Deciding to continue to the Joint Genotyping workflow from the Running GATK Best Practices Google tutorial, I came across the error below. The error has been addressed in a previous issue. The solution that worked for the user is this:

java -Dsystem.input-read-limits.lines=500000 -jar /cromwell-34.jar

If this is still the recommended solution, where would I add this modification given that this is running on the Google Cloud Platform?

Command run: 

$ gcloud alpha genomics pipelines run --pipeline-file wdl_pipeline.yaml --regions us-central1 --inputs-from-file WDL=${GATK_GOOGLE_DIR}/JointGenotypingWf.wdl,WORKFLOW_INPUTS=${GATK_GOOGLE_DIR}/JointGenotypingWf.hg38.inputs.json,WORKFLOW_OPTIONS=${GATK_GOOGLE_DIR}/JointGenotypingWf.options.json --env-vars WORKSPACE=${GATK_OUTPUT_DIR}/work,OUTPUTS=${GATK_OUTPUT_DIR}/output --logging ${GATK_OUTPUT_DIR}/logging/

End of error log: 

2020-05-02 21:05:32,203 cromwell-system-akka.dispatchers.engine-dispatcher-28 INFO - Not triggering log of token queue status. Effective log interval = None
2020-05-02 21:05:32,270 cromwell_driver INFO: Job submitted to Cromwell. job id: 9eec64d6-5959-4c27-8a13-6b57ffbe034a
2020-05-02 21:05:48,283 cromwell-system-akka.dispatchers.engine-dispatcher-9 INFO - 1 new workflows fetched
2020-05-02 21:05:48,284 cromwell-system-akka.dispatchers.engine-dispatcher-9 INFO - WorkflowManagerActor Starting workflow UUID(9eec64d6-5959-4c27-8a13-6b57ffbe034a)
2020-05-02 21:05:48,288 cromwell-system-akka.dispatchers.engine-dispatcher-9 INFO - WorkflowManagerActor Successfully started WorkflowActor-9eec64d6-5959-4c27-8a13-6b57ffbe034a
2020-05-02 21:05:48,291 cromwell-system-akka.dispatchers.engine-dispatcher-9 INFO - Retrieved 1 workflows from the WorkflowStoreActor
2020-05-02 21:05:48,300 cromwell-system-akka.dispatchers.engine-dispatcher-30 INFO - WorkflowStoreHeartbeatWriteActor configured to flush with batch size 10000 and process rate 2 minutes.
2020-05-02 21:05:48,592 cromwell-system-akka.dispatchers.engine-dispatcher-29 INFO - MaterializeWorkflowDescriptorActor [UUID(9eec64d6)]: Parsing workflow as WDL draft-2
2020-05-02 21:05:50,495 cromwell-system-akka.dispatchers.engine-dispatcher-29 INFO - MaterializeWorkflowDescriptorActor [UUID(9eec64d6)]: Call-to-Backend assignments: JointGenotyping.SNPGatherTranches -> JES, JointGenotyping.FinalGatherVcf -> JES, JointGenotyping.SNPsVariantRecalibratorCreateModel -> JES, JointGenotyping.IndelsVariantRecalibrator -> JES, JointGenotyping.SNPsVariantRecalibratorScattered -> JES, JointGenotyping.CollectMetricsOnFullVcf -> JES, JointGenotyping.HardFilterAndMakeSitesOnlyVcf -> JES, JointGenotyping.SNPsVariantRecalibratorClassic -> JES, JointGenotyping.DynamicallyCombineIntervals -> JES, JointGenotyping.CollectMetricsSharded -> JES, JointGenotyping.ApplyRecalibration -> JES, JointGenotyping.GenotypeGVCFs -> JES, JointGenotyping.GatherMetrics -> JES, JointGenotyping.SitesOnlyGatherVcf -> JES, JointGenotyping.ImportGVCFs -> JES
2020-05-02 21:06:09,092 cromwell-system-akka.dispatchers.engine-dispatcher-29 ERROR - WorkflowManagerActor Workflow 9eec64d6-5959-4c27-8a13-6b57ffbe034a failed (during ExecutingWorkflowState): java.lang.RuntimeException: Failed to evaluate 'JointGenotyping.num_of_original_intervals' (reason 1 of 1): Evaluating length(read_lines(unpadded_intervals_file)) failed: [Attempted 1 time(s)] - IOException: Could not read from gs://gatk-test-data/intervals/hg38.even.handcurated.20k.intervals: File gs://gatk-test-data/intervals/hg38.even.handcurated.20k.intervals is larger than 128000 Bytes. Maximum read limits can be adjusted in the configuration under system.input-read-limits.
at cromwell.engine.workflow.lifecycle.execution.keys.ExpressionKey.processRunnable(ExpressionKey.scala:29)
at cromwell.engine.workflow.lifecycle.execution.WorkflowExecutionActor.$anonfun$startRunnableNodes$7(WorkflowExecutionActor.scala:523)
at cats.instances.ListInstances$$anon$1.$anonfun$traverse$2(list.scala:74)
at cats.instances.ListInstances$$anon$1.loop$2(list.scala:64)
at cats.instances.ListInstances$$anon$1.$anonfun$foldRight$1(list.scala:64)
at cats.Eval$.loop$1(Eval.scala:336)
at cats.Eval$.cats$Eval$$evaluate(Eval.scala:368)
at cats.Eval$Defer.value(Eval.scala:257)
at cats.instances.ListInstances$$anon$1.traverse(list.scala:73)
at cats.instances.ListInstances$$anon$1.traverse(list.scala:12)
at cats.Traverse$Ops.traverse(Traverse.scala:19)
at cats.Traverse$Ops.traverse$(Traverse.scala:19)
at cats.Traverse$ToTraverseOps$$anon$3.traverse(Traverse.scala:19)
at cromwell.engine.workflow.lifecycle.execution.WorkflowExecutionActor.cromwell$engine$workflow$lifecycle$execution$WorkflowExecutionActor$$startRunnableNodes(WorkflowExecutionActor.scala:517)
at cromwell.engine.workflow.lifecycle.execution.WorkflowExecutionActor$$anonfun$5.applyOrElse(WorkflowExecutionActor.scala:188)
at cromwell.engine.workflow.lifecycle.execution.WorkflowExecutionActor$$anonfun$5.applyOrElse(WorkflowExecutionActor.scala:186)
at scala.PartialFunction$OrElse.apply(PartialFunction.scala:168)
at akka.actor.FSM.processEvent(FSM.scala:687)
at akka.actor.FSM.processEvent$(FSM.scala:681)
at cromwell.engine.workflow.lifecycle.execution.WorkflowExecutionActor.akka$actor$LoggingFSM$$super$processEvent(WorkflowExecutionActor.scala:51)
at akka.actor.LoggingFSM.processEvent(FSM.scala:820)
at akka.actor.LoggingFSM.processEvent$(FSM.scala:802)
at cromwell.engine.workflow.lifecycle.execution.WorkflowExecutionActor.processEvent(WorkflowExecutionActor.scala:51)
at akka.actor.FSM.akka$actor$FSM$$processMsg(FSM.scala:678)
at akka.actor.FSM$$anonfun$receive$1.applyOrElse(FSM.scala:672)
at akka.actor.Actor.aroundReceive(Actor.scala:517)
at akka.actor.Actor.aroundReceive$(Actor.scala:515)
at cromwell.engine.workflow.lifecycle.execution.WorkflowExecutionActor.akka$actor$Timers$$super$aroundReceive(WorkflowExecutionActor.scala:51)
at akka.actor.Timers.aroundReceive(Timers.scala:51)
at akka.actor.Timers.aroundReceive$(Timers.scala:40)
at cromwell.engine.workflow.lifecycle.execution.WorkflowExecutionActor.aroundReceive(WorkflowExecutionActor.scala:51)
at akka.actor.ActorCell.receiveMessage(ActorCell.scala:588)
at akka.actor.ActorCell.invoke(ActorCell.scala:557)
at akka.dispatch.Mailbox.processMailbox(Mailbox.scala:258)
at akka.dispatch.Mailbox.run(Mailbox.scala:225)
at akka.dispatch.Mailbox.exec(Mailbox.scala:235)
at akka.dispatch.forkjoin.ForkJoinTask.doExec(ForkJoinTask.java:260)
at akka.dispatch.forkjoin.ForkJoinPool$WorkQueue.runTask(ForkJoinPool.java:1339)
at akka.dispatch.forkjoin.ForkJoinPool.runWorker(ForkJoinPool.java:1979)
at akka.dispatch.forkjoin.ForkJoinWorkerThread.run(ForkJoinWorkerThread.java:107)

2020-05-02 21:06:09,120 cromwell-system-akka.dispatchers.engine-dispatcher-29 INFO - WorkflowManagerActor WorkflowActor-9eec64d6-5959-4c27-8a13-6b57ffbe034a is in a terminal state: WorkflowFailedState
ERROR: Status of job is not Submitted, Running, or Succeeded: Failed