FailedConsole Output

Skipping 3,446 KB.. Full Log
a: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/adamTestdLUBupA/deleteMePleaseThisIsNoLongerNeeded/spark-2.4.3-bin-without-hadoop-scala-2.12/python/lib/py4j-0.10.7-src.zip/py4j/protocol.py:328: Py4JJavaError
----------------------------- Captured stderr call -----------------------------
2019-05-15 13:41:22 WARN  Utils:66 - Service 'SparkUI' could not bind on port 4040. Attempting port 4041.
2019-05-15 13:41:22 WARN  Utils:66 - Service 'SparkUI' could not bind on port 4041. Attempting port 4042.
______________ 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:236: in loadGenotypes
    _toJava(stringency, self._jvm))
/tmp/adamTestdLUBupA/deleteMePleaseThisIsNoLongerNeeded/spark-2.4.3-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-2.4.3-bin-without-hadoop-scala-2.12/python/pyspark/sql/utils.py:63: in deco
    return f(*a, **kw)
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 

answer = 'xro5911'
gateway_client = <py4j.java_gateway.GatewayClient object at 0x7f9a60794550>
target_id = 'o5909', 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 o5909.loadGenotypes.
E                   : java.lang.ArrayIndexOutOfBoundsException: 17418
E                   	at com.thoughtworks.paranamer.BytecodeReadingParanamer$ClassReader.accept(BytecodeReadingParanamer.java:563)
E                   	at com.thoughtworks.paranamer.BytecodeReadingParanamer$ClassReader.access$200(BytecodeReadingParanamer.java:338)
E                   	at com.thoughtworks.paranamer.BytecodeReadingParanamer.lookupParameterNames(BytecodeReadingParanamer.java:103)
E                   	at com.thoughtworks.paranamer.CachingParanamer.lookupParameterNames(CachingParanamer.java:90)
E                   	at com.fasterxml.jackson.module.scala.introspect.BeanIntrospector$.getCtorParams(BeanIntrospector.scala:44)
E                   	at com.fasterxml.jackson.module.scala.introspect.BeanIntrospector$.$anonfun$apply$1(BeanIntrospector.scala:58)
E                   	at com.fasterxml.jackson.module.scala.introspect.BeanIntrospector$.$anonfun$apply$1$adapted(BeanIntrospector.scala:58)
E                   	at scala.collection.TraversableLike.$anonfun$flatMap$1(TraversableLike.scala:244)
E                   	at scala.collection.Iterator.foreach(Iterator.scala:941)
E                   	at scala.collection.Iterator.foreach$(Iterator.scala:941)
E                   	at scala.collection.AbstractIterator.foreach(Iterator.scala:1429)
E                   	at scala.collection.IterableLike.foreach(IterableLike.scala:74)
E                   	at scala.collection.IterableLike.foreach$(IterableLike.scala:73)
E                   	at scala.collection.AbstractIterable.foreach(Iterable.scala:56)
E                   	at scala.collection.TraversableLike.flatMap(TraversableLike.scala:244)
E                   	at scala.collection.TraversableLike.flatMap$(TraversableLike.scala:241)
E                   	at scala.collection.AbstractTraversable.flatMap(Traversable.scala:108)
E                   	at com.fasterxml.jackson.module.scala.introspect.BeanIntrospector$.findConstructorParam$1(BeanIntrospector.scala:58)
E                   	at com.fasterxml.jackson.module.scala.introspect.BeanIntrospector$.$anonfun$apply$19(BeanIntrospector.scala:176)
E                   	at scala.collection.TraversableLike.$anonfun$map$1(TraversableLike.scala:237)
E                   	at scala.collection.IndexedSeqOptimized.foreach(IndexedSeqOptimized.scala:36)
E                   	at scala.collection.IndexedSeqOptimized.foreach$(IndexedSeqOptimized.scala:33)
E                   	at scala.collection.mutable.ArrayOps$ofRef.foreach(ArrayOps.scala:198)
E                   	at scala.collection.TraversableLike.map(TraversableLike.scala:237)
E                   	at scala.collection.TraversableLike.map$(TraversableLike.scala:230)
E                   	at scala.collection.mutable.ArrayOps$ofRef.map(ArrayOps.scala:198)
E                   	at com.fasterxml.jackson.module.scala.introspect.BeanIntrospector$.$anonfun$apply$14(BeanIntrospector.scala:170)
E                   	at com.fasterxml.jackson.module.scala.introspect.BeanIntrospector$.$anonfun$apply$14$adapted(BeanIntrospector.scala:169)
E                   	at scala.collection.TraversableLike.$anonfun$flatMap$1(TraversableLike.scala:244)
E                   	at scala.collection.immutable.List.foreach(List.scala:392)
E                   	at scala.collection.TraversableLike.flatMap(TraversableLike.scala:244)
E                   	at scala.collection.TraversableLike.flatMap$(TraversableLike.scala:241)
E                   	at scala.collection.immutable.List.flatMap(List.scala:355)
E                   	at com.fasterxml.jackson.module.scala.introspect.BeanIntrospector$.apply(BeanIntrospector.scala:169)
E                   	at com.fasterxml.jackson.module.scala.introspect.ScalaAnnotationIntrospector$._descriptorFor(ScalaAnnotationIntrospectorModule.scala:22)
E                   	at com.fasterxml.jackson.module.scala.introspect.ScalaAnnotationIntrospector$.fieldName(ScalaAnnotationIntrospectorModule.scala:30)
E                   	at com.fasterxml.jackson.module.scala.introspect.ScalaAnnotationIntrospector$.findImplicitPropertyName(ScalaAnnotationIntrospectorModule.scala:78)
E                   	at com.fasterxml.jackson.databind.introspect.AnnotationIntrospectorPair.findImplicitPropertyName(AnnotationIntrospectorPair.java:467)
E                   	at com.fasterxml.jackson.databind.introspect.POJOPropertiesCollector._addFields(POJOPropertiesCollector.java:351)
E                   	at com.fasterxml.jackson.databind.introspect.POJOPropertiesCollector.collectAll(POJOPropertiesCollector.java:283)
E                   	at com.fasterxml.jackson.databind.introspect.POJOPropertiesCollector.getJsonValueMethod(POJOPropertiesCollector.java:169)
E                   	at com.fasterxml.jackson.databind.introspect.BasicBeanDescription.findJsonValueMethod(BasicBeanDescription.java:223)
E                   	at com.fasterxml.jackson.databind.ser.BasicSerializerFactory.findSerializerByAnnotations(BasicSerializerFactory.java:348)
E                   	at com.fasterxml.jackson.databind.ser.BeanSerializerFactory._createSerializer2(BeanSerializerFactory.java:210)
E                   	at com.fasterxml.jackson.databind.ser.BeanSerializerFactory.createSerializer(BeanSerializerFactory.java:153)
E                   	at com.fasterxml.jackson.databind.SerializerProvider._createUntypedSerializer(SerializerProvider.java:1203)
E                   	at com.fasterxml.jackson.databind.SerializerProvider._createAndCacheUntypedSerializer(SerializerProvider.java:1157)
E                   	at com.fasterxml.jackson.databind.SerializerProvider.findValueSerializer(SerializerProvider.java:481)
E                   	at com.fasterxml.jackson.databind.SerializerProvider.findTypedValueSerializer(SerializerProvider.java:679)
E                   	at com.fasterxml.jackson.databind.ser.DefaultSerializerProvider.serializeValue(DefaultSerializerProvider.java:107)
E                   	at com.fasterxml.jackson.databind.ObjectMapper._configAndWriteValue(ObjectMapper.java:3559)
E                   	at com.fasterxml.jackson.databind.ObjectMapper.writeValueAsString(ObjectMapper.java:2927)
E                   	at org.apache.spark.rdd.RDDOperationScope.toJson(RDDOperationScope.scala:52)
E                   	at org.apache.spark.rdd.RDDOperationScope$.withScope(RDDOperationScope.scala:145)
E                   	at org.apache.spark.rdd.RDDOperationScope$.withScope(RDDOperationScope.scala:112)
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:2151)
E                   	at org.bdgenomics.adam.rdd.ADAMContext.$anonfun$loadVcf$1(ADAMContext.scala:2169)
E                   	at scala.Option.fold(Option.scala:175)
E                   	at org.apache.spark.rdd.Timer.time(Timer.scala:48)
E                   	at org.bdgenomics.adam.rdd.ADAMContext.loadVcf(ADAMContext.scala:2166)
E                   	at org.bdgenomics.adam.rdd.ADAMContext.$anonfun$loadGenotypes$1(ADAMContext.scala:3187)
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:3185)
E                   	at org.bdgenomics.adam.api.java.JavaADAMContext.loadGenotypes(JavaADAMContext.scala:353)
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/adamTestdLUBupA/deleteMePleaseThisIsNoLongerNeeded/spark-2.4.3-bin-without-hadoop-scala-2.12/python/lib/py4j-0.10.7-src.zip/py4j/protocol.py:328: Py4JJavaError
----------------------------- Captured stderr call -----------------------------
2019-05-15 13:41:22 WARN  Utils:66 - Service 'SparkUI' could not bind on port 4040. Attempting port 4041.
2019-05-15 13:41:22 WARN  Utils:66 - Service 'SparkUI' could not bind on port 4041. Attempting port 4042.
________________ 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:236: in loadGenotypes
    _toJava(stringency, self._jvm))
/tmp/adamTestdLUBupA/deleteMePleaseThisIsNoLongerNeeded/spark-2.4.3-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-2.4.3-bin-without-hadoop-scala-2.12/python/pyspark/sql/utils.py:63: in deco
    return f(*a, **kw)
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 

answer = 'xro6032'
gateway_client = <py4j.java_gateway.GatewayClient object at 0x7f9a60794550>
target_id = 'o6030', 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 o6030.loadGenotypes.
E                   : java.lang.ArrayIndexOutOfBoundsException: 17418
E                   	at com.thoughtworks.paranamer.BytecodeReadingParanamer$ClassReader.accept(BytecodeReadingParanamer.java:563)
E                   	at com.thoughtworks.paranamer.BytecodeReadingParanamer$ClassReader.access$200(BytecodeReadingParanamer.java:338)
E                   	at com.thoughtworks.paranamer.BytecodeReadingParanamer.lookupParameterNames(BytecodeReadingParanamer.java:103)
E                   	at com.thoughtworks.paranamer.CachingParanamer.lookupParameterNames(CachingParanamer.java:90)
E                   	at com.fasterxml.jackson.module.scala.introspect.BeanIntrospector$.getCtorParams(BeanIntrospector.scala:44)
E                   	at com.fasterxml.jackson.module.scala.introspect.BeanIntrospector$.$anonfun$apply$1(BeanIntrospector.scala:58)
E                   	at com.fasterxml.jackson.module.scala.introspect.BeanIntrospector$.$anonfun$apply$1$adapted(BeanIntrospector.scala:58)
E                   	at scala.collection.TraversableLike.$anonfun$flatMap$1(TraversableLike.scala:244)
E                   	at scala.collection.Iterator.foreach(Iterator.scala:941)
E                   	at scala.collection.Iterator.foreach$(Iterator.scala:941)
E                   	at scala.collection.AbstractIterator.foreach(Iterator.scala:1429)
E                   	at scala.collection.IterableLike.foreach(IterableLike.scala:74)
E                   	at scala.collection.IterableLike.foreach$(IterableLike.scala:73)
E                   	at scala.collection.AbstractIterable.foreach(Iterable.scala:56)
E                   	at scala.collection.TraversableLike.flatMap(TraversableLike.scala:244)
E                   	at scala.collection.TraversableLike.flatMap$(TraversableLike.scala:241)
E                   	at scala.collection.AbstractTraversable.flatMap(Traversable.scala:108)
E                   	at com.fasterxml.jackson.module.scala.introspect.BeanIntrospector$.findConstructorParam$1(BeanIntrospector.scala:58)
E                   	at com.fasterxml.jackson.module.scala.introspect.BeanIntrospector$.$anonfun$apply$19(BeanIntrospector.scala:176)
E                   	at scala.collection.TraversableLike.$anonfun$map$1(TraversableLike.scala:237)
E                   	at scala.collection.IndexedSeqOptimized.foreach(IndexedSeqOptimized.scala:36)
E                   	at scala.collection.IndexedSeqOptimized.foreach$(IndexedSeqOptimized.scala:33)
E                   	at scala.collection.mutable.ArrayOps$ofRef.foreach(ArrayOps.scala:198)
E                   	at scala.collection.TraversableLike.map(TraversableLike.scala:237)
E                   	at scala.collection.TraversableLike.map$(TraversableLike.scala:230)
E                   	at scala.collection.mutable.ArrayOps$ofRef.map(ArrayOps.scala:198)
E                   	at com.fasterxml.jackson.module.scala.introspect.BeanIntrospector$.$anonfun$apply$14(BeanIntrospector.scala:170)
E                   	at com.fasterxml.jackson.module.scala.introspect.BeanIntrospector$.$anonfun$apply$14$adapted(BeanIntrospector.scala:169)
E                   	at scala.collection.TraversableLike.$anonfun$flatMap$1(TraversableLike.scala:244)
E                   	at scala.collection.immutable.List.foreach(List.scala:392)
E                   	at scala.collection.TraversableLike.flatMap(TraversableLike.scala:244)
E                   	at scala.collection.TraversableLike.flatMap$(TraversableLike.scala:241)
E                   	at scala.collection.immutable.List.flatMap(List.scala:355)
E                   	at com.fasterxml.jackson.module.scala.introspect.BeanIntrospector$.apply(BeanIntrospector.scala:169)
E                   	at com.fasterxml.jackson.module.scala.introspect.ScalaAnnotationIntrospector$._descriptorFor(ScalaAnnotationIntrospectorModule.scala:22)
E                   	at com.fasterxml.jackson.module.scala.introspect.ScalaAnnotationIntrospector$.fieldName(ScalaAnnotationIntrospectorModule.scala:30)
E                   	at com.fasterxml.jackson.module.scala.introspect.ScalaAnnotationIntrospector$.findImplicitPropertyName(ScalaAnnotationIntrospectorModule.scala:78)
E                   	at com.fasterxml.jackson.databind.introspect.AnnotationIntrospectorPair.findImplicitPropertyName(AnnotationIntrospectorPair.java:467)
E                   	at com.fasterxml.jackson.databind.introspect.POJOPropertiesCollector._addFields(POJOPropertiesCollector.java:351)
E                   	at com.fasterxml.jackson.databind.introspect.POJOPropertiesCollector.collectAll(POJOPropertiesCollector.java:283)
E                   	at com.fasterxml.jackson.databind.introspect.POJOPropertiesCollector.getJsonValueMethod(POJOPropertiesCollector.java:169)
E                   	at com.fasterxml.jackson.databind.introspect.BasicBeanDescription.findJsonValueMethod(BasicBeanDescription.java:223)
E                   	at com.fasterxml.jackson.databind.ser.BasicSerializerFactory.findSerializerByAnnotations(BasicSerializerFactory.java:348)
E                   	at com.fasterxml.jackson.databind.ser.BeanSerializerFactory._createSerializer2(BeanSerializerFactory.java:210)
E                   	at com.fasterxml.jackson.databind.ser.BeanSerializerFactory.createSerializer(BeanSerializerFactory.java:153)
E                   	at com.fasterxml.jackson.databind.SerializerProvider._createUntypedSerializer(SerializerProvider.java:1203)
E                   	at com.fasterxml.jackson.databind.SerializerProvider._createAndCacheUntypedSerializer(SerializerProvider.java:1157)
E                   	at com.fasterxml.jackson.databind.SerializerProvider.findValueSerializer(SerializerProvider.java:481)
E                   	at com.fasterxml.jackson.databind.SerializerProvider.findTypedValueSerializer(SerializerProvider.java:679)
E                   	at com.fasterxml.jackson.databind.ser.DefaultSerializerProvider.serializeValue(DefaultSerializerProvider.java:107)
E                   	at com.fasterxml.jackson.databind.ObjectMapper._configAndWriteValue(ObjectMapper.java:3559)
E                   	at com.fasterxml.jackson.databind.ObjectMapper.writeValueAsString(ObjectMapper.java:2927)
E                   	at org.apache.spark.rdd.RDDOperationScope.toJson(RDDOperationScope.scala:52)
E                   	at org.apache.spark.rdd.RDDOperationScope$.withScope(RDDOperationScope.scala:145)
E                   	at org.apache.spark.rdd.RDDOperationScope$.withScope(RDDOperationScope.scala:112)
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:2151)
E                   	at org.bdgenomics.adam.rdd.ADAMContext.$anonfun$loadVcf$1(ADAMContext.scala:2169)
E                   	at scala.Option.fold(Option.scala:175)
E                   	at org.apache.spark.rdd.Timer.time(Timer.scala:48)
E                   	at org.bdgenomics.adam.rdd.ADAMContext.loadVcf(ADAMContext.scala:2166)
E                   	at org.bdgenomics.adam.rdd.ADAMContext.$anonfun$loadGenotypes$1(ADAMContext.scala:3187)
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:3185)
E                   	at org.bdgenomics.adam.api.java.JavaADAMContext.loadGenotypes(JavaADAMContext.scala:353)
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/adamTestdLUBupA/deleteMePleaseThisIsNoLongerNeeded/spark-2.4.3-bin-without-hadoop-scala-2.12/python/lib/py4j-0.10.7-src.zip/py4j/protocol.py:328: Py4JJavaError
----------------------------- Captured stderr call -----------------------------
2019-05-15 13:41:23 WARN  Utils:66 - Service 'SparkUI' could not bind on port 4040. Attempting port 4041.
2019-05-15 13:41:23 WARN  Utils:66 - Service 'SparkUI' could not bind on port 4041. Attempting port 4042.
____________ 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:236: in loadGenotypes
    _toJava(stringency, self._jvm))
/tmp/adamTestdLUBupA/deleteMePleaseThisIsNoLongerNeeded/spark-2.4.3-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-2.4.3-bin-without-hadoop-scala-2.12/python/pyspark/sql/utils.py:63: in deco
    return f(*a, **kw)
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 

answer = 'xro6153'
gateway_client = <py4j.java_gateway.GatewayClient object at 0x7f9a60794550>
target_id = 'o6151', 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 o6151.loadGenotypes.
E                   : java.lang.ArrayIndexOutOfBoundsException: 17418
E                   	at com.thoughtworks.paranamer.BytecodeReadingParanamer$ClassReader.accept(BytecodeReadingParanamer.java:563)
E                   	at com.thoughtworks.paranamer.BytecodeReadingParanamer$ClassReader.access$200(BytecodeReadingParanamer.java:338)
E                   	at com.thoughtworks.paranamer.BytecodeReadingParanamer.lookupParameterNames(BytecodeReadingParanamer.java:103)
E                   	at com.thoughtworks.paranamer.CachingParanamer.lookupParameterNames(CachingParanamer.java:90)
E                   	at com.fasterxml.jackson.module.scala.introspect.BeanIntrospector$.getCtorParams(BeanIntrospector.scala:44)
E                   	at com.fasterxml.jackson.module.scala.introspect.BeanIntrospector$.$anonfun$apply$1(BeanIntrospector.scala:58)
E                   	at com.fasterxml.jackson.module.scala.introspect.BeanIntrospector$.$anonfun$apply$1$adapted(BeanIntrospector.scala:58)
E                   	at scala.collection.TraversableLike.$anonfun$flatMap$1(TraversableLike.scala:244)
E                   	at scala.collection.Iterator.foreach(Iterator.scala:941)
E                   	at scala.collection.Iterator.foreach$(Iterator.scala:941)
E                   	at scala.collection.AbstractIterator.foreach(Iterator.scala:1429)
E                   	at scala.collection.IterableLike.foreach(IterableLike.scala:74)
E                   	at scala.collection.IterableLike.foreach$(IterableLike.scala:73)
E                   	at scala.collection.AbstractIterable.foreach(Iterable.scala:56)
E                   	at scala.collection.TraversableLike.flatMap(TraversableLike.scala:244)
E                   	at scala.collection.TraversableLike.flatMap$(TraversableLike.scala:241)
E                   	at scala.collection.AbstractTraversable.flatMap(Traversable.scala:108)
E                   	at com.fasterxml.jackson.module.scala.introspect.BeanIntrospector$.findConstructorParam$1(BeanIntrospector.scala:58)
E                   	at com.fasterxml.jackson.module.scala.introspect.BeanIntrospector$.$anonfun$apply$19(BeanIntrospector.scala:176)
E                   	at scala.collection.TraversableLike.$anonfun$map$1(TraversableLike.scala:237)
E                   	at scala.collection.IndexedSeqOptimized.foreach(IndexedSeqOptimized.scala:36)
E                   	at scala.collection.IndexedSeqOptimized.foreach$(IndexedSeqOptimized.scala:33)
E                   	at scala.collection.mutable.ArrayOps$ofRef.foreach(ArrayOps.scala:198)
E                   	at scala.collection.TraversableLike.map(TraversableLike.scala:237)
E                   	at scala.collection.TraversableLike.map$(TraversableLike.scala:230)
E                   	at scala.collection.mutable.ArrayOps$ofRef.map(ArrayOps.scala:198)
E                   	at com.fasterxml.jackson.module.scala.introspect.BeanIntrospector$.$anonfun$apply$14(BeanIntrospector.scala:170)
E                   	at com.fasterxml.jackson.module.scala.introspect.BeanIntrospector$.$anonfun$apply$14$adapted(BeanIntrospector.scala:169)
E                   	at scala.collection.TraversableLike.$anonfun$flatMap$1(TraversableLike.scala:244)
E                   	at scala.collection.immutable.List.foreach(List.scala:392)
E                   	at scala.collection.TraversableLike.flatMap(TraversableLike.scala:244)
E                   	at scala.collection.TraversableLike.flatMap$(TraversableLike.scala:241)
E                   	at scala.collection.immutable.List.flatMap(List.scala:355)
E                   	at com.fasterxml.jackson.module.scala.introspect.BeanIntrospector$.apply(BeanIntrospector.scala:169)
E                   	at com.fasterxml.jackson.module.scala.introspect.ScalaAnnotationIntrospector$._descriptorFor(ScalaAnnotationIntrospectorModule.scala:22)
E                   	at com.fasterxml.jackson.module.scala.introspect.ScalaAnnotationIntrospector$.fieldName(ScalaAnnotationIntrospectorModule.scala:30)
E                   	at com.fasterxml.jackson.module.scala.introspect.ScalaAnnotationIntrospector$.findImplicitPropertyName(ScalaAnnotationIntrospectorModule.scala:78)
E                   	at com.fasterxml.jackson.databind.introspect.AnnotationIntrospectorPair.findImplicitPropertyName(AnnotationIntrospectorPair.java:467)
E                   	at com.fasterxml.jackson.databind.introspect.POJOPropertiesCollector._addFields(POJOPropertiesCollector.java:351)
E                   	at com.fasterxml.jackson.databind.introspect.POJOPropertiesCollector.collectAll(POJOPropertiesCollector.java:283)
E                   	at com.fasterxml.jackson.databind.introspect.POJOPropertiesCollector.getJsonValueMethod(POJOPropertiesCollector.java:169)
E                   	at com.fasterxml.jackson.databind.introspect.BasicBeanDescription.findJsonValueMethod(BasicBeanDescription.java:223)
E                   	at com.fasterxml.jackson.databind.ser.BasicSerializerFactory.findSerializerByAnnotations(BasicSerializerFactory.java:348)
E                   	at com.fasterxml.jackson.databind.ser.BeanSerializerFactory._createSerializer2(BeanSerializerFactory.java:210)
E                   	at com.fasterxml.jackson.databind.ser.BeanSerializerFactory.createSerializer(BeanSerializerFactory.java:153)
E                   	at com.fasterxml.jackson.databind.SerializerProvider._createUntypedSerializer(SerializerProvider.java:1203)
E                   	at com.fasterxml.jackson.databind.SerializerProvider._createAndCacheUntypedSerializer(SerializerProvider.java:1157)
E                   	at com.fasterxml.jackson.databind.SerializerProvider.findValueSerializer(SerializerProvider.java:481)
E                   	at com.fasterxml.jackson.databind.SerializerProvider.findTypedValueSerializer(SerializerProvider.java:679)
E                   	at com.fasterxml.jackson.databind.ser.DefaultSerializerProvider.serializeValue(DefaultSerializerProvider.java:107)
E                   	at com.fasterxml.jackson.databind.ObjectMapper._configAndWriteValue(ObjectMapper.java:3559)
E                   	at com.fasterxml.jackson.databind.ObjectMapper.writeValueAsString(ObjectMapper.java:2927)
E                   	at org.apache.spark.rdd.RDDOperationScope.toJson(RDDOperationScope.scala:52)
E                   	at org.apache.spark.rdd.RDDOperationScope$.withScope(RDDOperationScope.scala:145)
E                   	at org.apache.spark.rdd.RDDOperationScope$.withScope(RDDOperationScope.scala:112)
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:2151)
E                   	at org.bdgenomics.adam.rdd.ADAMContext.$anonfun$loadVcf$1(ADAMContext.scala:2169)
E                   	at scala.Option.fold(Option.scala:175)
E                   	at org.apache.spark.rdd.Timer.time(Timer.scala:48)
E                   	at org.bdgenomics.adam.rdd.ADAMContext.loadVcf(ADAMContext.scala:2166)
E                   	at org.bdgenomics.adam.rdd.ADAMContext.$anonfun$loadGenotypes$1(ADAMContext.scala:3187)
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:3185)
E                   	at org.bdgenomics.adam.api.java.JavaADAMContext.loadGenotypes(JavaADAMContext.scala:353)
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/adamTestdLUBupA/deleteMePleaseThisIsNoLongerNeeded/spark-2.4.3-bin-without-hadoop-scala-2.12/python/lib/py4j-0.10.7-src.zip/py4j/protocol.py:328: Py4JJavaError
----------------------------- Captured stderr call -----------------------------
2019-05-15 13:41:24 WARN  Utils:66 - Service 'SparkUI' could not bind on port 4040. Attempting port 4041.
2019-05-15 13:41:24 WARN  Utils:66 - Service 'SparkUI' could not bind on port 4041. Attempting port 4042.
________________ 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:236: in loadGenotypes
    _toJava(stringency, self._jvm))
/tmp/adamTestdLUBupA/deleteMePleaseThisIsNoLongerNeeded/spark-2.4.3-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-2.4.3-bin-without-hadoop-scala-2.12/python/pyspark/sql/utils.py:63: in deco
    return f(*a, **kw)
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 

answer = 'xro6274'
gateway_client = <py4j.java_gateway.GatewayClient object at 0x7f9a60794550>
target_id = 'o6272', 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 o6272.loadGenotypes.
E                   : java.lang.ArrayIndexOutOfBoundsException: 17418
E                   	at com.thoughtworks.paranamer.BytecodeReadingParanamer$ClassReader.accept(BytecodeReadingParanamer.java:563)
E                   	at com.thoughtworks.paranamer.BytecodeReadingParanamer$ClassReader.access$200(BytecodeReadingParanamer.java:338)
E                   	at com.thoughtworks.paranamer.BytecodeReadingParanamer.lookupParameterNames(BytecodeReadingParanamer.java:103)
E                   	at com.thoughtworks.paranamer.CachingParanamer.lookupParameterNames(CachingParanamer.java:90)
E                   	at com.fasterxml.jackson.module.scala.introspect.BeanIntrospector$.getCtorParams(BeanIntrospector.scala:44)
E                   	at com.fasterxml.jackson.module.scala.introspect.BeanIntrospector$.$anonfun$apply$1(BeanIntrospector.scala:58)
E                   	at com.fasterxml.jackson.module.scala.introspect.BeanIntrospector$.$anonfun$apply$1$adapted(BeanIntrospector.scala:58)
E                   	at scala.collection.TraversableLike.$anonfun$flatMap$1(TraversableLike.scala:244)
E                   	at scala.collection.Iterator.foreach(Iterator.scala:941)
E                   	at scala.collection.Iterator.foreach$(Iterator.scala:941)
E                   	at scala.collection.AbstractIterator.foreach(Iterator.scala:1429)
E                   	at scala.collection.IterableLike.foreach(IterableLike.scala:74)
E                   	at scala.collection.IterableLike.foreach$(IterableLike.scala:73)
E                   	at scala.collection.AbstractIterable.foreach(Iterable.scala:56)
E                   	at scala.collection.TraversableLike.flatMap(TraversableLike.scala:244)
E                   	at scala.collection.TraversableLike.flatMap$(TraversableLike.scala:241)
E                   	at scala.collection.AbstractTraversable.flatMap(Traversable.scala:108)
E                   	at com.fasterxml.jackson.module.scala.introspect.BeanIntrospector$.findConstructorParam$1(BeanIntrospector.scala:58)
E                   	at com.fasterxml.jackson.module.scala.introspect.BeanIntrospector$.$anonfun$apply$19(BeanIntrospector.scala:176)
E                   	at scala.collection.TraversableLike.$anonfun$map$1(TraversableLike.scala:237)
E                   	at scala.collection.IndexedSeqOptimized.foreach(IndexedSeqOptimized.scala:36)
E                   	at scala.collection.IndexedSeqOptimized.foreach$(IndexedSeqOptimized.scala:33)
E                   	at scala.collection.mutable.ArrayOps$ofRef.foreach(ArrayOps.scala:198)
E                   	at scala.collection.TraversableLike.map(TraversableLike.scala:237)
E                   	at scala.collection.TraversableLike.map$(TraversableLike.scala:230)
E                   	at scala.collection.mutable.ArrayOps$ofRef.map(ArrayOps.scala:198)
E                   	at com.fasterxml.jackson.module.scala.introspect.BeanIntrospector$.$anonfun$apply$14(BeanIntrospector.scala:170)
E                   	at com.fasterxml.jackson.module.scala.introspect.BeanIntrospector$.$anonfun$apply$14$adapted(BeanIntrospector.scala:169)
E                   	at scala.collection.TraversableLike.$anonfun$flatMap$1(TraversableLike.scala:244)
E                   	at scala.collection.immutable.List.foreach(List.scala:392)
E                   	at scala.collection.TraversableLike.flatMap(TraversableLike.scala:244)
E                   	at scala.collection.TraversableLike.flatMap$(TraversableLike.scala:241)
E                   	at scala.collection.immutable.List.flatMap(List.scala:355)
E                   	at com.fasterxml.jackson.module.scala.introspect.BeanIntrospector$.apply(BeanIntrospector.scala:169)
E                   	at com.fasterxml.jackson.module.scala.introspect.ScalaAnnotationIntrospector$._descriptorFor(ScalaAnnotationIntrospectorModule.scala:22)
E                   	at com.fasterxml.jackson.module.scala.introspect.ScalaAnnotationIntrospector$.fieldName(ScalaAnnotationIntrospectorModule.scala:30)
E                   	at com.fasterxml.jackson.module.scala.introspect.ScalaAnnotationIntrospector$.findImplicitPropertyName(ScalaAnnotationIntrospectorModule.scala:78)
E                   	at com.fasterxml.jackson.databind.introspect.AnnotationIntrospectorPair.findImplicitPropertyName(AnnotationIntrospectorPair.java:467)
E                   	at com.fasterxml.jackson.databind.introspect.POJOPropertiesCollector._addFields(POJOPropertiesCollector.java:351)
E                   	at com.fasterxml.jackson.databind.introspect.POJOPropertiesCollector.collectAll(POJOPropertiesCollector.java:283)
E                   	at com.fasterxml.jackson.databind.introspect.POJOPropertiesCollector.getJsonValueMethod(POJOPropertiesCollector.java:169)
E                   	at com.fasterxml.jackson.databind.introspect.BasicBeanDescription.findJsonValueMethod(BasicBeanDescription.java:223)
E                   	at com.fasterxml.jackson.databind.ser.BasicSerializerFactory.findSerializerByAnnotations(BasicSerializerFactory.java:348)
E                   	at com.fasterxml.jackson.databind.ser.BeanSerializerFactory._createSerializer2(BeanSerializerFactory.java:210)
E                   	at com.fasterxml.jackson.databind.ser.BeanSerializerFactory.createSerializer(BeanSerializerFactory.java:153)
E                   	at com.fasterxml.jackson.databind.SerializerProvider._createUntypedSerializer(SerializerProvider.java:1203)
E                   	at com.fasterxml.jackson.databind.SerializerProvider._createAndCacheUntypedSerializer(SerializerProvider.java:1157)
E                   	at com.fasterxml.jackson.databind.SerializerProvider.findValueSerializer(SerializerProvider.java:481)
E                   	at com.fasterxml.jackson.databind.SerializerProvider.findTypedValueSerializer(SerializerProvider.java:679)
E                   	at com.fasterxml.jackson.databind.ser.DefaultSerializerProvider.serializeValue(DefaultSerializerProvider.java:107)
E                   	at com.fasterxml.jackson.databind.ObjectMapper._configAndWriteValue(ObjectMapper.java:3559)
E                   	at com.fasterxml.jackson.databind.ObjectMapper.writeValueAsString(ObjectMapper.java:2927)
E                   	at org.apache.spark.rdd.RDDOperationScope.toJson(RDDOperationScope.scala:52)
E                   	at org.apache.spark.rdd.RDDOperationScope$.withScope(RDDOperationScope.scala:145)
E                   	at org.apache.spark.rdd.RDDOperationScope$.withScope(RDDOperationScope.scala:112)
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:2151)
E                   	at org.bdgenomics.adam.rdd.ADAMContext.$anonfun$loadVcf$1(ADAMContext.scala:2169)
E                   	at scala.Option.fold(Option.scala:175)
E                   	at org.apache.spark.rdd.Timer.time(Timer.scala:48)
E                   	at org.bdgenomics.adam.rdd.ADAMContext.loadVcf(ADAMContext.scala:2166)
E                   	at org.bdgenomics.adam.rdd.ADAMContext.$anonfun$loadGenotypes$1(ADAMContext.scala:3187)
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:3185)
E                   	at org.bdgenomics.adam.api.java.JavaADAMContext.loadGenotypes(JavaADAMContext.scala:353)
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/adamTestdLUBupA/deleteMePleaseThisIsNoLongerNeeded/spark-2.4.3-bin-without-hadoop-scala-2.12/python/lib/py4j-0.10.7-src.zip/py4j/protocol.py:328: Py4JJavaError
----------------------------- Captured stderr call -----------------------------
2019-05-15 13:41:24 WARN  Utils:66 - Service 'SparkUI' could not bind on port 4040. Attempting port 4041.
2019-05-15 13:41:24 WARN  Utils:66 - Service 'SparkUI' could not bind on port 4041. Attempting port 4042.
_______________ 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:236: in loadGenotypes
    _toJava(stringency, self._jvm))
/tmp/adamTestdLUBupA/deleteMePleaseThisIsNoLongerNeeded/spark-2.4.3-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-2.4.3-bin-without-hadoop-scala-2.12/python/pyspark/sql/utils.py:63: in deco
    return f(*a, **kw)
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 

answer = 'xro6395'
gateway_client = <py4j.java_gateway.GatewayClient object at 0x7f9a60794550>
target_id = 'o6393', 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 o6393.loadGenotypes.
E                   : java.lang.ArrayIndexOutOfBoundsException: 17418
E                   	at com.thoughtworks.paranamer.BytecodeReadingParanamer$ClassReader.accept(BytecodeReadingParanamer.java:563)
E                   	at com.thoughtworks.paranamer.BytecodeReadingParanamer$ClassReader.access$200(BytecodeReadingParanamer.java:338)
E                   	at com.thoughtworks.paranamer.BytecodeReadingParanamer.lookupParameterNames(BytecodeReadingParanamer.java:103)
E                   	at com.thoughtworks.paranamer.CachingParanamer.lookupParameterNames(CachingParanamer.java:90)
E                   	at com.fasterxml.jackson.module.scala.introspect.BeanIntrospector$.getCtorParams(BeanIntrospector.scala:44)
E                   	at com.fasterxml.jackson.module.scala.introspect.BeanIntrospector$.$anonfun$apply$1(BeanIntrospector.scala:58)
E                   	at com.fasterxml.jackson.module.scala.introspect.BeanIntrospector$.$anonfun$apply$1$adapted(BeanIntrospector.scala:58)
E                   	at scala.collection.TraversableLike.$anonfun$flatMap$1(TraversableLike.scala:244)
E                   	at scala.collection.Iterator.foreach(Iterator.scala:941)
E                   	at scala.collection.Iterator.foreach$(Iterator.scala:941)
E                   	at scala.collection.AbstractIterator.foreach(Iterator.scala:1429)
E                   	at scala.collection.IterableLike.foreach(IterableLike.scala:74)
E                   	at scala.collection.IterableLike.foreach$(IterableLike.scala:73)
E                   	at scala.collection.AbstractIterable.foreach(Iterable.scala:56)
E                   	at scala.collection.TraversableLike.flatMap(TraversableLike.scala:244)
E                   	at scala.collection.TraversableLike.flatMap$(TraversableLike.scala:241)
E                   	at scala.collection.AbstractTraversable.flatMap(Traversable.scala:108)
E                   	at com.fasterxml.jackson.module.scala.introspect.BeanIntrospector$.findConstructorParam$1(BeanIntrospector.scala:58)
E                   	at com.fasterxml.jackson.module.scala.introspect.BeanIntrospector$.$anonfun$apply$19(BeanIntrospector.scala:176)
E                   	at scala.collection.TraversableLike.$anonfun$map$1(TraversableLike.scala:237)
E                   	at scala.collection.IndexedSeqOptimized.foreach(IndexedSeqOptimized.scala:36)
E                   	at scala.collection.IndexedSeqOptimized.foreach$(IndexedSeqOptimized.scala:33)
E                   	at scala.collection.mutable.ArrayOps$ofRef.foreach(ArrayOps.scala:198)
E                   	at scala.collection.TraversableLike.map(TraversableLike.scala:237)
E                   	at scala.collection.TraversableLike.map$(TraversableLike.scala:230)
E                   	at scala.collection.mutable.ArrayOps$ofRef.map(ArrayOps.scala:198)
E                   	at com.fasterxml.jackson.module.scala.introspect.BeanIntrospector$.$anonfun$apply$14(BeanIntrospector.scala:170)
E                   	at com.fasterxml.jackson.module.scala.introspect.BeanIntrospector$.$anonfun$apply$14$adapted(BeanIntrospector.scala:169)
E                   	at scala.collection.TraversableLike.$anonfun$flatMap$1(TraversableLike.scala:244)
E                   	at scala.collection.immutable.List.foreach(List.scala:392)
E                   	at scala.collection.TraversableLike.flatMap(TraversableLike.scala:244)
E                   	at scala.collection.TraversableLike.flatMap$(TraversableLike.scala:241)
E                   	at scala.collection.immutable.List.flatMap(List.scala:355)
E                   	at com.fasterxml.jackson.module.scala.introspect.BeanIntrospector$.apply(BeanIntrospector.scala:169)
E                   	at com.fasterxml.jackson.module.scala.introspect.ScalaAnnotationIntrospector$._descriptorFor(ScalaAnnotationIntrospectorModule.scala:22)
E                   	at com.fasterxml.jackson.module.scala.introspect.ScalaAnnotationIntrospector$.fieldName(ScalaAnnotationIntrospectorModule.scala:30)
E                   	at com.fasterxml.jackson.module.scala.introspect.ScalaAnnotationIntrospector$.findImplicitPropertyName(ScalaAnnotationIntrospectorModule.scala:78)
E                   	at com.fasterxml.jackson.databind.introspect.AnnotationIntrospectorPair.findImplicitPropertyName(AnnotationIntrospectorPair.java:467)
E                   	at com.fasterxml.jackson.databind.introspect.POJOPropertiesCollector._addFields(POJOPropertiesCollector.java:351)
E                   	at com.fasterxml.jackson.databind.introspect.POJOPropertiesCollector.collectAll(POJOPropertiesCollector.java:283)
E                   	at com.fasterxml.jackson.databind.introspect.POJOPropertiesCollector.getJsonValueMethod(POJOPropertiesCollector.java:169)
E                   	at com.fasterxml.jackson.databind.introspect.BasicBeanDescription.findJsonValueMethod(BasicBeanDescription.java:223)
E                   	at com.fasterxml.jackson.databind.ser.BasicSerializerFactory.findSerializerByAnnotations(BasicSerializerFactory.java:348)
E                   	at com.fasterxml.jackson.databind.ser.BeanSerializerFactory._createSerializer2(BeanSerializerFactory.java:210)
E                   	at com.fasterxml.jackson.databind.ser.BeanSerializerFactory.createSerializer(BeanSerializerFactory.java:153)
E                   	at com.fasterxml.jackson.databind.SerializerProvider._createUntypedSerializer(SerializerProvider.java:1203)
E                   	at com.fasterxml.jackson.databind.SerializerProvider._createAndCacheUntypedSerializer(SerializerProvider.java:1157)
E                   	at com.fasterxml.jackson.databind.SerializerProvider.findValueSerializer(SerializerProvider.java:481)
E                   	at com.fasterxml.jackson.databind.SerializerProvider.findTypedValueSerializer(SerializerProvider.java:679)
E                   	at com.fasterxml.jackson.databind.ser.DefaultSerializerProvider.serializeValue(DefaultSerializerProvider.java:107)
E                   	at com.fasterxml.jackson.databind.ObjectMapper._configAndWriteValue(ObjectMapper.java:3559)
E                   	at com.fasterxml.jackson.databind.ObjectMapper.writeValueAsString(ObjectMapper.java:2927)
E                   	at org.apache.spark.rdd.RDDOperationScope.toJson(RDDOperationScope.scala:52)
E                   	at org.apache.spark.rdd.RDDOperationScope$.withScope(RDDOperationScope.scala:145)
E                   	at org.apache.spark.rdd.RDDOperationScope$.withScope(RDDOperationScope.scala:112)
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:2151)
E                   	at org.bdgenomics.adam.rdd.ADAMContext.$anonfun$loadVcf$1(ADAMContext.scala:2169)
E                   	at scala.Option.fold(Option.scala:175)
E                   	at org.apache.spark.rdd.Timer.time(Timer.scala:48)
E                   	at org.bdgenomics.adam.rdd.ADAMContext.loadVcf(ADAMContext.scala:2166)
E                   	at org.bdgenomics.adam.rdd.ADAMContext.$anonfun$loadGenotypes$1(ADAMContext.scala:3187)
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:3185)
E                   	at org.bdgenomics.adam.api.java.JavaADAMContext.loadGenotypes(JavaADAMContext.scala:353)
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/adamTestdLUBupA/deleteMePleaseThisIsNoLongerNeeded/spark-2.4.3-bin-without-hadoop-scala-2.12/python/lib/py4j-0.10.7-src.zip/py4j/protocol.py:328: Py4JJavaError
----------------------------- Captured stderr call -----------------------------
2019-05-15 13:41:25 WARN  Utils:66 - Service 'SparkUI' could not bind on port 4040. Attempting port 4041.
2019-05-15 13:41:25 WARN  Utils:66 - Service 'SparkUI' could not bind on port 4041. Attempting port 4042.
_______________ 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:236: in loadGenotypes
    _toJava(stringency, self._jvm))
/tmp/adamTestdLUBupA/deleteMePleaseThisIsNoLongerNeeded/spark-2.4.3-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-2.4.3-bin-without-hadoop-scala-2.12/python/pyspark/sql/utils.py:63: in deco
    return f(*a, **kw)
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 

answer = 'xro6516'
gateway_client = <py4j.java_gateway.GatewayClient object at 0x7f9a60794550>
target_id = 'o6514', 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 o6514.loadGenotypes.
E                   : java.lang.ArrayIndexOutOfBoundsException: 17418
E                   	at com.thoughtworks.paranamer.BytecodeReadingParanamer$ClassReader.accept(BytecodeReadingParanamer.java:563)
E                   	at com.thoughtworks.paranamer.BytecodeReadingParanamer$ClassReader.access$200(BytecodeReadingParanamer.java:338)
E                   	at com.thoughtworks.paranamer.BytecodeReadingParanamer.lookupParameterNames(BytecodeReadingParanamer.java:103)
E                   	at com.thoughtworks.paranamer.CachingParanamer.lookupParameterNames(CachingParanamer.java:90)
E                   	at com.fasterxml.jackson.module.scala.introspect.BeanIntrospector$.getCtorParams(BeanIntrospector.scala:44)
E                   	at com.fasterxml.jackson.module.scala.introspect.BeanIntrospector$.$anonfun$apply$1(BeanIntrospector.scala:58)
E                   	at com.fasterxml.jackson.module.scala.introspect.BeanIntrospector$.$anonfun$apply$1$adapted(BeanIntrospector.scala:58)
E                   	at scala.collection.TraversableLike.$anonfun$flatMap$1(TraversableLike.scala:244)
E                   	at scala.collection.Iterator.foreach(Iterator.scala:941)
E                   	at scala.collection.Iterator.foreach$(Iterator.scala:941)
E                   	at scala.collection.AbstractIterator.foreach(Iterator.scala:1429)
E                   	at scala.collection.IterableLike.foreach(IterableLike.scala:74)
E                   	at scala.collection.IterableLike.foreach$(IterableLike.scala:73)
E                   	at scala.collection.AbstractIterable.foreach(Iterable.scala:56)
E                   	at scala.collection.TraversableLike.flatMap(TraversableLike.scala:244)
E                   	at scala.collection.TraversableLike.flatMap$(TraversableLike.scala:241)
E                   	at scala.collection.AbstractTraversable.flatMap(Traversable.scala:108)
E                   	at com.fasterxml.jackson.module.scala.introspect.BeanIntrospector$.findConstructorParam$1(BeanIntrospector.scala:58)
E                   	at com.fasterxml.jackson.module.scala.introspect.BeanIntrospector$.$anonfun$apply$19(BeanIntrospector.scala:176)
E                   	at scala.collection.TraversableLike.$anonfun$map$1(TraversableLike.scala:237)
E                   	at scala.collection.IndexedSeqOptimized.foreach(IndexedSeqOptimized.scala:36)
E                   	at scala.collection.IndexedSeqOptimized.foreach$(IndexedSeqOptimized.scala:33)
E                   	at scala.collection.mutable.ArrayOps$ofRef.foreach(ArrayOps.scala:198)
E                   	at scala.collection.TraversableLike.map(TraversableLike.scala:237)
E                   	at scala.collection.TraversableLike.map$(TraversableLike.scala:230)
E                   	at scala.collection.mutable.ArrayOps$ofRef.map(ArrayOps.scala:198)
E                   	at com.fasterxml.jackson.module.scala.introspect.BeanIntrospector$.$anonfun$apply$14(BeanIntrospector.scala:170)
E                   	at com.fasterxml.jackson.module.scala.introspect.BeanIntrospector$.$anonfun$apply$14$adapted(BeanIntrospector.scala:169)
E                   	at scala.collection.TraversableLike.$anonfun$flatMap$1(TraversableLike.scala:244)
E                   	at scala.collection.immutable.List.foreach(List.scala:392)
E                   	at scala.collection.TraversableLike.flatMap(TraversableLike.scala:244)
E                   	at scala.collection.TraversableLike.flatMap$(TraversableLike.scala:241)
E                   	at scala.collection.immutable.List.flatMap(List.scala:355)
E                   	at com.fasterxml.jackson.module.scala.introspect.BeanIntrospector$.apply(BeanIntrospector.scala:169)
E                   	at com.fasterxml.jackson.module.scala.introspect.ScalaAnnotationIntrospector$._descriptorFor(ScalaAnnotationIntrospectorModule.scala:22)
E                   	at com.fasterxml.jackson.module.scala.introspect.ScalaAnnotationIntrospector$.fieldName(ScalaAnnotationIntrospectorModule.scala:30)
E                   	at com.fasterxml.jackson.module.scala.introspect.ScalaAnnotationIntrospector$.findImplicitPropertyName(ScalaAnnotationIntrospectorModule.scala:78)
E                   	at com.fasterxml.jackson.databind.introspect.AnnotationIntrospectorPair.findImplicitPropertyName(AnnotationIntrospectorPair.java:467)
E                   	at com.fasterxml.jackson.databind.introspect.POJOPropertiesCollector._addFields(POJOPropertiesCollector.java:351)
E                   	at com.fasterxml.jackson.databind.introspect.POJOPropertiesCollector.collectAll(POJOPropertiesCollector.java:283)
E                   	at com.fasterxml.jackson.databind.introspect.POJOPropertiesCollector.getJsonValueMethod(POJOPropertiesCollector.java:169)
E                   	at com.fasterxml.jackson.databind.introspect.BasicBeanDescription.findJsonValueMethod(BasicBeanDescription.java:223)
E                   	at com.fasterxml.jackson.databind.ser.BasicSerializerFactory.findSerializerByAnnotations(BasicSerializerFactory.java:348)
E                   	at com.fasterxml.jackson.databind.ser.BeanSerializerFactory._createSerializer2(BeanSerializerFactory.java:210)
E                   	at com.fasterxml.jackson.databind.ser.BeanSerializerFactory.createSerializer(BeanSerializerFactory.java:153)
E                   	at com.fasterxml.jackson.databind.SerializerProvider._createUntypedSerializer(SerializerProvider.java:1203)
E                   	at com.fasterxml.jackson.databind.SerializerProvider._createAndCacheUntypedSerializer(SerializerProvider.java:1157)
E                   	at com.fasterxml.jackson.databind.SerializerProvider.findValueSerializer(SerializerProvider.java:481)
E                   	at com.fasterxml.jackson.databind.SerializerProvider.findTypedValueSerializer(SerializerProvider.java:679)
E                   	at com.fasterxml.jackson.databind.ser.DefaultSerializerProvider.serializeValue(DefaultSerializerProvider.java:107)
E                   	at com.fasterxml.jackson.databind.ObjectMapper._configAndWriteValue(ObjectMapper.java:3559)
E                   	at com.fasterxml.jackson.databind.ObjectMapper.writeValueAsString(ObjectMapper.java:2927)
E                   	at org.apache.spark.rdd.RDDOperationScope.toJson(RDDOperationScope.scala:52)
E                   	at org.apache.spark.rdd.RDDOperationScope$.withScope(RDDOperationScope.scala:145)
E                   	at org.apache.spark.rdd.RDDOperationScope$.withScope(RDDOperationScope.scala:112)
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:2151)
E                   	at org.bdgenomics.adam.rdd.ADAMContext.$anonfun$loadVcf$1(ADAMContext.scala:2169)
E                   	at scala.Option.fold(Option.scala:175)
E                   	at org.apache.spark.rdd.Timer.time(Timer.scala:48)
E                   	at org.bdgenomics.adam.rdd.ADAMContext.loadVcf(ADAMContext.scala:2166)
E                   	at org.bdgenomics.adam.rdd.ADAMContext.$anonfun$loadGenotypes$1(ADAMContext.scala:3187)
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:3185)
E                   	at org.bdgenomics.adam.api.java.JavaADAMContext.loadGenotypes(JavaADAMContext.scala:353)
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/adamTestdLUBupA/deleteMePleaseThisIsNoLongerNeeded/spark-2.4.3-bin-without-hadoop-scala-2.12/python/lib/py4j-0.10.7-src.zip/py4j/protocol.py:328: Py4JJavaError
----------------------------- Captured stderr call -----------------------------
2019-05-15 13:41:26 WARN  Utils:66 - Service 'SparkUI' could not bind on port 4040. Attempting port 4041.
2019-05-15 13:41:26 WARN  Utils:66 - Service 'SparkUI' could not bind on port 4041. Attempting port 4042.
_________________ 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:236: in loadGenotypes
    _toJava(stringency, self._jvm))
/tmp/adamTestdLUBupA/deleteMePleaseThisIsNoLongerNeeded/spark-2.4.3-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-2.4.3-bin-without-hadoop-scala-2.12/python/pyspark/sql/utils.py:63: in deco
    return f(*a, **kw)
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 

answer = 'xro6637'
gateway_client = <py4j.java_gateway.GatewayClient object at 0x7f9a60794550>
target_id = 'o6635', 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 o6635.loadGenotypes.
E                   : java.lang.ArrayIndexOutOfBoundsException: 17418
E                   	at com.thoughtworks.paranamer.BytecodeReadingParanamer$ClassReader.accept(BytecodeReadingParanamer.java:563)
E                   	at com.thoughtworks.paranamer.BytecodeReadingParanamer$ClassReader.access$200(BytecodeReadingParanamer.java:338)
E                   	at com.thoughtworks.paranamer.BytecodeReadingParanamer.lookupParameterNames(BytecodeReadingParanamer.java:103)
E                   	at com.thoughtworks.paranamer.CachingParanamer.lookupParameterNames(CachingParanamer.java:90)
E                   	at com.fasterxml.jackson.module.scala.introspect.BeanIntrospector$.getCtorParams(BeanIntrospector.scala:44)
E                   	at com.fasterxml.jackson.module.scala.introspect.BeanIntrospector$.$anonfun$apply$1(BeanIntrospector.scala:58)
E                   	at com.fasterxml.jackson.module.scala.introspect.BeanIntrospector$.$anonfun$apply$1$adapted(BeanIntrospector.scala:58)
E                   	at scala.collection.TraversableLike.$anonfun$flatMap$1(TraversableLike.scala:244)
E                   	at scala.collection.Iterator.foreach(Iterator.scala:941)
E                   	at scala.collection.Iterator.foreach$(Iterator.scala:941)
E                   	at scala.collection.AbstractIterator.foreach(Iterator.scala:1429)
E                   	at scala.collection.IterableLike.foreach(IterableLike.scala:74)
E                   	at scala.collection.IterableLike.foreach$(IterableLike.scala:73)
E                   	at scala.collection.AbstractIterable.foreach(Iterable.scala:56)
E                   	at scala.collection.TraversableLike.flatMap(TraversableLike.scala:244)
E                   	at scala.collection.TraversableLike.flatMap$(TraversableLike.scala:241)
E                   	at scala.collection.AbstractTraversable.flatMap(Traversable.scala:108)
E                   	at com.fasterxml.jackson.module.scala.introspect.BeanIntrospector$.findConstructorParam$1(BeanIntrospector.scala:58)
E                   	at com.fasterxml.jackson.module.scala.introspect.BeanIntrospector$.$anonfun$apply$19(BeanIntrospector.scala:176)
E                   	at scala.collection.TraversableLike.$anonfun$map$1(TraversableLike.scala:237)
E                   	at scala.collection.IndexedSeqOptimized.foreach(IndexedSeqOptimized.scala:36)
E                   	at scala.collection.IndexedSeqOptimized.foreach$(IndexedSeqOptimized.scala:33)
E                   	at scala.collection.mutable.ArrayOps$ofRef.foreach(ArrayOps.scala:198)
E                   	at scala.collection.TraversableLike.map(TraversableLike.scala:237)
E                   	at scala.collection.TraversableLike.map$(TraversableLike.scala:230)
E                   	at scala.collection.mutable.ArrayOps$ofRef.map(ArrayOps.scala:198)
E                   	at com.fasterxml.jackson.module.scala.introspect.BeanIntrospector$.$anonfun$apply$14(BeanIntrospector.scala:170)
E                   	at com.fasterxml.jackson.module.scala.introspect.BeanIntrospector$.$anonfun$apply$14$adapted(BeanIntrospector.scala:169)
E                   	at scala.collection.TraversableLike.$anonfun$flatMap$1(TraversableLike.scala:244)
E                   	at scala.collection.immutable.List.foreach(List.scala:392)
E                   	at scala.collection.TraversableLike.flatMap(TraversableLike.scala:244)
E                   	at scala.collection.TraversableLike.flatMap$(TraversableLike.scala:241)
E                   	at scala.collection.immutable.List.flatMap(List.scala:355)
E                   	at com.fasterxml.jackson.module.scala.introspect.BeanIntrospector$.apply(BeanIntrospector.scala:169)
E                   	at com.fasterxml.jackson.module.scala.introspect.ScalaAnnotationIntrospector$._descriptorFor(ScalaAnnotationIntrospectorModule.scala:22)
E                   	at com.fasterxml.jackson.module.scala.introspect.ScalaAnnotationIntrospector$.fieldName(ScalaAnnotationIntrospectorModule.scala:30)
E                   	at com.fasterxml.jackson.module.scala.introspect.ScalaAnnotationIntrospector$.findImplicitPropertyName(ScalaAnnotationIntrospectorModule.scala:78)
E                   	at com.fasterxml.jackson.databind.introspect.AnnotationIntrospectorPair.findImplicitPropertyName(AnnotationIntrospectorPair.java:467)
E                   	at com.fasterxml.jackson.databind.introspect.POJOPropertiesCollector._addFields(POJOPropertiesCollector.java:351)
E                   	at com.fasterxml.jackson.databind.introspect.POJOPropertiesCollector.collectAll(POJOPropertiesCollector.java:283)
E                   	at com.fasterxml.jackson.databind.introspect.POJOPropertiesCollector.getJsonValueMethod(POJOPropertiesCollector.java:169)
E                   	at com.fasterxml.jackson.databind.introspect.BasicBeanDescription.findJsonValueMethod(BasicBeanDescription.java:223)
E                   	at com.fasterxml.jackson.databind.ser.BasicSerializerFactory.findSerializerByAnnotations(BasicSerializerFactory.java:348)
E                   	at com.fasterxml.jackson.databind.ser.BeanSerializerFactory._createSerializer2(BeanSerializerFactory.java:210)
E                   	at com.fasterxml.jackson.databind.ser.BeanSerializerFactory.createSerializer(BeanSerializerFactory.java:153)
E                   	at com.fasterxml.jackson.databind.SerializerProvider._createUntypedSerializer(SerializerProvider.java:1203)
E                   	at com.fasterxml.jackson.databind.SerializerProvider._createAndCacheUntypedSerializer(SerializerProvider.java:1157)
E                   	at com.fasterxml.jackson.databind.SerializerProvider.findValueSerializer(SerializerProvider.java:481)
E                   	at com.fasterxml.jackson.databind.SerializerProvider.findTypedValueSerializer(SerializerProvider.java:679)
E                   	at com.fasterxml.jackson.databind.ser.DefaultSerializerProvider.serializeValue(DefaultSerializerProvider.java:107)
E                   	at com.fasterxml.jackson.databind.ObjectMapper._configAndWriteValue(ObjectMapper.java:3559)
E                   	at com.fasterxml.jackson.databind.ObjectMapper.writeValueAsString(ObjectMapper.java:2927)
E                   	at org.apache.spark.rdd.RDDOperationScope.toJson(RDDOperationScope.scala:52)
E                   	at org.apache.spark.rdd.RDDOperationScope$.withScope(RDDOperationScope.scala:145)
E                   	at org.apache.spark.rdd.RDDOperationScope$.withScope(RDDOperationScope.scala:112)
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:2151)
E                   	at org.bdgenomics.adam.rdd.ADAMContext.$anonfun$loadVcf$1(ADAMContext.scala:2169)
E                   	at scala.Option.fold(Option.scala:175)
E                   	at org.apache.spark.rdd.Timer.time(Timer.scala:48)
E                   	at org.bdgenomics.adam.rdd.ADAMContext.loadVcf(ADAMContext.scala:2166)
E                   	at org.bdgenomics.adam.rdd.ADAMContext.$anonfun$loadGenotypes$1(ADAMContext.scala:3187)
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:3185)
E                   	at org.bdgenomics.adam.api.java.JavaADAMContext.loadGenotypes(JavaADAMContext.scala:353)
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/adamTestdLUBupA/deleteMePleaseThisIsNoLongerNeeded/spark-2.4.3-bin-without-hadoop-scala-2.12/python/lib/py4j-0.10.7-src.zip/py4j/protocol.py:328: Py4JJavaError
----------------------------- Captured stderr call -----------------------------
2019-05-15 13:41:26 WARN  Utils:66 - Service 'SparkUI' could not bind on port 4040. Attempting port 4041.
2019-05-15 13:41:26 WARN  Utils:66 - Service 'SparkUI' could not bind on port 4041. Attempting port 4042.
_________________ 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:236: in loadGenotypes
    _toJava(stringency, self._jvm))
/tmp/adamTestdLUBupA/deleteMePleaseThisIsNoLongerNeeded/spark-2.4.3-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-2.4.3-bin-without-hadoop-scala-2.12/python/pyspark/sql/utils.py:63: in deco
    return f(*a, **kw)
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 

answer = 'xro6758'
gateway_client = <py4j.java_gateway.GatewayClient object at 0x7f9a60794550>
target_id = 'o6756', 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 o6756.loadGenotypes.
E                   : java.lang.ArrayIndexOutOfBoundsException: 17418
E                   	at com.thoughtworks.paranamer.BytecodeReadingParanamer$ClassReader.accept(BytecodeReadingParanamer.java:563)
E                   	at com.thoughtworks.paranamer.BytecodeReadingParanamer$ClassReader.access$200(BytecodeReadingParanamer.java:338)
E                   	at com.thoughtworks.paranamer.BytecodeReadingParanamer.lookupParameterNames(BytecodeReadingParanamer.java:103)
E                   	at com.thoughtworks.paranamer.CachingParanamer.lookupParameterNames(CachingParanamer.java:90)
E                   	at com.fasterxml.jackson.module.scala.introspect.BeanIntrospector$.getCtorParams(BeanIntrospector.scala:44)
E                   	at com.fasterxml.jackson.module.scala.introspect.BeanIntrospector$.$anonfun$apply$1(BeanIntrospector.scala:58)
E                   	at com.fasterxml.jackson.module.scala.introspect.BeanIntrospector$.$anonfun$apply$1$adapted(BeanIntrospector.scala:58)
E                   	at scala.collection.TraversableLike.$anonfun$flatMap$1(TraversableLike.scala:244)
E                   	at scala.collection.Iterator.foreach(Iterator.scala:941)
E                   	at scala.collection.Iterator.foreach$(Iterator.scala:941)
E                   	at scala.collection.AbstractIterator.foreach(Iterator.scala:1429)
E                   	at scala.collection.IterableLike.foreach(IterableLike.scala:74)
E                   	at scala.collection.IterableLike.foreach$(IterableLike.scala:73)
E                   	at scala.collection.AbstractIterable.foreach(Iterable.scala:56)
E                   	at scala.collection.TraversableLike.flatMap(TraversableLike.scala:244)
E                   	at scala.collection.TraversableLike.flatMap$(TraversableLike.scala:241)
E                   	at scala.collection.AbstractTraversable.flatMap(Traversable.scala:108)
E                   	at com.fasterxml.jackson.module.scala.introspect.BeanIntrospector$.findConstructorParam$1(BeanIntrospector.scala:58)
E                   	at com.fasterxml.jackson.module.scala.introspect.BeanIntrospector$.$anonfun$apply$19(BeanIntrospector.scala:176)
E                   	at scala.collection.TraversableLike.$anonfun$map$1(TraversableLike.scala:237)
E                   	at scala.collection.IndexedSeqOptimized.foreach(IndexedSeqOptimized.scala:36)
E                   	at scala.collection.IndexedSeqOptimized.foreach$(IndexedSeqOptimized.scala:33)
E                   	at scala.collection.mutable.ArrayOps$ofRef.foreach(ArrayOps.scala:198)
E                   	at scala.collection.TraversableLike.map(TraversableLike.scala:237)
E                   	at scala.collection.TraversableLike.map$(TraversableLike.scala:230)
E                   	at scala.collection.mutable.ArrayOps$ofRef.map(ArrayOps.scala:198)
E                   	at com.fasterxml.jackson.module.scala.introspect.BeanIntrospector$.$anonfun$apply$14(BeanIntrospector.scala:170)
E                   	at com.fasterxml.jackson.module.scala.introspect.BeanIntrospector$.$anonfun$apply$14$adapted(BeanIntrospector.scala:169)
E                   	at scala.collection.TraversableLike.$anonfun$flatMap$1(TraversableLike.scala:244)
E                   	at scala.collection.immutable.List.foreach(List.scala:392)
E                   	at scala.collection.TraversableLike.flatMap(TraversableLike.scala:244)
E                   	at scala.collection.TraversableLike.flatMap$(TraversableLike.scala:241)
E                   	at scala.collection.immutable.List.flatMap(List.scala:355)
E                   	at com.fasterxml.jackson.module.scala.introspect.BeanIntrospector$.apply(BeanIntrospector.scala:169)
E                   	at com.fasterxml.jackson.module.scala.introspect.ScalaAnnotationIntrospector$._descriptorFor(ScalaAnnotationIntrospectorModule.scala:22)
E                   	at com.fasterxml.jackson.module.scala.introspect.ScalaAnnotationIntrospector$.fieldName(ScalaAnnotationIntrospectorModule.scala:30)
E                   	at com.fasterxml.jackson.module.scala.introspect.ScalaAnnotationIntrospector$.findImplicitPropertyName(ScalaAnnotationIntrospectorModule.scala:78)
E                   	at com.fasterxml.jackson.databind.introspect.AnnotationIntrospectorPair.findImplicitPropertyName(AnnotationIntrospectorPair.java:467)
E                   	at com.fasterxml.jackson.databind.introspect.POJOPropertiesCollector._addFields(POJOPropertiesCollector.java:351)
E                   	at com.fasterxml.jackson.databind.introspect.POJOPropertiesCollector.collectAll(POJOPropertiesCollector.java:283)
E                   	at com.fasterxml.jackson.databind.introspect.POJOPropertiesCollector.getJsonValueMethod(POJOPropertiesCollector.java:169)
E                   	at com.fasterxml.jackson.databind.introspect.BasicBeanDescription.findJsonValueMethod(BasicBeanDescription.java:223)
E                   	at com.fasterxml.jackson.databind.ser.BasicSerializerFactory.findSerializerByAnnotations(BasicSerializerFactory.java:348)
E                   	at com.fasterxml.jackson.databind.ser.BeanSerializerFactory._createSerializer2(BeanSerializerFactory.java:210)
E                   	at com.fasterxml.jackson.databind.ser.BeanSerializerFactory.createSerializer(BeanSerializerFactory.java:153)
E                   	at com.fasterxml.jackson.databind.SerializerProvider._createUntypedSerializer(SerializerProvider.java:1203)
E                   	at com.fasterxml.jackson.databind.SerializerProvider._createAndCacheUntypedSerializer(SerializerProvider.java:1157)
E                   	at com.fasterxml.jackson.databind.SerializerProvider.findValueSerializer(SerializerProvider.java:481)
E                   	at com.fasterxml.jackson.databind.SerializerProvider.findTypedValueSerializer(SerializerProvider.java:679)
E                   	at com.fasterxml.jackson.databind.ser.DefaultSerializerProvider.serializeValue(DefaultSerializerProvider.java:107)
E                   	at com.fasterxml.jackson.databind.ObjectMapper._configAndWriteValue(ObjectMapper.java:3559)
E                   	at com.fasterxml.jackson.databind.ObjectMapper.writeValueAsString(ObjectMapper.java:2927)
E                   	at org.apache.spark.rdd.RDDOperationScope.toJson(RDDOperationScope.scala:52)
E                   	at org.apache.spark.rdd.RDDOperationScope$.withScope(RDDOperationScope.scala:145)
E                   	at org.apache.spark.rdd.RDDOperationScope$.withScope(RDDOperationScope.scala:112)
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:2151)
E                   	at org.bdgenomics.adam.rdd.ADAMContext.$anonfun$loadVcf$1(ADAMContext.scala:2169)
E                   	at scala.Option.fold(Option.scala:175)
E                   	at org.apache.spark.rdd.Timer.time(Timer.scala:48)
E                   	at org.bdgenomics.adam.rdd.ADAMContext.loadVcf(ADAMContext.scala:2166)
E                   	at org.bdgenomics.adam.rdd.ADAMContext.$anonfun$loadGenotypes$1(ADAMContext.scala:3187)
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:3185)
E                   	at org.bdgenomics.adam.api.java.JavaADAMContext.loadGenotypes(JavaADAMContext.scala:353)
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/adamTestdLUBupA/deleteMePleaseThisIsNoLongerNeeded/spark-2.4.3-bin-without-hadoop-scala-2.12/python/lib/py4j-0.10.7-src.zip/py4j/protocol.py:328: Py4JJavaError
----------------------------- Captured stderr call -----------------------------
2019-05-15 13:41:27 WARN  Utils:66 - Service 'SparkUI' could not bind on port 4040. Attempting port 4041.
2019-05-15 13:41:27 WARN  Utils:66 - Service 'SparkUI' could not bind on port 4041. Attempting port 4042.
___________________ 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:236: in loadGenotypes
    _toJava(stringency, self._jvm))
/tmp/adamTestdLUBupA/deleteMePleaseThisIsNoLongerNeeded/spark-2.4.3-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-2.4.3-bin-without-hadoop-scala-2.12/python/pyspark/sql/utils.py:63: in deco
    return f(*a, **kw)
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 

answer = 'xro6879'
gateway_client = <py4j.java_gateway.GatewayClient object at 0x7f9a60794550>
target_id = 'o6877', 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 o6877.loadGenotypes.
E                   : java.lang.ArrayIndexOutOfBoundsException: 17418
E                   	at com.thoughtworks.paranamer.BytecodeReadingParanamer$ClassReader.accept(BytecodeReadingParanamer.java:563)
E                   	at com.thoughtworks.paranamer.BytecodeReadingParanamer$ClassReader.access$200(BytecodeReadingParanamer.java:338)
E                   	at com.thoughtworks.paranamer.BytecodeReadingParanamer.lookupParameterNames(BytecodeReadingParanamer.java:103)
E                   	at com.thoughtworks.paranamer.CachingParanamer.lookupParameterNames(CachingParanamer.java:90)
E                   	at com.fasterxml.jackson.module.scala.introspect.BeanIntrospector$.getCtorParams(BeanIntrospector.scala:44)
E                   	at com.fasterxml.jackson.module.scala.introspect.BeanIntrospector$.$anonfun$apply$1(BeanIntrospector.scala:58)
E                   	at com.fasterxml.jackson.module.scala.introspect.BeanIntrospector$.$anonfun$apply$1$adapted(BeanIntrospector.scala:58)
E                   	at scala.collection.TraversableLike.$anonfun$flatMap$1(TraversableLike.scala:244)
E                   	at scala.collection.Iterator.foreach(Iterator.scala:941)
E                   	at scala.collection.Iterator.foreach$(Iterator.scala:941)
E                   	at scala.collection.AbstractIterator.foreach(Iterator.scala:1429)
E                   	at scala.collection.IterableLike.foreach(IterableLike.scala:74)
E                   	at scala.collection.IterableLike.foreach$(IterableLike.scala:73)
E                   	at scala.collection.AbstractIterable.foreach(Iterable.scala:56)
E                   	at scala.collection.TraversableLike.flatMap(TraversableLike.scala:244)
E                   	at scala.collection.TraversableLike.flatMap$(TraversableLike.scala:241)
E                   	at scala.collection.AbstractTraversable.flatMap(Traversable.scala:108)
E                   	at com.fasterxml.jackson.module.scala.introspect.BeanIntrospector$.findConstructorParam$1(BeanIntrospector.scala:58)
E                   	at com.fasterxml.jackson.module.scala.introspect.BeanIntrospector$.$anonfun$apply$19(BeanIntrospector.scala:176)
E                   	at scala.collection.TraversableLike.$anonfun$map$1(TraversableLike.scala:237)
E                   	at scala.collection.IndexedSeqOptimized.foreach(IndexedSeqOptimized.scala:36)
E                   	at scala.collection.IndexedSeqOptimized.foreach$(IndexedSeqOptimized.scala:33)
E                   	at scala.collection.mutable.ArrayOps$ofRef.foreach(ArrayOps.scala:198)
E                   	at scala.collection.TraversableLike.map(TraversableLike.scala:237)
E                   	at scala.collection.TraversableLike.map$(TraversableLike.scala:230)
E                   	at scala.collection.mutable.ArrayOps$ofRef.map(ArrayOps.scala:198)
E                   	at com.fasterxml.jackson.module.scala.introspect.BeanIntrospector$.$anonfun$apply$14(BeanIntrospector.scala:170)
E                   	at com.fasterxml.jackson.module.scala.introspect.BeanIntrospector$.$anonfun$apply$14$adapted(BeanIntrospector.scala:169)
E                   	at scala.collection.TraversableLike.$anonfun$flatMap$1(TraversableLike.scala:244)
E                   	at scala.collection.immutable.List.foreach(List.scala:392)
E                   	at scala.collection.TraversableLike.flatMap(TraversableLike.scala:244)
E                   	at scala.collection.TraversableLike.flatMap$(TraversableLike.scala:241)
E                   	at scala.collection.immutable.List.flatMap(List.scala:355)
E                   	at com.fasterxml.jackson.module.scala.introspect.BeanIntrospector$.apply(BeanIntrospector.scala:169)
E                   	at com.fasterxml.jackson.module.scala.introspect.ScalaAnnotationIntrospector$._descriptorFor(ScalaAnnotationIntrospectorModule.scala:22)
E                   	at com.fasterxml.jackson.module.scala.introspect.ScalaAnnotationIntrospector$.fieldName(ScalaAnnotationIntrospectorModule.scala:30)
E                   	at com.fasterxml.jackson.module.scala.introspect.ScalaAnnotationIntrospector$.findImplicitPropertyName(ScalaAnnotationIntrospectorModule.scala:78)
E                   	at com.fasterxml.jackson.databind.introspect.AnnotationIntrospectorPair.findImplicitPropertyName(AnnotationIntrospectorPair.java:467)
E                   	at com.fasterxml.jackson.databind.introspect.POJOPropertiesCollector._addFields(POJOPropertiesCollector.java:351)
E                   	at com.fasterxml.jackson.databind.introspect.POJOPropertiesCollector.collectAll(POJOPropertiesCollector.java:283)
E                   	at com.fasterxml.jackson.databind.introspect.POJOPropertiesCollector.getJsonValueMethod(POJOPropertiesCollector.java:169)
E                   	at com.fasterxml.jackson.databind.introspect.BasicBeanDescription.findJsonValueMethod(BasicBeanDescription.java:223)
E                   	at com.fasterxml.jackson.databind.ser.BasicSerializerFactory.findSerializerByAnnotations(BasicSerializerFactory.java:348)
E                   	at com.fasterxml.jackson.databind.ser.BeanSerializerFactory._createSerializer2(BeanSerializerFactory.java:210)
E                   	at com.fasterxml.jackson.databind.ser.BeanSerializerFactory.createSerializer(BeanSerializerFactory.java:153)
E                   	at com.fasterxml.jackson.databind.SerializerProvider._createUntypedSerializer(SerializerProvider.java:1203)
E                   	at com.fasterxml.jackson.databind.SerializerProvider._createAndCacheUntypedSerializer(SerializerProvider.java:1157)
E                   	at com.fasterxml.jackson.databind.SerializerProvider.findValueSerializer(SerializerProvider.java:481)
E                   	at com.fasterxml.jackson.databind.SerializerProvider.findTypedValueSerializer(SerializerProvider.java:679)
E                   	at com.fasterxml.jackson.databind.ser.DefaultSerializerProvider.serializeValue(DefaultSerializerProvider.java:107)
E                   	at com.fasterxml.jackson.databind.ObjectMapper._configAndWriteValue(ObjectMapper.java:3559)
E                   	at com.fasterxml.jackson.databind.ObjectMapper.writeValueAsString(ObjectMapper.java:2927)
E                   	at org.apache.spark.rdd.RDDOperationScope.toJson(RDDOperationScope.scala:52)
E                   	at org.apache.spark.rdd.RDDOperationScope$.withScope(RDDOperationScope.scala:145)
E                   	at org.apache.spark.rdd.RDDOperationScope$.withScope(RDDOperationScope.scala:112)
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:2151)
E                   	at org.bdgenomics.adam.rdd.ADAMContext.$anonfun$loadVcf$1(ADAMContext.scala:2169)
E                   	at scala.Option.fold(Option.scala:175)
E                   	at org.apache.spark.rdd.Timer.time(Timer.scala:48)
E                   	at org.bdgenomics.adam.rdd.ADAMContext.loadVcf(ADAMContext.scala:2166)
E                   	at org.bdgenomics.adam.rdd.ADAMContext.$anonfun$loadGenotypes$1(ADAMContext.scala:3187)
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:3185)
E                   	at org.bdgenomics.adam.api.java.JavaADAMContext.loadGenotypes(JavaADAMContext.scala:353)
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/adamTestdLUBupA/deleteMePleaseThisIsNoLongerNeeded/spark-2.4.3-bin-without-hadoop-scala-2.12/python/lib/py4j-0.10.7-src.zip/py4j/protocol.py:328: Py4JJavaError
----------------------------- Captured stderr call -----------------------------
2019-05-15 13:41:28 WARN  Utils:66 - Service 'SparkUI' could not bind on port 4040. Attempting port 4041.
2019-05-15 13:41:28 WARN  Utils:66 - Service 'SparkUI' could not bind on port 4041. Attempting port 4042.
______________________ 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:236: in loadGenotypes
    _toJava(stringency, self._jvm))
/tmp/adamTestdLUBupA/deleteMePleaseThisIsNoLongerNeeded/spark-2.4.3-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-2.4.3-bin-without-hadoop-scala-2.12/python/pyspark/sql/utils.py:63: in deco
    return f(*a, **kw)
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 

answer = 'xro7000'
gateway_client = <py4j.java_gateway.GatewayClient object at 0x7f9a60794550>
target_id = 'o6998', 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 o6998.loadGenotypes.
E                   : java.lang.ArrayIndexOutOfBoundsException: 17418
E                   	at com.thoughtworks.paranamer.BytecodeReadingParanamer$ClassReader.accept(BytecodeReadingParanamer.java:563)
E                   	at com.thoughtworks.paranamer.BytecodeReadingParanamer$ClassReader.access$200(BytecodeReadingParanamer.java:338)
E                   	at com.thoughtworks.paranamer.BytecodeReadingParanamer.lookupParameterNames(BytecodeReadingParanamer.java:103)
E                   	at com.thoughtworks.paranamer.CachingParanamer.lookupParameterNames(CachingParanamer.java:90)
E                   	at com.fasterxml.jackson.module.scala.introspect.BeanIntrospector$.getCtorParams(BeanIntrospector.scala:44)
E                   	at com.fasterxml.jackson.module.scala.introspect.BeanIntrospector$.$anonfun$apply$1(BeanIntrospector.scala:58)
E                   	at com.fasterxml.jackson.module.scala.introspect.BeanIntrospector$.$anonfun$apply$1$adapted(BeanIntrospector.scala:58)
E                   	at scala.collection.TraversableLike.$anonfun$flatMap$1(TraversableLike.scala:244)
E                   	at scala.collection.Iterator.foreach(Iterator.scala:941)
E                   	at scala.collection.Iterator.foreach$(Iterator.scala:941)
E                   	at scala.collection.AbstractIterator.foreach(Iterator.scala:1429)
E                   	at scala.collection.IterableLike.foreach(IterableLike.scala:74)
E                   	at scala.collection.IterableLike.foreach$(IterableLike.scala:73)
E                   	at scala.collection.AbstractIterable.foreach(Iterable.scala:56)
E                   	at scala.collection.TraversableLike.flatMap(TraversableLike.scala:244)
E                   	at scala.collection.TraversableLike.flatMap$(TraversableLike.scala:241)
E                   	at scala.collection.AbstractTraversable.flatMap(Traversable.scala:108)
E                   	at com.fasterxml.jackson.module.scala.introspect.BeanIntrospector$.findConstructorParam$1(BeanIntrospector.scala:58)
E                   	at com.fasterxml.jackson.module.scala.introspect.BeanIntrospector$.$anonfun$apply$19(BeanIntrospector.scala:176)
E                   	at scala.collection.TraversableLike.$anonfun$map$1(TraversableLike.scala:237)
E                   	at scala.collection.IndexedSeqOptimized.foreach(IndexedSeqOptimized.scala:36)
E                   	at scala.collection.IndexedSeqOptimized.foreach$(IndexedSeqOptimized.scala:33)
E                   	at scala.collection.mutable.ArrayOps$ofRef.foreach(ArrayOps.scala:198)
E                   	at scala.collection.TraversableLike.map(TraversableLike.scala:237)
E                   	at scala.collection.TraversableLike.map$(TraversableLike.scala:230)
E                   	at scala.collection.mutable.ArrayOps$ofRef.map(ArrayOps.scala:198)
E                   	at com.fasterxml.jackson.module.scala.introspect.BeanIntrospector$.$anonfun$apply$14(BeanIntrospector.scala:170)
E                   	at com.fasterxml.jackson.module.scala.introspect.BeanIntrospector$.$anonfun$apply$14$adapted(BeanIntrospector.scala:169)
E                   	at scala.collection.TraversableLike.$anonfun$flatMap$1(TraversableLike.scala:244)
E                   	at scala.collection.immutable.List.foreach(List.scala:392)
E                   	at scala.collection.TraversableLike.flatMap(TraversableLike.scala:244)
E                   	at scala.collection.TraversableLike.flatMap$(TraversableLike.scala:241)
E                   	at scala.collection.immutable.List.flatMap(List.scala:355)
E                   	at com.fasterxml.jackson.module.scala.introspect.BeanIntrospector$.apply(BeanIntrospector.scala:169)
E                   	at com.fasterxml.jackson.module.scala.introspect.ScalaAnnotationIntrospector$._descriptorFor(ScalaAnnotationIntrospectorModule.scala:22)
E                   	at com.fasterxml.jackson.module.scala.introspect.ScalaAnnotationIntrospector$.fieldName(ScalaAnnotationIntrospectorModule.scala:30)
E                   	at com.fasterxml.jackson.module.scala.introspect.ScalaAnnotationIntrospector$.findImplicitPropertyName(ScalaAnnotationIntrospectorModule.scala:78)
E                   	at com.fasterxml.jackson.databind.introspect.AnnotationIntrospectorPair.findImplicitPropertyName(AnnotationIntrospectorPair.java:467)
E                   	at com.fasterxml.jackson.databind.introspect.POJOPropertiesCollector._addFields(POJOPropertiesCollector.java:351)
E                   	at com.fasterxml.jackson.databind.introspect.POJOPropertiesCollector.collectAll(POJOPropertiesCollector.java:283)
E                   	at com.fasterxml.jackson.databind.introspect.POJOPropertiesCollector.getJsonValueMethod(POJOPropertiesCollector.java:169)
E                   	at com.fasterxml.jackson.databind.introspect.BasicBeanDescription.findJsonValueMethod(BasicBeanDescription.java:223)
E                   	at com.fasterxml.jackson.databind.ser.BasicSerializerFactory.findSerializerByAnnotations(BasicSerializerFactory.java:348)
E                   	at com.fasterxml.jackson.databind.ser.BeanSerializerFactory._createSerializer2(BeanSerializerFactory.java:210)
E                   	at com.fasterxml.jackson.databind.ser.BeanSerializerFactory.createSerializer(BeanSerializerFactory.java:153)
E                   	at com.fasterxml.jackson.databind.SerializerProvider._createUntypedSerializer(SerializerProvider.java:1203)
E                   	at com.fasterxml.jackson.databind.SerializerProvider._createAndCacheUntypedSerializer(SerializerProvider.java:1157)
E                   	at com.fasterxml.jackson.databind.SerializerProvider.findValueSerializer(SerializerProvider.java:481)
E                   	at com.fasterxml.jackson.databind.SerializerProvider.findTypedValueSerializer(SerializerProvider.java:679)
E                   	at com.fasterxml.jackson.databind.ser.DefaultSerializerProvider.serializeValue(DefaultSerializerProvider.java:107)
E                   	at com.fasterxml.jackson.databind.ObjectMapper._configAndWriteValue(ObjectMapper.java:3559)
E                   	at com.fasterxml.jackson.databind.ObjectMapper.writeValueAsString(ObjectMapper.java:2927)
E                   	at org.apache.spark.rdd.RDDOperationScope.toJson(RDDOperationScope.scala:52)
E                   	at org.apache.spark.rdd.RDDOperationScope$.withScope(RDDOperationScope.scala:145)
E                   	at org.apache.spark.rdd.RDDOperationScope$.withScope(RDDOperationScope.scala:112)
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:2151)
E                   	at org.bdgenomics.adam.rdd.ADAMContext.$anonfun$loadVcf$1(ADAMContext.scala:2169)
E                   	at scala.Option.fold(Option.scala:175)
E                   	at org.apache.spark.rdd.Timer.time(Timer.scala:48)
E                   	at org.bdgenomics.adam.rdd.ADAMContext.loadVcf(ADAMContext.scala:2166)
E                   	at org.bdgenomics.adam.rdd.ADAMContext.$anonfun$loadGenotypes$1(ADAMContext.scala:3187)
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:3185)
E                   	at org.bdgenomics.adam.api.java.JavaADAMContext.loadGenotypes(JavaADAMContext.scala:353)
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/adamTestdLUBupA/deleteMePleaseThisIsNoLongerNeeded/spark-2.4.3-bin-without-hadoop-scala-2.12/python/lib/py4j-0.10.7-src.zip/py4j/protocol.py:328: Py4JJavaError
----------------------------- Captured stderr call -----------------------------
2019-05-15 13:41:28 WARN  Utils:66 - Service 'SparkUI' could not bind on port 4040. Attempting port 4041.
2019-05-15 13:41:28 WARN  Utils:66 - Service 'SparkUI' could not bind on port 4041. Attempting port 4042.
____________________ 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:236: in loadGenotypes
    _toJava(stringency, self._jvm))
/tmp/adamTestdLUBupA/deleteMePleaseThisIsNoLongerNeeded/spark-2.4.3-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-2.4.3-bin-without-hadoop-scala-2.12/python/pyspark/sql/utils.py:63: in deco
    return f(*a, **kw)
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 

answer = 'xro7121'
gateway_client = <py4j.java_gateway.GatewayClient object at 0x7f9a60794550>
target_id = 'o7119', 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 o7119.loadGenotypes.
E                   : java.lang.ArrayIndexOutOfBoundsException: 17418
E                   	at com.thoughtworks.paranamer.BytecodeReadingParanamer$ClassReader.accept(BytecodeReadingParanamer.java:563)
E                   	at com.thoughtworks.paranamer.BytecodeReadingParanamer$ClassReader.access$200(BytecodeReadingParanamer.java:338)
E                   	at com.thoughtworks.paranamer.BytecodeReadingParanamer.lookupParameterNames(BytecodeReadingParanamer.java:103)
E                   	at com.thoughtworks.paranamer.CachingParanamer.lookupParameterNames(CachingParanamer.java:90)
E                   	at com.fasterxml.jackson.module.scala.introspect.BeanIntrospector$.getCtorParams(BeanIntrospector.scala:44)
E                   	at com.fasterxml.jackson.module.scala.introspect.BeanIntrospector$.$anonfun$apply$1(BeanIntrospector.scala:58)
E                   	at com.fasterxml.jackson.module.scala.introspect.BeanIntrospector$.$anonfun$apply$1$adapted(BeanIntrospector.scala:58)
E                   	at scala.collection.TraversableLike.$anonfun$flatMap$1(TraversableLike.scala:244)
E                   	at scala.collection.Iterator.foreach(Iterator.scala:941)
E                   	at scala.collection.Iterator.foreach$(Iterator.scala:941)
E                   	at scala.collection.AbstractIterator.foreach(Iterator.scala:1429)
E                   	at scala.collection.IterableLike.foreach(IterableLike.scala:74)
E                   	at scala.collection.IterableLike.foreach$(IterableLike.scala:73)
E                   	at scala.collection.AbstractIterable.foreach(Iterable.scala:56)
E                   	at scala.collection.TraversableLike.flatMap(TraversableLike.scala:244)
E                   	at scala.collection.TraversableLike.flatMap$(TraversableLike.scala:241)
E                   	at scala.collection.AbstractTraversable.flatMap(Traversable.scala:108)
E                   	at com.fasterxml.jackson.module.scala.introspect.BeanIntrospector$.findConstructorParam$1(BeanIntrospector.scala:58)
E                   	at com.fasterxml.jackson.module.scala.introspect.BeanIntrospector$.$anonfun$apply$19(BeanIntrospector.scala:176)
E                   	at scala.collection.TraversableLike.$anonfun$map$1(TraversableLike.scala:237)
E                   	at scala.collection.IndexedSeqOptimized.foreach(IndexedSeqOptimized.scala:36)
E                   	at scala.collection.IndexedSeqOptimized.foreach$(IndexedSeqOptimized.scala:33)
E                   	at scala.collection.mutable.ArrayOps$ofRef.foreach(ArrayOps.scala:198)
E                   	at scala.collection.TraversableLike.map(TraversableLike.scala:237)
E                   	at scala.collection.TraversableLike.map$(TraversableLike.scala:230)
E                   	at scala.collection.mutable.ArrayOps$ofRef.map(ArrayOps.scala:198)
E                   	at com.fasterxml.jackson.module.scala.introspect.BeanIntrospector$.$anonfun$apply$14(BeanIntrospector.scala:170)
E                   	at com.fasterxml.jackson.module.scala.introspect.BeanIntrospector$.$anonfun$apply$14$adapted(BeanIntrospector.scala:169)
E                   	at scala.collection.TraversableLike.$anonfun$flatMap$1(TraversableLike.scala:244)
E                   	at scala.collection.immutable.List.foreach(List.scala:392)
E                   	at scala.collection.TraversableLike.flatMap(TraversableLike.scala:244)
E                   	at scala.collection.TraversableLike.flatMap$(TraversableLike.scala:241)
E                   	at scala.collection.immutable.List.flatMap(List.scala:355)
E                   	at com.fasterxml.jackson.module.scala.introspect.BeanIntrospector$.apply(BeanIntrospector.scala:169)
E                   	at com.fasterxml.jackson.module.scala.introspect.ScalaAnnotationIntrospector$._descriptorFor(ScalaAnnotationIntrospectorModule.scala:22)
E                   	at com.fasterxml.jackson.module.scala.introspect.ScalaAnnotationIntrospector$.fieldName(ScalaAnnotationIntrospectorModule.scala:30)
E                   	at com.fasterxml.jackson.module.scala.introspect.ScalaAnnotationIntrospector$.findImplicitPropertyName(ScalaAnnotationIntrospectorModule.scala:78)
E                   	at com.fasterxml.jackson.databind.introspect.AnnotationIntrospectorPair.findImplicitPropertyName(AnnotationIntrospectorPair.java:467)
E                   	at com.fasterxml.jackson.databind.introspect.POJOPropertiesCollector._addFields(POJOPropertiesCollector.java:351)
E                   	at com.fasterxml.jackson.databind.introspect.POJOPropertiesCollector.collectAll(POJOPropertiesCollector.java:283)
E                   	at com.fasterxml.jackson.databind.introspect.POJOPropertiesCollector.getJsonValueMethod(POJOPropertiesCollector.java:169)
E                   	at com.fasterxml.jackson.databind.introspect.BasicBeanDescription.findJsonValueMethod(BasicBeanDescription.java:223)
E                   	at com.fasterxml.jackson.databind.ser.BasicSerializerFactory.findSerializerByAnnotations(BasicSerializerFactory.java:348)
E                   	at com.fasterxml.jackson.databind.ser.BeanSerializerFactory._createSerializer2(BeanSerializerFactory.java:210)
E                   	at com.fasterxml.jackson.databind.ser.BeanSerializerFactory.createSerializer(BeanSerializerFactory.java:153)
E                   	at com.fasterxml.jackson.databind.SerializerProvider._createUntypedSerializer(SerializerProvider.java:1203)
E                   	at com.fasterxml.jackson.databind.SerializerProvider._createAndCacheUntypedSerializer(SerializerProvider.java:1157)
E                   	at com.fasterxml.jackson.databind.SerializerProvider.findValueSerializer(SerializerProvider.java:481)
E                   	at com.fasterxml.jackson.databind.SerializerProvider.findTypedValueSerializer(SerializerProvider.java:679)
E                   	at com.fasterxml.jackson.databind.ser.DefaultSerializerProvider.serializeValue(DefaultSerializerProvider.java:107)
E                   	at com.fasterxml.jackson.databind.ObjectMapper._configAndWriteValue(ObjectMapper.java:3559)
E                   	at com.fasterxml.jackson.databind.ObjectMapper.writeValueAsString(ObjectMapper.java:2927)
E                   	at org.apache.spark.rdd.RDDOperationScope.toJson(RDDOperationScope.scala:52)
E                   	at org.apache.spark.rdd.RDDOperationScope$.withScope(RDDOperationScope.scala:145)
E                   	at org.apache.spark.rdd.RDDOperationScope$.withScope(RDDOperationScope.scala:112)
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:2151)
E                   	at org.bdgenomics.adam.rdd.ADAMContext.$anonfun$loadVcf$1(ADAMContext.scala:2169)
E                   	at scala.Option.fold(Option.scala:175)
E                   	at org.apache.spark.rdd.Timer.time(Timer.scala:48)
E                   	at org.bdgenomics.adam.rdd.ADAMContext.loadVcf(ADAMContext.scala:2166)
E                   	at org.bdgenomics.adam.rdd.ADAMContext.$anonfun$loadGenotypes$1(ADAMContext.scala:3187)
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:3185)
E                   	at org.bdgenomics.adam.api.java.JavaADAMContext.loadGenotypes(JavaADAMContext.scala:353)
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/adamTestdLUBupA/deleteMePleaseThisIsNoLongerNeeded/spark-2.4.3-bin-without-hadoop-scala-2.12/python/lib/py4j-0.10.7-src.zip/py4j/protocol.py:328: Py4JJavaError
----------------------------- Captured stderr call -----------------------------
2019-05-15 13:41:29 WARN  Utils:66 - Service 'SparkUI' could not bind on port 4040. Attempting port 4041.
2019-05-15 13:41:29 WARN  Utils:66 - Service 'SparkUI' could not bind on port 4041. Attempting port 4042.
______________________ 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:255: in loadVariants
    _toJava(stringency, self._jvm))
/tmp/adamTestdLUBupA/deleteMePleaseThisIsNoLongerNeeded/spark-2.4.3-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-2.4.3-bin-without-hadoop-scala-2.12/python/pyspark/sql/utils.py:63: in deco
    return f(*a, **kw)
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 

answer = 'xro7242'
gateway_client = <py4j.java_gateway.GatewayClient object at 0x7f9a60794550>
target_id = 'o7240', 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 o7240.loadVariants.
E                   : java.lang.ArrayIndexOutOfBoundsException: 17418
E                   	at com.thoughtworks.paranamer.BytecodeReadingParanamer$ClassReader.accept(BytecodeReadingParanamer.java:563)
E                   	at com.thoughtworks.paranamer.BytecodeReadingParanamer$ClassReader.access$200(BytecodeReadingParanamer.java:338)
E                   	at com.thoughtworks.paranamer.BytecodeReadingParanamer.lookupParameterNames(BytecodeReadingParanamer.java:103)
E                   	at com.thoughtworks.paranamer.CachingParanamer.lookupParameterNames(CachingParanamer.java:90)
E                   	at com.fasterxml.jackson.module.scala.introspect.BeanIntrospector$.getCtorParams(BeanIntrospector.scala:44)
E                   	at com.fasterxml.jackson.module.scala.introspect.BeanIntrospector$.$anonfun$apply$1(BeanIntrospector.scala:58)
E                   	at com.fasterxml.jackson.module.scala.introspect.BeanIntrospector$.$anonfun$apply$1$adapted(BeanIntrospector.scala:58)
E                   	at scala.collection.TraversableLike.$anonfun$flatMap$1(TraversableLike.scala:244)
E                   	at scala.collection.Iterator.foreach(Iterator.scala:941)
E                   	at scala.collection.Iterator.foreach$(Iterator.scala:941)
E                   	at scala.collection.AbstractIterator.foreach(Iterator.scala:1429)
E                   	at scala.collection.IterableLike.foreach(IterableLike.scala:74)
E                   	at scala.collection.IterableLike.foreach$(IterableLike.scala:73)
E                   	at scala.collection.AbstractIterable.foreach(Iterable.scala:56)
E                   	at scala.collection.TraversableLike.flatMap(TraversableLike.scala:244)
E                   	at scala.collection.TraversableLike.flatMap$(TraversableLike.scala:241)
E                   	at scala.collection.AbstractTraversable.flatMap(Traversable.scala:108)
E                   	at com.fasterxml.jackson.module.scala.introspect.BeanIntrospector$.findConstructorParam$1(BeanIntrospector.scala:58)
E                   	at com.fasterxml.jackson.module.scala.introspect.BeanIntrospector$.$anonfun$apply$19(BeanIntrospector.scala:176)
E                   	at scala.collection.TraversableLike.$anonfun$map$1(TraversableLike.scala:237)
E                   	at scala.collection.IndexedSeqOptimized.foreach(IndexedSeqOptimized.scala:36)
E                   	at scala.collection.IndexedSeqOptimized.foreach$(IndexedSeqOptimized.scala:33)
E                   	at scala.collection.mutable.ArrayOps$ofRef.foreach(ArrayOps.scala:198)
E                   	at scala.collection.TraversableLike.map(TraversableLike.scala:237)
E                   	at scala.collection.TraversableLike.map$(TraversableLike.scala:230)
E                   	at scala.collection.mutable.ArrayOps$ofRef.map(ArrayOps.scala:198)
E                   	at com.fasterxml.jackson.module.scala.introspect.BeanIntrospector$.$anonfun$apply$14(BeanIntrospector.scala:170)
E                   	at com.fasterxml.jackson.module.scala.introspect.BeanIntrospector$.$anonfun$apply$14$adapted(BeanIntrospector.scala:169)
E                   	at scala.collection.TraversableLike.$anonfun$flatMap$1(TraversableLike.scala:244)
E                   	at scala.collection.immutable.List.foreach(List.scala:392)
E                   	at scala.collection.TraversableLike.flatMap(TraversableLike.scala:244)
E                   	at scala.collection.TraversableLike.flatMap$(TraversableLike.scala:241)
E                   	at scala.collection.immutable.List.flatMap(List.scala:355)
E                   	at com.fasterxml.jackson.module.scala.introspect.BeanIntrospector$.apply(BeanIntrospector.scala:169)
E                   	at com.fasterxml.jackson.module.scala.introspect.ScalaAnnotationIntrospector$._descriptorFor(ScalaAnnotationIntrospectorModule.scala:22)
E                   	at com.fasterxml.jackson.module.scala.introspect.ScalaAnnotationIntrospector$.fieldName(ScalaAnnotationIntrospectorModule.scala:30)
E                   	at com.fasterxml.jackson.module.scala.introspect.ScalaAnnotationIntrospector$.findImplicitPropertyName(ScalaAnnotationIntrospectorModule.scala:78)
E                   	at com.fasterxml.jackson.databind.introspect.AnnotationIntrospectorPair.findImplicitPropertyName(AnnotationIntrospectorPair.java:467)
E                   	at com.fasterxml.jackson.databind.introspect.POJOPropertiesCollector._addFields(POJOPropertiesCollector.java:351)
E                   	at com.fasterxml.jackson.databind.introspect.POJOPropertiesCollector.collectAll(POJOPropertiesCollector.java:283)
E                   	at com.fasterxml.jackson.databind.introspect.POJOPropertiesCollector.getJsonValueMethod(POJOPropertiesCollector.java:169)
E                   	at com.fasterxml.jackson.databind.introspect.BasicBeanDescription.findJsonValueMethod(BasicBeanDescription.java:223)
E                   	at com.fasterxml.jackson.databind.ser.BasicSerializerFactory.findSerializerByAnnotations(BasicSerializerFactory.java:348)
E                   	at com.fasterxml.jackson.databind.ser.BeanSerializerFactory._createSerializer2(BeanSerializerFactory.java:210)
E                   	at com.fasterxml.jackson.databind.ser.BeanSerializerFactory.createSerializer(BeanSerializerFactory.java:153)
E                   	at com.fasterxml.jackson.databind.SerializerProvider._createUntypedSerializer(SerializerProvider.java:1203)
E                   	at com.fasterxml.jackson.databind.SerializerProvider._createAndCacheUntypedSerializer(SerializerProvider.java:1157)
E                   	at com.fasterxml.jackson.databind.SerializerProvider.findValueSerializer(SerializerProvider.java:481)
E                   	at com.fasterxml.jackson.databind.SerializerProvider.findTypedValueSerializer(SerializerProvider.java:679)
E                   	at com.fasterxml.jackson.databind.ser.DefaultSerializerProvider.serializeValue(DefaultSerializerProvider.java:107)
E                   	at com.fasterxml.jackson.databind.ObjectMapper._configAndWriteValue(ObjectMapper.java:3559)
E                   	at com.fasterxml.jackson.databind.ObjectMapper.writeValueAsString(ObjectMapper.java:2927)
E                   	at org.apache.spark.rdd.RDDOperationScope.toJson(RDDOperationScope.scala:52)
E                   	at org.apache.spark.rdd.RDDOperationScope$.withScope(RDDOperationScope.scala:145)
E                   	at org.apache.spark.rdd.RDDOperationScope$.withScope(RDDOperationScope.scala:112)
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:2151)
E                   	at org.bdgenomics.adam.rdd.ADAMContext.$anonfun$loadVcf$1(ADAMContext.scala:2169)
E                   	at scala.Option.fold(Option.scala:175)
E                   	at org.apache.spark.rdd.Timer.time(Timer.scala:48)
E                   	at org.bdgenomics.adam.rdd.ADAMContext.loadVcf(ADAMContext.scala:2166)
E                   	at org.bdgenomics.adam.rdd.ADAMContext.$anonfun$loadVariants$1(ADAMContext.scala:3221)
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:3219)
E                   	at org.bdgenomics.adam.api.java.JavaADAMContext.loadVariants(JavaADAMContext.scala:387)
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/adamTestdLUBupA/deleteMePleaseThisIsNoLongerNeeded/spark-2.4.3-bin-without-hadoop-scala-2.12/python/lib/py4j-0.10.7-src.zip/py4j/protocol.py:328: Py4JJavaError
----------------------------- Captured stderr call -----------------------------
2019-05-15 13:41:30 WARN  Utils:66 - Service 'SparkUI' could not bind on port 4040. Attempting port 4041.
2019-05-15 13:41:30 WARN  Utils:66 - Service 'SparkUI' could not bind on port 4041. Attempting port 4042.
____________________ 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:255: in loadVariants
    _toJava(stringency, self._jvm))
/tmp/adamTestdLUBupA/deleteMePleaseThisIsNoLongerNeeded/spark-2.4.3-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-2.4.3-bin-without-hadoop-scala-2.12/python/pyspark/sql/utils.py:63: in deco
    return f(*a, **kw)
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ 

answer = 'xro7363'
gateway_client = <py4j.java_gateway.GatewayClient object at 0x7f9a60794550>
target_id = 'o7361', 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 o7361.loadVariants.
E                   : java.lang.ArrayIndexOutOfBoundsException: 17418
E                   	at com.thoughtworks.paranamer.BytecodeReadingParanamer$ClassReader.accept(BytecodeReadingParanamer.java:563)
E                   	at com.thoughtworks.paranamer.BytecodeReadingParanamer$ClassReader.access$200(BytecodeReadingParanamer.java:338)
E                   	at com.thoughtworks.paranamer.BytecodeReadingParanamer.lookupParameterNames(BytecodeReadingParanamer.java:103)
E                   	at com.thoughtworks.paranamer.CachingParanamer.lookupParameterNames(CachingParanamer.java:90)
E                   	at com.fasterxml.jackson.module.scala.introspect.BeanIntrospector$.getCtorParams(BeanIntrospector.scala:44)
E                   	at com.fasterxml.jackson.module.scala.introspect.BeanIntrospector$.$anonfun$apply$1(BeanIntrospector.scala:58)
E                   	at com.fasterxml.jackson.module.scala.introspect.BeanIntrospector$.$anonfun$apply$1$adapted(BeanIntrospector.scala:58)
E                   	at scala.collection.TraversableLike.$anonfun$flatMap$1(TraversableLike.scala:244)
E                   	at scala.collection.Iterator.foreach(Iterator.scala:941)
E                   	at scala.collection.Iterator.foreach$(Iterator.scala:941)
E                   	at scala.collection.AbstractIterator.foreach(Iterator.scala:1429)
E                   	at scala.collection.IterableLike.foreach(IterableLike.scala:74)
E                   	at scala.collection.IterableLike.foreach$(IterableLike.scala:73)
E                   	at scala.collection.AbstractIterable.foreach(Iterable.scala:56)
E                   	at scala.collection.TraversableLike.flatMap(TraversableLike.scala:244)
E                   	at scala.collection.TraversableLike.flatMap$(TraversableLike.scala:241)
E                   	at scala.collection.AbstractTraversable.flatMap(Traversable.scala:108)
E                   	at com.fasterxml.jackson.module.scala.introspect.BeanIntrospector$.findConstructorParam$1(BeanIntrospector.scala:58)
E                   	at com.fasterxml.jackson.module.scala.introspect.BeanIntrospector$.$anonfun$apply$19(BeanIntrospector.scala:176)
E                   	at scala.collection.TraversableLike.$anonfun$map$1(TraversableLike.scala:237)
E                   	at scala.collection.IndexedSeqOptimized.foreach(IndexedSeqOptimized.scala:36)
E                   	at scala.collection.IndexedSeqOptimized.foreach$(IndexedSeqOptimized.scala:33)
E                   	at scala.collection.mutable.ArrayOps$ofRef.foreach(ArrayOps.scala:198)
E                   	at scala.collection.TraversableLike.map(TraversableLike.scala:237)
E                   	at scala.collection.TraversableLike.map$(TraversableLike.scala:230)
E                   	at scala.collection.mutable.ArrayOps$ofRef.map(ArrayOps.scala:198)
E                   	at com.fasterxml.jackson.module.scala.introspect.BeanIntrospector$.$anonfun$apply$14(BeanIntrospector.scala:170)
E                   	at com.fasterxml.jackson.module.scala.introspect.BeanIntrospector$.$anonfun$apply$14$adapted(BeanIntrospector.scala:169)
E                   	at scala.collection.TraversableLike.$anonfun$flatMap$1(TraversableLike.scala:244)
E                   	at scala.collection.immutable.List.foreach(List.scala:392)
E                   	at scala.collection.TraversableLike.flatMap(TraversableLike.scala:244)
E                   	at scala.collection.TraversableLike.flatMap$(TraversableLike.scala:241)
E                   	at scala.collection.immutable.List.flatMap(List.scala:355)
E                   	at com.fasterxml.jackson.module.scala.introspect.BeanIntrospector$.apply(BeanIntrospector.scala:169)
E                   	at com.fasterxml.jackson.module.scala.introspect.ScalaAnnotationIntrospector$._descriptorFor(ScalaAnnotationIntrospectorModule.scala:22)
E                   	at com.fasterxml.jackson.module.scala.introspect.ScalaAnnotationIntrospector$.fieldName(ScalaAnnotationIntrospectorModule.scala:30)
E                   	at com.fasterxml.jackson.module.scala.introspect.ScalaAnnotationIntrospector$.findImplicitPropertyName(ScalaAnnotationIntrospectorModule.scala:78)
E                   	at com.fasterxml.jackson.databind.introspect.AnnotationIntrospectorPair.findImplicitPropertyName(AnnotationIntrospectorPair.java:467)
E                   	at com.fasterxml.jackson.databind.introspect.POJOPropertiesCollector._addFields(POJOPropertiesCollector.java:351)
E                   	at com.fasterxml.jackson.databind.introspect.POJOPropertiesCollector.collectAll(POJOPropertiesCollector.java:283)
E                   	at com.fasterxml.jackson.databind.introspect.POJOPropertiesCollector.getJsonValueMethod(POJOPropertiesCollector.java:169)
E                   	at com.fasterxml.jackson.databind.introspect.BasicBeanDescription.findJsonValueMethod(BasicBeanDescription.java:223)
E                   	at com.fasterxml.jackson.databind.ser.BasicSerializerFactory.findSerializerByAnnotations(BasicSerializerFactory.java:348)
E                   	at com.fasterxml.jackson.databind.ser.BeanSerializerFactory._createSerializer2(BeanSerializerFactory.java:210)
E                   	at com.fasterxml.jackson.databind.ser.BeanSerializerFactory.createSerializer(BeanSerializerFactory.java:153)
E                   	at com.fasterxml.jackson.databind.SerializerProvider._createUntypedSerializer(SerializerProvider.java:1203)
E                   	at com.fasterxml.jackson.databind.SerializerProvider._createAndCacheUntypedSerializer(SerializerProvider.java:1157)
E                   	at com.fasterxml.jackson.databind.SerializerProvider.findValueSerializer(SerializerProvider.java:481)
E                   	at com.fasterxml.jackson.databind.SerializerProvider.findTypedValueSerializer(SerializerProvider.java:679)
E                   	at com.fasterxml.jackson.databind.ser.DefaultSerializerProvider.serializeValue(DefaultSerializerProvider.java:107)
E                   	at com.fasterxml.jackson.databind.ObjectMapper._configAndWriteValue(ObjectMapper.java:3559)
E                   	at com.fasterxml.jackson.databind.ObjectMapper.writeValueAsString(ObjectMapper.java:2927)
E                   	at org.apache.spark.rdd.RDDOperationScope.toJson(RDDOperationScope.scala:52)
E                   	at org.apache.spark.rdd.RDDOperationScope$.withScope(RDDOperationScope.scala:145)
E                   	at org.apache.spark.rdd.RDDOperationScope$.withScope(RDDOperationScope.scala:112)
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:2151)
E                   	at org.bdgenomics.adam.rdd.ADAMContext.$anonfun$loadVcf$1(ADAMContext.scala:2169)
E                   	at scala.Option.fold(Option.scala:175)
E                   	at org.apache.spark.rdd.Timer.time(Timer.scala:48)
E                   	at org.bdgenomics.adam.rdd.ADAMContext.loadVcf(ADAMContext.scala:2166)
E                   	at org.bdgenomics.adam.rdd.ADAMContext.$anonfun$loadVariants$1(ADAMContext.scala:3221)
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:3219)
E                   	at org.bdgenomics.adam.api.java.JavaADAMContext.loadVariants(JavaADAMContext.scala:387)
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/adamTestdLUBupA/deleteMePleaseThisIsNoLongerNeeded/spark-2.4.3-bin-without-hadoop-scala-2.12/python/lib/py4j-0.10.7-src.zip/py4j/protocol.py:328: Py4JJavaError
----------------------------- Captured stderr call -----------------------------
2019-05-15 13:41:30 WARN  Utils:66 - Service 'SparkUI' could not bind on port 4040. Attempting port 4041.
2019-05-15 13:41:30 WARN  Utils:66 - Service 'SparkUI' could not bind on port 4041. Attempting port 4042.
- generated xml file: /tmp/adamTestdLUBupA/deleteMePleaseThisIsNoLongerNeeded/adam-python/target/pytest-reports/tests.xml -
========================== 62 failed in 47.86 seconds ==========================
make: *** [test] Error 1
Makefile:83: recipe for target 'test' failed
[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 [  9.625 s]
[INFO] ADAM_2.12: Shader workaround ....................... SUCCESS [  7.674 s]
[INFO] ADAM_2.12: Avro-to-Dataset codegen utils ........... SUCCESS [  9.434 s]
[INFO] ADAM_2.12: Core .................................... SUCCESS [01:37 min]
[INFO] ADAM_2.12: APIs for Java, Python ................... SUCCESS [ 18.692 s]
[INFO] ADAM_2.12: CLI ..................................... SUCCESS [ 26.814 s]
[INFO] ADAM_2.12: Assembly ................................ SUCCESS [ 15.967 s]
[INFO] ADAM_2.12: Python APIs ............................. FAILURE [01:17 min]
[INFO] ADAM_2.12: R APIs .................................. SKIPPED
[INFO] ADAM_2.12: Distribution ............................ SKIPPED
[INFO] ------------------------------------------------------------------------
[INFO] BUILD FAILURE
[INFO] ------------------------------------------------------------------------
[INFO] Total time: 04:23 min
[INFO] Finished at: 2019-05-15T13:41:32-07:00
[INFO] Final Memory: 89M/1486M
[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/8f09a5504fee4f06243a20b42b534b17aef33d46
Finished: FAILURE