REQUIRED for all errors and issues:
a) GATK version used: gatk4-mitochondria-pipeline/1.1.0/
b) Exact command used: java -jar cromwell-33.1.jar run ./gatk4-mitochondria-pipeline/mitochondria-pipeline.wdl --inputs ./gatk4-mitochondria-pipeline/mitochondria-pipeline.inputs.local.json 
c) Entire program log: 

 java -jar cromwell-33.1.jar run ./gatk4-mitochondria-pipeline/mitochondria-pipeline.wdl --inputs ./gatk4-mitochondria-pipeline/mitochondria-pipeline.inputs.local.json 
Picked up _JAVA_OPTIONS: -Xmx64G
[2022-03-08 10:08:22,77] [info] Running with database db.url = jdbc:hsqldb:mem:106e419f-3004-4ca8-b8be-16ae1479c715;shutdown=false;hsqldb.tx=mvcc
[2022-03-08 10:08:28,06] [info] Running migration RenameWorkflowOptionsInMetadata with a read batch size of 100000 and a write batch size of 100000
[2022-03-08 10:08:28,07] [info] [RenameWorkflowOptionsInMetadata] 100%
[2022-03-08 10:08:28,12] [info] Running with database db.url = jdbc:hsqldb:mem:cd438e5b-ef38-42ea-8335-f1bf07b7f4c1;shutdown=false;hsqldb.tx=mvcc
[2022-03-08 10:08:28,37] [info] Slf4jLogger started
[2022-03-08 10:08:28,53] [info] Workflow heartbeat configuration:
{
  "cromwellId" : "cromid-0c6604b",
  "heartbeatInterval" : "2 minutes",
  "ttl" : "10 minutes",
  "writeBatchSize" : 10000,
  "writeThreshold" : 10000
}
[2022-03-08 10:08:28,56] [info] Metadata summary refreshing every 2 seconds.
[2022-03-08 10:08:28,58] [info] KvWriteActor configured to flush with batch size 200 and process rate 5 seconds.
[2022-03-08 10:08:28,58] [info] WriteMetadataActor configured to flush with batch size 200 and process rate 5 seconds.
[2022-03-08 10:08:28,59] [info] CallCacheWriteActor configured to flush with batch size 100 and process rate 3 seconds.
[2022-03-08 10:08:28,96] [info] JobExecutionTokenDispenser - Distribution rate: 50 per 1 seconds.
[2022-03-08 10:08:28,97] [info] SingleWorkflowRunnerActor: Submitting workflow
[2022-03-08 10:08:29,00] [info] Unspecified type (Unspecified version) workflow 90228a49-6fd4-4627-9752-7c3b92eb674e submitted
[2022-03-08 10:08:29,02] [info] SingleWorkflowRunnerActor: Workflow submitted 90228a49-6fd4-4627-9752-7c3b92eb674e
[2022-03-08 10:08:29,02] [info] 1 new workflows fetched
[2022-03-08 10:08:29,02] [info] WorkflowManagerActor Starting workflow 90228a49-6fd4-4627-9752-7c3b92eb674e
[2022-03-08 10:08:29,02] [info] WorkflowManagerActor Successfully started WorkflowActor-90228a49-6fd4-4627-9752-7c3b92eb674e
[2022-03-08 10:08:29,02] [info] Retrieved 1 workflows from the WorkflowStoreActor
[2022-03-08 10:08:29,03] [warn] SingleWorkflowRunnerActor: received unexpected message: Done in state RunningSwraData
[2022-03-08 10:08:29,03] [warn] Couldn't find a suitable DSN, defaulting to a Noop one.
[2022-03-08 10:08:29,04] [info] Using noop to send events.
[2022-03-08 10:08:29,19] [info] WorkflowStoreHeartbeatWriteActor configured to flush with batch size 10000 and process rate 2 minutes.
[2022-03-08 10:08:29,19] [info] MaterializeWorkflowDescriptorActor [90228a49]: Parsing workflow as WDL 1.0
[2022-03-08 10:08:30,17] [error] WorkflowManagerActor Workflow 90228a49-6fd4-4627-9752-7c3b92eb674e failed (during MaterializingWorkflowDescriptorState): cromwell.engine.workflow.lifecycle.materialization.MaterializeWorkflowDescriptorActor$$anon$1: Workflow input processing failed:
Failed to import 'https://raw.githubusercontent.com/gatk-workflows/gatk4-mitochondria-pipeline/1.1.0/tasks/align-and-call.wdl' (reason 1 of 1): Failed to import 'https://raw.githubusercontent.com/gatk-workflows/gatk4-mitochondria-pipeline/1.1.0/tasks/alignment-pipeline.wdl' (reason 1 of 1): Unrecognized token on line 181, column 20:

    String version = read_string(stdout())
                   ^
    at cromwell.engine.workflow.lifecycle.materialization.MaterializeWorkflowDescriptorActor.cromwell$engine$workflow$lifecycle$materialization$MaterializeWorkflowDescriptorActor$$workflowInitializationFailed(MaterializeWorkflowDescriptorActor.scala:200)
    at cromwell.engine.workflow.lifecycle.materialization.MaterializeWorkflowDescriptorActor$$anonfun$2.applyOrElse(MaterializeWorkflowDescriptorActor.scala:170)
    at cromwell.engine.workflow.lifecycle.materialization.MaterializeWorkflowDescriptorActor$$anonfun$2.applyOrElse(MaterializeWorkflowDescriptorActor.scala:165)
    at scala.runtime.AbstractPartialFunction.apply(AbstractPartialFunction.scala:34)
    at akka.actor.FSM.processEvent(FSM.scala:665)
    at akka.actor.FSM.processEvent$(FSM.scala:662)
    at cromwell.engine.workflow.lifecycle.materialization.MaterializeWorkflowDescriptorActor.akka$actor$LoggingFSM$$super$processEvent(MaterializeWorkflowDescriptorActor.scala:123)
    at akka.actor.LoggingFSM.processEvent(FSM.scala:801)
    at akka.actor.LoggingFSM.processEvent$(FSM.scala:783)
    at cromwell.engine.workflow.lifecycle.materialization.MaterializeWorkflowDescriptorActor.processEvent(MaterializeWorkflowDescriptorActor.scala:123)
    at akka.actor.FSM.akka$actor$FSM$$processMsg(FSM.scala:659)
    at akka.actor.FSM$$anonfun$receive$1.applyOrElse(FSM.scala:653)
    at akka.actor.Actor.aroundReceive(Actor.scala:514)
    at akka.actor.Actor.aroundReceive$(Actor.scala:512)
    at cromwell.engine.workflow.lifecycle.materialization.MaterializeWorkflowDescriptorActor.aroundReceive(MaterializeWorkflowDescriptorActor.scala:123)
    at akka.actor.ActorCell.receiveMessage(ActorCell.scala:527)
    at akka.actor.ActorCell.invoke(ActorCell.scala:496)
    at akka.dispatch.Mailbox.processMailbox(Mailbox.scala:257)
    at akka.dispatch.Mailbox.run(Mailbox.scala:224)
    at akka.dispatch.Mailbox.exec(Mailbox.scala:234)
    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)

[2022-03-08 10:08:30,17] [info] WorkflowManagerActor WorkflowActor-90228a49-6fd4-4627-9752-7c3b92eb674e is in a terminal state: WorkflowFailedState
[2022-03-08 10:08:35,33] [info] SingleWorkflowRunnerActor workflow finished with status 'Failed'.
[2022-03-08 10:08:38,59] [info] Workflow polling stopped
[2022-03-08 10:08:38,59] [info] Shutting down WorkflowStoreActor - Timeout = 5 seconds
[2022-03-08 10:08:38,60] [info] Shutting down WorkflowLogCopyRouter - Timeout = 5 seconds
[2022-03-08 10:08:38,60] [info] Aborting all running workflows.
[2022-03-08 10:08:38,60] [info] Shutting down JobExecutionTokenDispenser - Timeout = 5 seconds
[2022-03-08 10:08:38,60] [info] JobExecutionTokenDispenser stopped
[2022-03-08 10:08:38,60] [info] WorkflowStoreActor stopped
[2022-03-08 10:08:38,60] [info] WorkflowLogCopyRouter stopped
[2022-03-08 10:08:38,60] [info] Shutting down WorkflowManagerActor - Timeout = 3600 seconds
[2022-03-08 10:08:38,60] [info] WorkflowManagerActor All workflows finished
[2022-03-08 10:08:38,60] [info] WorkflowManagerActor stopped
[2022-03-08 10:08:38,60] [info] Connection pools shut down
[2022-03-08 10:08:38,60] [info] Shutting down SubWorkflowStoreActor - Timeout = 1800 seconds
[2022-03-08 10:08:38,60] [info] Shutting down JobStoreActor - Timeout = 1800 seconds
[2022-03-08 10:08:38,60] [info] SubWorkflowStoreActor stopped
[2022-03-08 10:08:38,60] [info] Shutting down CallCacheWriteActor - Timeout = 1800 seconds
[2022-03-08 10:08:38,60] [info] Shutting down ServiceRegistryActor - Timeout = 1800 seconds
[2022-03-08 10:08:38,60] [info] CallCacheWriteActor Shutting down: 0 queued messages to process
[2022-03-08 10:08:38,60] [info] JobStoreActor stopped
[2022-03-08 10:08:38,61] [info] CallCacheWriteActor stopped
[2022-03-08 10:08:38,61] [info] Shutting down DockerHashActor - Timeout = 1800 seconds
[2022-03-08 10:08:38,61] [info] Shutting down IoProxy - Timeout = 1800 seconds
[2022-03-08 10:08:38,61] [info] WriteMetadataActor Shutting down: 0 queued messages to process
[2022-03-08 10:08:38,61] [info] KvWriteActor Shutting down: 0 queued messages to process
[2022-03-08 10:08:38,61] [info] DockerHashActor stopped
[2022-03-08 10:08:38,61] [info] ServiceRegistryActor stopped
[2022-03-08 10:08:38,61] [info] IoProxy stopped
[2022-03-08 10:08:38,62] [info] Database closed
[2022-03-08 10:08:38,62] [info] Stream materializer shut down
Workflow 90228a49-6fd4-4627-9752-7c3b92eb674e transitioned to state Failed
[2022-03-08 10:08:38,64] [info] Automatic shutdown of the async connection
[2022-03-08 10:08:38,64] [info] Gracefully shutdown sentry threads.
[2022-03-08 10:08:38,64] [info] Shutdown finished.

Dear GATK Support Team,

running a local wdl cromwell instance to execute the GATK mitochondria pipeline gives following error message:

Failed to import 'https://raw.githubusercontent.com/gatk-workflows/gatk4-mitochondria-pipeline/1.1.0/tasks/align-and-call.wdl' (reason 1 of 1): Failed to import 'https://raw.githubusercontent.com/gatk-workflows/gatk4-mitochondria-pipeline/1.1.0/tasks/alignment-pipeline.wdl' (reason 1 of 1): Unrecognized token on line 181, column 20...

The download of the file using wget on the command line works and in principle the file accessible through the internet. Further for running the local instance all the mtDNA reference data was downloaded locally and set in the input json. 

Looking forward for your support and reply regarding this issue. Many thanks in advance.

See forum topic details at forum guidelines page: https://gatk.broadinstitute.org/hc/en-us/articles/360053845952-Forum-Guidelines