Google Dataflow batch job reading from Pub Sub - google-cloud-dataflow

Question

I'm having trouble running a dataflow pipeline in batch mode using PubsubIO.Read as the source. I have tried using both .maxNumRecords and .maxReadTime in order to make it a bounded collection. However, my job hangs on the read step and I get Socket Timeout Exceptions. Only when I publish a message to the topic while the job is running does it process queued messages. I was under the impression that if I specify a subscription for the pipeline that it would process any messages that it missed on startup. I'm using the Dataflow SDK 1.9 for Java. Below is a snippet of my code.
AuditPipelineOptions options = PipelineOptionsFactory.fromArgs(args).withValidation()
.as(AuditPipelineOptions.class);
options.setRunner(TemplatingDataflowPipelineRunner.class);
Pipeline p = Pipeline.create(options);
p.apply(PubsubIO.Read.subscription(options.getPubSubSubscription()).withCoder(StringUtf8Coder.of()).maxReadTime(new Duration(1000 * 60)))
.apply(ParDo.of(new CreateEntitiesFn(options.getNamespace(),options.getIgnoreKeys())))
.apply(DatastoreIO.v1().write().withProjectId(options.getProject()));
p.run();
Here is the full exception:
exception thrown while executing request
java.net.SocketTimeoutException: Read timed out
at java.net.SocketInputStream.socketRead0(Native Method)
at java.net.SocketInputStream.socketRead(SocketInputStream.java:116)
at java.net.SocketInputStream.read(SocketInputStream.java:170)
at java.net.SocketInputStream.read(SocketInputStream.java:141)
at sun.security.ssl.InputRecord.readFully(InputRecord.java:465)
at sun.security.ssl.InputRecord.read(InputRecord.java:503)
at sun.security.ssl.SSLSocketImpl.readRecord(SSLSocketImpl.java:983)
at sun.security.ssl.SSLSocketImpl.readDataRecord(SSLSocketImpl.java:940)
at sun.security.ssl.AppInputStream.read(AppInputStream.java:105)
at java.io.BufferedInputStream.fill(BufferedInputStream.java:246)
at java.io.BufferedInputStream.read1(BufferedInputStream.java:286)
at java.io.BufferedInputStream.read(BufferedInputStream.java:345)
at sun.net.www.http.HttpClient.parseHTTPHeader(HttpClient.java:704)
at sun.net.www.http.HttpClient.parseHTTP(HttpClient.java:647)
at sun.net.www.protocol.http.HttpURLConnection.getInputStream0(HttpURLConnection.java:1536)
at sun.net.www.protocol.http.HttpURLConnection.getInputStream(HttpURLConnection.java:1441)
at java.net.HttpURLConnection.getResponseCode(HttpURLConnection.java:480)
at sun.net.www.protocol.https.HttpsURLConnectionImpl.getResponseCode(HttpsURLConnectionImpl.java:338)
at com.google.api.client.http.javanet.NetHttpResponse.<init>(NetHttpResponse.java:37)
at com.google.api.client.http.javanet.NetHttpRequest.execute(NetHttpRequest.java:94)
at com.google.api.client.http.HttpRequest.execute(HttpRequest.java:981)
at com.google.api.client.googleapis.services.AbstractGoogleClientRequest.executeUnparsed(AbstractGoogleClientRequest.java:419)
at com.google.api.client.googleapis.services.AbstractGoogleClientRequest.executeUnparsed(AbstractGoogleClientRequest.java:352)
at com.google.api.client.googleapis.services.AbstractGoogleClientRequest.execute(AbstractGoogleClientRequest.java:469)
at com.google.cloud.dataflow.sdk.util.PubsubJsonClient.pull(PubsubJsonClient.java:171)
at com.google.cloud.dataflow.sdk.io.PubsubIO$Read$Bound$PubsubReader.processElement(PubsubIO.java:886)
at com.google.cloud.dataflow.sdk.util.SimpleDoFnRunner.invokeProcessElement(SimpleDoFnRunner.java:49)
at com.google.cloud.dataflow.sdk.util.DoFnRunnerBase.processElement(DoFnRunnerBase.java:139)
at com.google.cloud.dataflow.sdk.runners.worker.SimpleParDoFn.processElement(SimpleParDoFn.java:188)
at com.google.cloud.dataflow.sdk.runners.worker.ForwardingParDoFn.processElement(ForwardingParDoFn.java:42)
at com.google.cloud.dataflow.sdk.runners.worker.DataflowWorkerLoggingParDoFn.processElement(DataflowWorkerLoggingParDoFn.java:47)
at com.google.cloud.dataflow.sdk.util.common.worker.ParDoOperation.process(ParDoOperation.java:55)
at com.google.cloud.dataflow.sdk.util.common.worker.OutputReceiver.process(OutputReceiver.java:52)
at com.google.cloud.dataflow.sdk.util.common.worker.ReadOperation.runReadLoop(ReadOperation.java:221)
at com.google.cloud.dataflow.sdk.util.common.worker.ReadOperation.start(ReadOperation.java:182)
at com.google.cloud.dataflow.sdk.util.common.worker.MapTaskExecutor.execute(MapTaskExecutor.java:69)
at com.google.cloud.dataflow.sdk.runners.worker.DataflowWorker.executeWork(DataflowWorker.java:285)
at com.google.cloud.dataflow.sdk.runners.worker.DataflowWorker.doWork(DataflowWorker.java:221)
at com.google.cloud.dataflow.sdk.runners.worker.DataflowWorker.getAndPerformWork(DataflowWorker.java:171)
at com.google.cloud.dataflow.sdk.runners.worker.DataflowWorkerHarness$WorkerThread.doWork(DataflowWorkerHarness.java:192)
at com.google.cloud.dataflow.sdk.runners.worker.DataflowWorkerHarness$WorkerThread.call(DataflowWorkerHarness.java:172)
at com.google.cloud.dataflow.sdk.runners.worker.DataflowWorkerHarness$WorkerThread.call(DataflowWorkerHarness.java:159)
at java.util.concurrent.FutureTask.run(FutureTask.java:266)
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
at java.lang.Thread.run(Thread.java:745)
Sample Job ID: 2017-05-17_12_07_37-2442852182886580802