThisIsNoLongerNeeded/spark-2.4.4-bin-without-hadoop-scala-2.12/python/lib/py4j-0.10.7-src.zip/py4j/java_gateway.py:1257: in __call__
    answer, self.gateway_client, self.target_id, self.name)
../spark-2.4.4-bin-without-hadoop-scala-2.12/python/pyspark/sql/utils.py:63: in deco
    return f(*a, **kw)
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 

answer = 'xro3859'
gateway_client = <py4j.java_gateway.GatewayClient object at 0x7f2f8c6ecbd0>
target_id = 'o3857', name = 'loadGenotypes'

    def get_return_value(answer, gateway_client, target_id=None, name=None):
        """Converts an answer received from the Java gateway into a Python object.
    
        For example, string representation of integers are converted to Python
        integer, string representation of objects are converted to JavaObject
        instances, etc.
    
        :param answer: the string returned by the Java gateway
        :param gateway_client: the gateway client used to communicate with the Java
            Gateway. Only necessary if the answer is a reference (e.g., object,
            list, map)
        :param target_id: the name of the object from which the answer comes from
            (e.g., *object1* in `object1.hello()`). Optional.
        :param name: the name of the member from which the answer comes from
            (e.g., *hello* in `object1.hello()`). Optional.
        """
        if is_error(answer)[0]:
            if len(answer) > 1:
                type = answer[1]
                value = OUTPUT_CONVERTER[type](answer[2:], gateway_client)
                if answer[1] == REFERENCE_TYPE:
                    raise Py4JJavaError(
                        "An error occurred while calling {0}{1}{2}.\n".
>                       format(target_id, ".", name), value)
E                   Py4JJavaError: An error occurred while calling o3857.loadGenotypes.
E                   : java.lang.NoClassDefFoundError: Could not initialize class org.apache.spark.rdd.RDDOperationScope$
E                   	at org.apache.spark.SparkContext.withScope(SparkContext.scala:699)
E                   	at org.apache.spark.SparkContext.newAPIHadoopFile(SparkContext.scala:1146)
E                   	at org.bdgenomics.adam.rdd.ADAMContext.readVcfRecords(ADAMContext.scala:2627)
E                   	at org.bdgenomics.adam.rdd.ADAMContext.$anonfun$loadVcf$1(ADAMContext.scala:2645)
E                   	at scala.Option.fold(Option.scala:175)
E                   	at org.apache.spark.rdd.Timer.time(Timer.scala:48)
E                   	at org.bdgenomics.adam.rdd.ADAMContext.loadVcf(ADAMContext.scala:2642)
E                   	at org.bdgenomics.adam.rdd.ADAMContext.$anonfun$loadGenotypes$1(ADAMContext.scala:3551)
E                   	at scala.Option.fold(Option.scala:175)
E                   	at org.apache.spark.rdd.Timer.time(Timer.scala:48)
E                   	at org.bdgenomics.adam.rdd.ADAMContext.loadGenotypes(ADAMContext.scala:3549)
E                   	at org.bdgenomics.adam.api.java.JavaADAMContext.loadGenotypes(JavaADAMContext.scala:333)
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:498)
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:282)
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:238)
E                   	at java.lang.Thread.run(Thread.java:748)

/tmp/adamTest1UPduEN/deleteMePleaseThisIsNoLongerNeeded/spark-2.4.4-bin-without-hadoop-scala-2.12/python/lib/py4j-0.10.7-src.zip/py4j/protocol.py:328: Py4JJavaError
___________________ GenotypeDatasetTest.test_vcf_round_trip ____________________

self = <bdgenomics.adam.test.genotypeDataset_test.GenotypeDatasetTest testMethod=test_vcf_round_trip>

    def test_vcf_round_trip(self):
    
        testFile = self.resourceFile("small.vcf")
        ac = ADAMContext(self.ss)
    
>       genotypes = ac.loadGenotypes(testFile)

bdgenomics/adam/test/genotypeDataset_test.py:47: 
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 
bdgenomics/adam/adamContext.py:218: in loadGenotypes
    _toJava(stringency, self._jvm))
/tmp/adamTest1UPduEN/deleteMePleaseThisIsNoLongerNeeded/spark-2.4.4-bin-without-hadoop-scala-2.12/python/lib/py4j-0.10.7-src.zip/py4j/java_gateway.py:1257: in __call__
    answer, self.gateway_client, self.target_id, self.name)
../spark-2.4.4-bin-without-hadoop-scala-2.12/python/pyspark/sql/utils.py:63: in deco
    return f(*a, **kw)
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 

answer = 'xro3927'
gateway_client = <py4j.java_gateway.GatewayClient object at 0x7f2f8c6ecbd0>
target_id = 'o3925', name = 'loadGenotypes'

    def get_return_value(answer, gateway_client, target_id=None, name=None):
        """Converts an answer received from the Java gateway into a Python object.
    
        For example, string representation of integers are converted to Python
        integer, string representation of objects are converted to JavaObject
        instances, etc.
    
        :param answer: the string returned by the Java gateway
        :param gateway_client: the gateway client used to communicate with the Java
            Gateway. Only necessary if the answer is a reference (e.g., object,
            list, map)
        :param target_id: the name of the object from which the answer comes from
            (e.g., *object1* in `object1.hello()`). Optional.
        :param name: the name of the member from which the answer comes from
            (e.g., *hello* in `object1.hello()`). Optional.
        """
        if is_error(answer)[0]:
            if len(answer) > 1:
                type = answer[1]
                value = OUTPUT_CONVERTER[type](answer[2:], gateway_client)
                if answer[1] == REFERENCE_TYPE:
                    raise Py4JJavaError(
                        "An error occurred while calling {0}{1}{2}.\n".
>                       format(target_id, ".", name), value)
E                   Py4JJavaError: An error occurred while calling o3925.loadGenotypes.
E                   : java.lang.NoClassDefFoundError: Could not initialize class org.apache.spark.rdd.RDDOperationScope$
E                   	at org.apache.spark.SparkContext.withScope(SparkContext.scala:699)
E                   	at org.apache.spark.SparkContext.newAPIHadoopFile(SparkContext.scala:1146)
E                   	at org.bdgenomics.adam.rdd.ADAMContext.readVcfRecords(ADAMContext.scala:2627)
E                   	at org.bdgenomics.adam.rdd.ADAMContext.$anonfun$loadVcf$1(ADAMContext.scala:2645)
E                   	at scala.Option.fold(Option.scala:175)
E                   	at org.apache.spark.rdd.Timer.time(Timer.scala:48)
E                   	at org.bdgenomics.adam.rdd.ADAMContext.loadVcf(ADAMContext.scala:2642)
E                   	at org.bdgenomics.adam.rdd.ADAMContext.$anonfun$loadGenotypes$1(ADAMContext.scala:3551)
E                   	at scala.Option.fold(Option.scala:175)
E                   	at org.apache.spark.rdd.Timer.time(Timer.scala:48)
E                   	at org.bdgenomics.adam.rdd.ADAMContext.loadGenotypes(ADAMContext.scala:3549)
E                   	at org.bdgenomics.adam.api.java.JavaADAMContext.loadGenotypes(JavaADAMContext.scala:333)
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:498)
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:282)
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:238)
E                   	at java.lang.Thread.run(Thread.java:748)

/tmp/adamTest1UPduEN/deleteMePleaseThisIsNoLongerNeeded/spark-2.4.4-bin-without-hadoop-scala-2.12/python/lib/py4j-0.10.7-src.zip/py4j/protocol.py:328: Py4JJavaError
______________________ GenotypeDatasetTest.test_vcf_sort _______________________

self = <bdgenomics.adam.test.genotypeDataset_test.GenotypeDatasetTest testMethod=test_vcf_sort>

    def test_vcf_sort(self):
    
        testFile = self.resourceFile("random.vcf")
        ac = ADAMContext(self.ss)
    
>       genotypes = ac.loadGenotypes(testFile)

bdgenomics/adam/test/genotypeDataset_test.py:222: 
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 
bdgenomics/adam/adamContext.py:218: in loadGenotypes
    _toJava(stringency, self._jvm))
/tmp/adamTest1UPduEN/deleteMePleaseThisIsNoLongerNeeded/spark-2.4.4-bin-without-hadoop-scala-2.12/python/lib/py4j-0.10.7-src.zip/py4j/java_gateway.py:1257: in __call__
    answer, self.gateway_client, self.target_id, self.name)
../spark-2.4.4-bin-without-hadoop-scala-2.12/python/pyspark/sql/utils.py:63: in deco
    return f(*a, **kw)
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 

answer = 'xro3995'
gateway_client = <py4j.java_gateway.GatewayClient object at 0x7f2f8c6ecbd0>
target_id = 'o3993', name = 'loadGenotypes'

    def get_return_value(answer, gateway_client, target_id=None, name=None):
        """Converts an answer received from the Java gateway into a Python object.
    
        For example, string representation of integers are converted to Python
        integer, string representation of objects are converted to JavaObject
        instances, etc.
    
        :param answer: the string returned by the Java gateway
        :param gateway_client: the gateway client used to communicate with the Java
            Gateway. Only necessary if the answer is a reference (e.g., object,
            list, map)
        :param target_id: the name of the object from which the answer comes from
            (e.g., *object1* in `object1.hello()`). Optional.
        :param name: the name of the member from which the answer comes from
            (e.g., *hello* in `object1.hello()`). Optional.
        """
        if is_error(answer)[0]:
            if len(answer) > 1:
                type = answer[1]
                value = OUTPUT_CONVERTER[type](answer[2:], gateway_client)
                if answer[1] == REFERENCE_TYPE:
                    raise Py4JJavaError(
                        "An error occurred while calling {0}{1}{2}.\n".
>                       format(target_id, ".", name), value)
E                   Py4JJavaError: An error occurred while calling o3993.loadGenotypes.
E                   : java.lang.NoClassDefFoundError: Could not initialize class org.apache.spark.rdd.RDDOperationScope$
E                   	at org.apache.spark.SparkContext.withScope(SparkContext.scala:699)
E                   	at org.apache.spark.SparkContext.newAPIHadoopFile(SparkContext.scala:1146)
E                   	at org.bdgenomics.adam.rdd.ADAMContext.readVcfRecords(ADAMContext.scala:2627)
E                   	at org.bdgenomics.adam.rdd.ADAMContext.$anonfun$loadVcf$1(ADAMContext.scala:2645)
E                   	at scala.Option.fold(Option.scala:175)
E                   	at org.apache.spark.rdd.Timer.time(Timer.scala:48)
E                   	at org.bdgenomics.adam.rdd.ADAMContext.loadVcf(ADAMContext.scala:2642)
E                   	at org.bdgenomics.adam.rdd.ADAMContext.$anonfun$loadGenotypes$1(ADAMContext.scala:3551)
E                   	at scala.Option.fold(Option.scala:175)
E                   	at org.apache.spark.rdd.Timer.time(Timer.scala:48)
E                   	at org.bdgenomics.adam.rdd.ADAMContext.loadGenotypes(ADAMContext.scala:3549)
E                   	at org.bdgenomics.adam.api.java.JavaADAMContext.loadGenotypes(JavaADAMContext.scala:333)
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:498)
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:282)
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:238)
E                   	at java.lang.Thread.run(Thread.java:748)

/tmp/adamTest1UPduEN/deleteMePleaseThisIsNoLongerNeeded/spark-2.4.4-bin-without-hadoop-scala-2.12/python/lib/py4j-0.10.7-src.zip/py4j/protocol.py:328: Py4JJavaError
____________________ GenotypeDatasetTest.test_vcf_sort_lex _____________________

self = <bdgenomics.adam.test.genotypeDataset_test.GenotypeDatasetTest testMethod=test_vcf_sort_lex>

    def test_vcf_sort_lex(self):
    
        testFile = self.resourceFile("random.vcf")
        ac = ADAMContext(self.ss)
    
>       genotypes = ac.loadGenotypes(testFile)

bdgenomics/adam/test/genotypeDataset_test.py:236: 
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 
bdgenomics/adam/adamContext.py:218: in loadGenotypes
    _toJava(stringency, self._jvm))
/tmp/adamTest1UPduEN/deleteMePleaseThisIsNoLongerNeeded/spark-2.4.4-bin-without-hadoop-scala-2.12/python/lib/py4j-0.10.7-src.zip/py4j/java_gateway.py:1257: in __call__
    answer, self.gateway_client, self.target_id, self.name)
../spark-2.4.4-bin-without-hadoop-scala-2.12/python/pyspark/sql/utils.py:63: in deco
    return f(*a, **kw)
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 

answer = 'xro4063'
gateway_client = <py4j.java_gateway.GatewayClient object at 0x7f2f8c6ecbd0>
target_id = 'o4061', name = 'loadGenotypes'

    def get_return_value(answer, gateway_client, target_id=None, name=None):
        """Converts an answer received from the Java gateway into a Python object.
    
        For example, string representation of integers are converted to Python
        integer, string representation of objects are converted to JavaObject
        instances, etc.
    
        :param answer: the string returned by the Java gateway
        :param gateway_client: the gateway client used to communicate with the Java
            Gateway. Only necessary if the answer is a reference (e.g., object,
            list, map)
        :param target_id: the name of the object from which the answer comes from
            (e.g., *object1* in `object1.hello()`). Optional.
        :param name: the name of the member from which the answer comes from
            (e.g., *hello* in `object1.hello()`). Optional.
        """
        if is_error(answer)[0]:
            if len(answer) > 1:
                type = answer[1]
                value = OUTPUT_CONVERTER[type](answer[2:], gateway_client)
                if answer[1] == REFERENCE_TYPE:
                    raise Py4JJavaError(
                        "An error occurred while calling {0}{1}{2}.\n".
>                       format(target_id, ".", name), value)
E                   Py4JJavaError: An error occurred while calling o4061.loadGenotypes.
E                   : java.lang.NoClassDefFoundError: Could not initialize class org.apache.spark.rdd.RDDOperationScope$
E                   	at org.apache.spark.SparkContext.withScope(SparkContext.scala:699)
E                   	at org.apache.spark.SparkContext.newAPIHadoopFile(SparkContext.scala:1146)
E                   	at org.bdgenomics.adam.rdd.ADAMContext.readVcfRecords(ADAMContext.scala:2627)
E                   	at org.bdgenomics.adam.rdd.ADAMContext.$anonfun$loadVcf$1(ADAMContext.scala:2645)
E                   	at scala.Option.fold(Option.scala:175)
E                   	at org.apache.spark.rdd.Timer.time(Timer.scala:48)
E                   	at org.bdgenomics.adam.rdd.ADAMContext.loadVcf(ADAMContext.scala:2642)
E                   	at org.bdgenomics.adam.rdd.ADAMContext.$anonfun$loadGenotypes$1(ADAMContext.scala:3551)
E                   	at scala.Option.fold(Option.scala:175)
E                   	at org.apache.spark.rdd.Timer.time(Timer.scala:48)
E                   	at org.bdgenomics.adam.rdd.ADAMContext.loadGenotypes(ADAMContext.scala:3549)
E                   	at org.bdgenomics.adam.api.java.JavaADAMContext.loadGenotypes(JavaADAMContext.scala:333)
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:498)
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:282)
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:238)
E                   	at java.lang.Thread.run(Thread.java:748)

/tmp/adamTest1UPduEN/deleteMePleaseThisIsNoLongerNeeded/spark-2.4.4-bin-without-hadoop-scala-2.12/python/lib/py4j-0.10.7-src.zip/py4j/protocol.py:328: Py4JJavaError
______________________ VariantDatasetTest.test_transform _______________________

self = <bdgenomics.adam.test.variantDataset_test.VariantDatasetTest testMethod=test_transform>

    def test_transform(self):
    
        variantPath = self.resourceFile("small.vcf")
        ac = ADAMContext(self.ss)
    
>       variants = ac.loadVariants(variantPath)

bdgenomics/adam/test/variantDataset_test.py:48: 
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 
bdgenomics/adam/adamContext.py:237: in loadVariants
    _toJava(stringency, self._jvm))
/tmp/adamTest1UPduEN/deleteMePleaseThisIsNoLongerNeeded/spark-2.4.4-bin-without-hadoop-scala-2.12/python/lib/py4j-0.10.7-src.zip/py4j/java_gateway.py:1257: in __call__
    answer, self.gateway_client, self.target_id, self.name)
../spark-2.4.4-bin-without-hadoop-scala-2.12/python/pyspark/sql/utils.py:63: in deco
    return f(*a, **kw)
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 

answer = 'xro4131'
gateway_client = <py4j.java_gateway.GatewayClient object at 0x7f2f8c6ecbd0>
target_id = 'o4129', name = 'loadVariants'

    def get_return_value(answer, gateway_client, target_id=None, name=None):
        """Converts an answer received from the Java gateway into a Python object.
    
        For example, string representation of integers are converted to Python
        integer, string representation of objects are converted to JavaObject
        instances, etc.
    
        :param answer: the string returned by the Java gateway
        :param gateway_client: the gateway client used to communicate with the Java
            Gateway. Only necessary if the answer is a reference (e.g., object,
            list, map)
        :param target_id: the name of the object from which the answer comes from
            (e.g., *object1* in `object1.hello()`). Optional.
        :param name: the name of the member from which the answer comes from
            (e.g., *hello* in `object1.hello()`). Optional.
        """
        if is_error(answer)[0]:
            if len(answer) > 1:
                type = answer[1]
                value = OUTPUT_CONVERTER[type](answer[2:], gateway_client)
                if answer[1] == REFERENCE_TYPE:
                    raise Py4JJavaError(
                        "An error occurred while calling {0}{1}{2}.\n".
>                       format(target_id, ".", name), value)
E                   Py4JJavaError: An error occurred while calling o4129.loadVariants.
E                   : java.lang.NoClassDefFoundError: Could not initialize class org.apache.spark.rdd.RDDOperationScope$
E                   	at org.apache.spark.SparkContext.withScope(SparkContext.scala:699)
E                   	at org.apache.spark.SparkContext.newAPIHadoopFile(SparkContext.scala:1146)
E                   	at org.bdgenomics.adam.rdd.ADAMContext.readVcfRecords(ADAMContext.scala:2627)
E                   	at org.bdgenomics.adam.rdd.ADAMContext.$anonfun$loadVcf$1(ADAMContext.scala:2645)
E                   	at scala.Option.fold(Option.scala:175)
E                   	at org.apache.spark.rdd.Timer.time(Timer.scala:48)
E                   	at org.bdgenomics.adam.rdd.ADAMContext.loadVcf(ADAMContext.scala:2642)
E                   	at org.bdgenomics.adam.rdd.ADAMContext.$anonfun$loadVariants$1(ADAMContext.scala:3585)
E                   	at scala.Option.fold(Option.scala:175)
E                   	at org.apache.spark.rdd.Timer.time(Timer.scala:48)
E                   	at org.bdgenomics.adam.rdd.ADAMContext.loadVariants(ADAMContext.scala:3583)
E                   	at org.bdgenomics.adam.api.java.JavaADAMContext.loadVariants(JavaADAMContext.scala:367)
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:498)
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:282)
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:238)
E                   	at java.lang.Thread.run(Thread.java:748)

/tmp/adamTest1UPduEN/deleteMePleaseThisIsNoLongerNeeded/spark-2.4.4-bin-without-hadoop-scala-2.12/python/lib/py4j-0.10.7-src.zip/py4j/protocol.py:328: Py4JJavaError
____________________ VariantDatasetTest.test_vcf_round_trip ____________________

self = <bdgenomics.adam.test.variantDataset_test.VariantDatasetTest testMethod=test_vcf_round_trip>

    def test_vcf_round_trip(self):
    
        testFile = self.resourceFile("small.vcf")
        ac = ADAMContext(self.ss)
    
>       variants = ac.loadVariants(testFile)

bdgenomics/adam/test/variantDataset_test.py:32: 
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 
bdgenomics/adam/adamContext.py:237: in loadVariants
    _toJava(stringency, self._jvm))
/tmp/adamTest1UPduEN/deleteMePleaseThisIsNoLongerNeeded/spark-2.4.4-bin-without-hadoop-scala-2.12/python/lib/py4j-0.10.7-src.zip/py4j/java_gateway.py:1257: in __call__
    answer, self.gateway_client, self.target_id, self.name)
../spark-2.4.4-bin-without-hadoop-scala-2.12/python/pyspark/sql/utils.py:63: in deco
    return f(*a, **kw)
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 

answer = 'xro4199'
gateway_client = <py4j.java_gateway.GatewayClient object at 0x7f2f8c6ecbd0>
target_id = 'o4197', name = 'loadVariants'

    def get_return_value(answer, gateway_client, target_id=None, name=None):
        """Converts an answer received from the Java gateway into a Python object.
    
        For example, string representation of integers are converted to Python
        integer, string representation of objects are converted to JavaObject
        instances, etc.
    
        :param answer: the string returned by the Java gateway
        :param gateway_client: the gateway client used to communicate with the Java
            Gateway. Only necessary if the answer is a reference (e.g., object,
            list, map)
        :param target_id: the name of the object from which the answer comes from
            (e.g., *object1* in `object1.hello()`). Optional.
        :param name: the name of the member from which the answer comes from
            (e.g., *hello* in `object1.hello()`). Optional.
        """
        if is_error(answer)[0]:
            if len(answer) > 1:
                type = answer[1]
                value = OUTPUT_CONVERTER[type](answer[2:], gateway_client)
                if answer[1] == REFERENCE_TYPE:
                    raise Py4JJavaError(
                        "An error occurred while calling {0}{1}{2}.\n".
>                       format(target_id, ".", name), value)
E                   Py4JJavaError: An error occurred while calling o4197.loadVariants.
E                   : java.lang.NoClassDefFoundError: Could not initialize class org.apache.spark.rdd.RDDOperationScope$
E                   	at org.apache.spark.SparkContext.withScope(SparkContext.scala:699)
E                   	at org.apache.spark.SparkContext.newAPIHadoopFile(SparkContext.scala:1146)
E                   	at org.bdgenomics.adam.rdd.ADAMContext.readVcfRecords(ADAMContext.scala:2627)
E                   	at org.bdgenomics.adam.rdd.ADAMContext.$anonfun$loadVcf$1(ADAMContext.scala:2645)
E                   	at scala.Option.fold(Option.scala:175)
E                   	at org.apache.spark.rdd.Timer.time(Timer.scala:48)
E                   	at org.bdgenomics.adam.rdd.ADAMContext.loadVcf(ADAMContext.scala:2642)
E                   	at org.bdgenomics.adam.rdd.ADAMContext.$anonfun$loadVariants$1(ADAMContext.scala:3585)
E                   	at scala.Option.fold(Option.scala:175)
E                   	at org.apache.spark.rdd.Timer.time(Timer.scala:48)
E                   	at org.bdgenomics.adam.rdd.ADAMContext.loadVariants(ADAMContext.scala:3583)
E                   	at org.bdgenomics.adam.api.java.JavaADAMContext.loadVariants(JavaADAMContext.scala:367)
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:498)
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:282)
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:238)
E                   	at java.lang.Thread.run(Thread.java:748)

/tmp/adamTest1UPduEN/deleteMePleaseThisIsNoLongerNeeded/spark-2.4.4-bin-without-hadoop-scala-2.12/python/lib/py4j-0.10.7-src.zip/py4j/protocol.py:328: Py4JJavaError
- generated xml file: /tmp/adamTest1UPduEN/deleteMePleaseThisIsNoLongerNeeded/adam-python/target/pytest-reports/tests.xml -
========================== 63 failed in 50.44 seconds ==========================
Makefile:83: recipe for target 'test' failed
make: *** [test] Error 1
[ERROR] Command execution failed.
org.apache.commons.exec.ExecuteException: Process exited with an error: 2 (Exit value: 2)
	at org.apache.commons.exec.DefaultExecutor.executeInternal(DefaultExecutor.java:404)
	at org.apache.commons.exec.DefaultExecutor.execute(DefaultExecutor.java:166)
	at org.codehaus.mojo.exec.ExecMojo.executeCommandLine(ExecMojo.java:764)
	at org.codehaus.mojo.exec.ExecMojo.executeCommandLine(ExecMojo.java:711)
	at org.codehaus.mojo.exec.ExecMojo.execute(ExecMojo.java:289)
	at org.apache.maven.plugin.DefaultBuildPluginManager.executeMojo(DefaultBuildPluginManager.java:134)
	at org.apache.maven.lifecycle.internal.MojoExecutor.execute(MojoExecutor.java:207)
	at org.apache.maven.lifecycle.internal.MojoExecutor.execute(MojoExecutor.java:153)
	at org.apache.maven.lifecycle.internal.MojoExecutor.execute(MojoExecutor.java:145)
	at org.apache.maven.lifecycle.internal.LifecycleModuleBuilder.buildProject(LifecycleModuleBuilder.java:116)
	at org.apache.maven.lifecycle.internal.LifecycleModuleBuilder.buildProject(LifecycleModuleBuilder.java:80)
	at org.apache.maven.lifecycle.internal.builder.singlethreaded.SingleThreadedBuilder.build(SingleThreadedBuilder.java:51)
	at org.apache.maven.lifecycle.internal.LifecycleStarter.execute(LifecycleStarter.java:128)
	at org.apache.maven.DefaultMaven.doExecute(DefaultMaven.java:307)
	at org.apache.maven.DefaultMaven.doExecute(DefaultMaven.java:193)
	at org.apache.maven.DefaultMaven.execute(DefaultMaven.java:106)
	at org.apache.maven.cli.MavenCli.execute(MavenCli.java:863)
	at org.apache.maven.cli.MavenCli.doMain(MavenCli.java:288)
	at org.apache.maven.cli.MavenCli.main(MavenCli.java:199)
	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.codehaus.plexus.classworlds.launcher.Launcher.launchEnhanced(Launcher.java:289)
	at org.codehaus.plexus.classworlds.launcher.Launcher.launch(Launcher.java:229)
	at org.codehaus.plexus.classworlds.launcher.Launcher.mainWithExitCode(Launcher.java:415)
	at org.codehaus.plexus.classworlds.launcher.Launcher.main(Launcher.java:356)
[INFO] ------------------------------------------------------------------------
[INFO] Reactor Summary:
[INFO] 
[INFO] ADAM_2.12 .......................................... SUCCESS [  8.722 s]
[INFO] ADAM_2.12: Avro-to-Dataset codegen utils ........... SUCCESS [ 11.011 s]
[INFO] ADAM_2.12: Core .................................... SUCCESS [01:42 min]
[INFO] ADAM_2.12: APIs for Java, Python ................... SUCCESS [ 22.682 s]
[INFO] ADAM_2.12: CLI ..................................... SUCCESS [ 28.315 s]
[INFO] ADAM_2.12: Assembly ................................ SUCCESS [ 23.806 s]
[INFO] ADAM_2.12: Python APIs ............................. FAILURE [ 58.573 s]
[INFO] ADAM_2.12: R APIs .................................. SKIPPED
[INFO] ADAM_2.12: Distribution ............................ SKIPPED
[INFO] ------------------------------------------------------------------------
[INFO] BUILD FAILURE
[INFO] ------------------------------------------------------------------------
[INFO] Total time: 04:16 min
[INFO] Finished at: 2020-01-24T12:31:09-08:00
[INFO] Final Memory: 100M/1510M
[INFO] ------------------------------------------------------------------------
[ERROR] Failed to execute goal org.codehaus.mojo:exec-maven-plugin:1.5.0:exec (test-python) on project adam-python-spark2_2.12: Command execution failed. Process exited with an error: 2 (Exit value: 2) -> [Help 1]
[ERROR] 
[ERROR] To see the full stack trace of the errors, re-run Maven with the -e switch.
[ERROR] Re-run Maven using the -X switch to enable full debug logging.
[ERROR] 
[ERROR] For more information about the errors and possible solutions, please read the following articles:
[ERROR] [Help 1] http://cwiki.apache.org/confluence/display/MAVEN/MojoExecutionException
[ERROR] 
[ERROR] After correcting the problems, you can resume the build with the command
[ERROR]   mvn <goals> -rf :adam-python-spark2_2.12
Build step 'Execute shell' marked build as failure
Recording test results
Publishing Scoverage XML and HTML report...
null
Setting commit status on GitHub for https://github.com/bigdatagenomics/adam/commit/9a16079f5a139ff66e00e34273154a8fc202520b
Finished: FAILURE