ProteinChainClassification.ipynb

[pwrose]

I get the following error below (on Windows). I think it's because we using a different dataset.

Take out the filter:

.filter(Pisces(sequenceIdentity=40,resolution=3.0))

and see if that fixes the problem (empty RDD).

Also, change the text:
Read MMTF File and create a non-redundant set (<=40% seq. identity) of L-protein clains

to:

Read MMTF File and create a set of L-protein chains.

---

Py4JJavaError Traceback (most recent call last)
in ()
----> 1 data = secondaryStructureExtractor.get_dataset(pdb)

~\Anaconda3\lib\site-packages\mmtfPyspark\datasets\secondaryStructureExtractor.py in get_dataset(structure)
48 "coil", "dsspQ8Code", "dsspQ3Code"]
49
---> 50 return pythonRDDToDataset.get_dataset(rows, colNames)
51
52

~\Anaconda3\lib\site-packages\mmtfPyspark\ml\pythonRDDToDataset.py in get_dataset(data, colNames)
26 '''
27
---> 28 row = data.first()
29 length = len(row)
30

~\Anaconda3\lib\site-packages\pyspark\rdd.py in first(self)
1374 ValueError: RDD is empty
1375 """
-> 1376 rs = self.take(1)
1377 if rs:
1378 return rs[0]

~\Anaconda3\lib\site-packages\pyspark\rdd.py in take(self, num)
1356
1357 p = range(partsScanned, min(partsScanned + numPartsToTry, totalParts))
-> 1358 res = self.context.runJob(self, takeUpToNumLeft, p)
1359
1360 items += res

~\Anaconda3\lib\site-packages\pyspark\context.py in runJob(self, rdd, partitionFunc, partitions, allowLocal)
999 # SparkContext#runJob.
1000 mappedRDD = rdd.mapPartitions(partitionFunc)
-> 1001 port = self._jvm.PythonRDD.runJob(self._jsc.sc(), mappedRDD._jrdd, partitions)
1002 return list(_load_from_socket(port, mappedRDD._jrdd_deserializer))
1003

~\Anaconda3\lib\site-packages\py4j\java_gateway.py in call(self, *args)
1158 answer = self.gateway_client.send_command(command)
1159 return_value = get_return_value(
-> 1160 answer, self.gateway_client, self.target_id, self.name)
1161
1162 for temp_arg in temp_args:

~\Anaconda3\lib\site-packages\py4j\protocol.py in get_return_value(answer, gateway_client, target_id, name)
318 raise Py4JJavaError(
319 "An error occurred while calling {0}{1}{2}.\n".
--> 320 format(target_id, ".", name), value)
321 else:
322 raise Py4JError(

Py4JJavaError: An error occurred while calling z:org.apache.spark.api.python.PythonRDD.runJob.
: org.apache.spark.SparkException: Job aborted due to stage failure: Task 0 in stage 1.0 failed 1 times, most recent failure: Lost task 0.0 in stage 1.0 (TID 1, localhost, executor driver): java.net.SocketException: Connection reset by peer: socket write error
at java.net.SocketOutputStream.socketWrite0(Native Method)
at java.net.SocketOutputStream.socketWrite(SocketOutputStream.java:111)
at java.net.SocketOutputStream.write(SocketOutputStream.java:155)
at java.io.BufferedOutputStream.write(BufferedOutputStream.java:122)
at java.io.DataOutputStream.write(DataOutputStream.java:107)
at java.io.FilterOutputStream.write(FilterOutputStream.java:97)
at org.apache.spark.api.python.PythonRDD$.org$apache$spark$api$python$PythonRDD$$write$1(PythonRDD.scala:192)
at org.apache.spark.api.python.PythonRDD$$anonfun$writeIteratorToStream$1.apply(PythonRDD.scala:204)
at org.apache.spark.api.python.PythonRDD$$anonfun$writeIteratorToStream$1.apply(PythonRDD.scala:204)
at scala.collection.Iterator$class.foreach(Iterator.scala:893)
at org.apache.spark.api.python.SerDeUtil$AutoBatchedPickler.foreach(SerDeUtil.scala:148)
at org.apache.spark.api.python.PythonRDD$.writeIteratorToStream(PythonRDD.scala:204)
at org.apache.spark.api.python.PythonRunner$$anon$2.writeIteratorToStream(PythonRunner.scala:407)
at org.apache.spark.api.python.BasePythonRunner$WriterThread$$anonfun$run$1.apply(PythonRunner.scala:215)
at org.apache.spark.util.Utils$.logUncaughtExceptions(Utils.scala:1988)
at org.apache.spark.api.python.BasePythonRunner$WriterThread.run(PythonRunner.scala:170)

Driver stacktrace:
at org.apache.spark.scheduler.DAGScheduler.org$apache$spark$scheduler$DAGScheduler$$failJobAndIndependentStages(DAGScheduler.scala:1599)
at org.apache.spark.scheduler.DAGScheduler$$anonfun$abortStage$1.apply(DAGScheduler.scala:1587)
at org.apache.spark.scheduler.DAGScheduler$$anonfun$abortStage$1.apply(DAGScheduler.scala:1586)
at scala.collection.mutable.ResizableArray$class.foreach(ResizableArray.scala:59)
at scala.collection.mutable.ArrayBuffer.foreach(ArrayBuffer.scala:48)
at org.apache.spark.scheduler.DAGScheduler.abortStage(DAGScheduler.scala:1586)
at org.apache.spark.scheduler.DAGScheduler$$anonfun$handleTaskSetFailed$1.apply(DAGScheduler.scala:831)
at org.apache.spark.scheduler.DAGScheduler$$anonfun$handleTaskSetFailed$1.apply(DAGScheduler.scala:831)
at scala.Option.foreach(Option.scala:257)
at org.apache.spark.scheduler.DAGScheduler.handleTaskSetFailed(DAGScheduler.scala:831)
at org.apache.spark.scheduler.DAGSchedulerEventProcessLoop.doOnReceive(DAGScheduler.scala:1820)
at org.apache.spark.scheduler.DAGSchedulerEventProcessLoop.onReceive(DAGScheduler.scala:1769)
at org.apache.spark.scheduler.DAGSchedulerEventProcessLoop.onReceive(DAGScheduler.scala:1758)
at org.apache.spark.util.EventLoop$$anon$1.run(EventLoop.scala:48)
at org.apache.spark.scheduler.DAGScheduler.runJob(DAGScheduler.scala:642)
at org.apache.spark.SparkContext.runJob(SparkContext.scala:2027)
at org.apache.spark.SparkContext.runJob(SparkContext.scala:2048)
at org.apache.spark.SparkContext.runJob(SparkContext.scala:2067)
at org.apache.spark.api.python.PythonRDD$.runJob(PythonRDD.scala:141)
at org.apache.spark.api.python.PythonRDD.runJob(PythonRDD.scala)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:498)
at py4j.reflection.MethodInvoker.invoke(MethodInvoker.java:244)
at py4j.reflection.ReflectionEngine.invoke(ReflectionEngine.java:357)
at py4j.Gateway.invoke(Gateway.java:282)
at py4j.commands.AbstractCommand.invokeMethod(AbstractCommand.java:132)
at py4j.commands.CallCommand.execute(CallCommand.java:79)
at py4j.GatewayConnection.run(GatewayConnection.java:214)
at java.lang.Thread.run(Thread.java:748)
Caused by: java.net.SocketException: Connection reset by peer: socket write error
at java.net.SocketOutputStream.socketWrite0(Native Method)
at java.net.SocketOutputStream.socketWrite(SocketOutputStream.java:111)
at java.net.SocketOutputStream.write(SocketOutputStream.java:155)
at java.io.BufferedOutputStream.write(BufferedOutputStream.java:122)
at java.io.DataOutputStream.write(DataOutputStream.java:107)
at java.io.FilterOutputStream.write(FilterOutputStream.java:97)
at org.apache.spark.api.python.PythonRDD$.org$apache$spark$api$python$PythonRDD$$write$1(PythonRDD.scala:192)
at org.apache.spark.api.python.PythonRDD$$anonfun$writeIteratorToStream$1.apply(PythonRDD.scala:204)
at org.apache.spark.api.python.PythonRDD$$anonfun$writeIteratorToStream$1.apply(PythonRDD.scala:204)
at scala.collection.Iterator$class.foreach(Iterator.scala:893)
at org.apache.spark.api.python.SerDeUtil$AutoBatchedPickler.foreach(SerDeUtil.scala:148)
at org.apache.spark.api.python.PythonRDD$.writeIteratorToStream(PythonRDD.scala:204)
at org.apache.spark.api.python.PythonRunner$$anon$2.writeIteratorToStream(PythonRunner.scala:407)
at org.apache.spark.api.python.BasePythonRunner$WriterThread$$anonfun$run$1.apply(PythonRunner.scala:215)
at org.apache.spark.util.Utils$.logUncaughtExceptions(Utils.scala:1988)
at org.apache.spark.api.python.BasePythonRunner$WriterThread.run(PythonRunner.scala:170)