search

broadinstitute / cromwell

Scientific workflow engine designed for simplicity & scalability. Trivially transition between one off use cases to massive scale production environments
http://cromwell.readthedocs.io/
BSD 3-Clause "New" or "Revised" License
988 stars 357 forks source link

sra not recognized as a valid filesytem #5793

Closed njbernstein closed 4 years ago

njbernstein commented 4 years ago

I cant get the sra filesystem to work. Here is the error:

[2020-08-21 11:08:59,62] [info] WorkflowManagerActor Workflow dbd5cdc0-c79a-42cd-b929-56ddb1115467 failed (during InitializingWorkflowState): common.exception.AggregatedMessageException: Failed to instantiate backend filesystem:
Cannot find a filesystem with name sra in the configuration. Available filesystems: ftp, s3, gcs, oss, drs, http
    at common.validation.Validation$ValidationChecked$.$anonfun$unsafe$2(Validation.scala:98)
    at cats.syntax.EitherOps$.valueOr$extension(either.scala:66)
    at common.validation.Validation$ValidationChecked$.unsafe$extension(Validation.scala:98)
    at cromwell.backend.BackendConfigurationDescriptor.configuredPathBuilderFactories$lzycompute(backend.scala:109)
    at cromwell.backend.BackendConfigurationDescriptor.configuredPathBuilderFactories(backend.scala:108)
    at cromwell.backend.BackendConfigurationDescriptor.pathBuilders(backend.scala:120)
    at cromwell.backend.standard.StandardInitializationActor.pathBuilders$lzycompute(StandardInitializationActor.scala:62)
    at cromwell.backend.standard.StandardInitializationActor.pathBuilders(StandardInitializationActor.scala:62)
    at cromwell.backend.google.pipelines.common.PipelinesApiInitializationActor.$anonfun$workflowPaths$2(PipelinesApiInitializationActor.scala:137)
    at scala.concurrent.Future.$anonfun$flatMap$1(Future.scala:307)
    at scala.concurrent.impl.Promise.$anonfun$transformWith$1(Promise.scala:41)
    at scala.concurrent.impl.CallbackRunnable.run(Promise.scala:64)
    at akka.dispatch.BatchingExecutor$AbstractBatch.processBatch(BatchingExecutor.scala:55)
    at akka.dispatch.BatchingExecutor$BlockableBatch.$anonfun$run$1(BatchingExecutor.scala:92)
    at scala.runtime.java8.JFunction0$mcV$sp.apply(JFunction0$mcV$sp.java:23)
    at scala.concurrent.BlockContext$.withBlockContext(BlockContext.scala:85)
    at akka.dispatch.BatchingExecutor$BlockableBatch.run(BatchingExecutor.scala:92)
    at akka.dispatch.TaskInvocation.run(AbstractDispatcher.scala:41)
    at akka.dispatch.ForkJoinExecutorConfigurator$AkkaForkJoinTask.exec(ForkJoinExecutorConfigurator.scala:49)
    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)

[2020-08-21 11:08:59,66] [info] WorkflowManagerActor WorkflowActor-dbd5cdc0-c79a-42cd-b929-56ddb1115467 is in a terminal state: WorkflowFailedState
[2020-08-21 11:09:00,66] [info] Not triggering log of token queue status. Effective log interval = None

Here is the relevant part of the wdl:

backend {
  default = PAPIv2
  providers {
    PAPIv2 {
      actor-factory = "cromwell.backend.google.pipelines.v2beta.PipelinesApiLifecycleActorFactory"
      config {
      concurrent-job-limit = 10000
      max-concurrent-workflows = 10000
      genomics-api-queries-per-100-seconds = 10000
      maximum-polling-interval = 300
      max-workflow-launch-count = 2000
// Google project
project = "calico-uk-biobank"
compute-service-account = "default"
// Base bucket for workflow executions
root = "nicholas-b-test"
// Polling for completion backs-off gradually for slower-running jobs.
// This is the maximum polling interval (in seconds):

// Optional Dockerhub Credentials. Can be used to access private docker images.
dockerhub {
  // account = ""
  // token = ""
}
genomics {
  // A reference to an auth defined in the `google` stanza at the top.  This auth is used to create
  // Pipelines and manipulate auth JSONs.
  auth = "application-default"
  // Endpoint for APIs, no reason to change this unless directed by Google.
  endpoint-url = "https://genomics.googleapis.com/"
}
filesystems {
  gcs {
    // A reference to a potentially different auth for manipulating files via engine functions.
    auth = "application-default"
  }
  sra {
class = "cromwell.filesystems.sra.SraPathBuilderFactory"
docker-image = "fusera/fusera:alpine"
ngc = "didnt want to put this up online"
  }
}
}
}
}
}

I ran this with cromwell 52. Any suggestions would be appreciated

njbernstein commented 4 years ago

Any thoughts here?

cjllanwarne commented 4 years ago

Answered on slack but for posterity:

According to the original PR, the sra filesystem should be referenced in the root filesystems stanza, not the one inside the PAPI filesystem. You might also need to add it inside the PAPI filesystem config too to enable it, but most of the config mentioned here (class, docker-image, ngc) looks like it belongs at the root level.

njbernstein commented 4 years ago

@cjllanwarne Thanks so much for your response.

I am unfortunately getting a new error. Which is as follows:

[2020-08-24 15:28:47,48] [error] 'nioPath' not implemented for SraPath
java.lang.UnsupportedOperationException: 'nioPath' not implemented for SraPath
    at cromwell.filesystems.sra.SraPath.nioPath(SraPathBuilder.scala:31)
    at cromwell.core.path.Path.nioPathPrivate(PathBuilder.scala:113)
    at cromwell.core.path.Path.nioPathPrivate$(PathBuilder.scala:113)
    at cromwell.filesystems.sra.SraPath.nioPathPrivate(SraPathBuilder.scala:26)
    at cromwell.core.path.PathObjectMethods.hashCode(PathObjectMethods.scala:18)
    at cromwell.core.path.PathObjectMethods.hashCode$(PathObjectMethods.scala:18)
    at cromwell.filesystems.sra.SraPath.hashCode(SraPathBuilder.scala:26)
    at scala.runtime.Statics.anyHash(Statics.java:122)
    at scala.util.hashing.MurmurHash3.productHash(MurmurHash3.scala:68)
    at scala.util.hashing.MurmurHash3$.productHash(MurmurHash3.scala:215)
    at scala.runtime.ScalaRunTime$._hashCode(ScalaRunTime.scala:149)
    at cromwell.core.io.DefaultIoCommand$DefaultIoSizeCommand.hashCode(DefaultIoCommand.scala:14)
    at scala.runtime.Statics.anyHash(Statics.java:122)
    at scala.util.hashing.MurmurHash3.productHash(MurmurHash3.scala:68)
    at scala.util.hashing.MurmurHash3$.productHash(MurmurHash3.scala:215)
    at scala.runtime.ScalaRunTime$._hashCode(ScalaRunTime.scala:149)
    at cromwell.core.io.IoPromiseProxyActor$IoCommandWithPromise.hashCode(IoPromiseProxyActor.scala:11)
    at com.google.common.base.Equivalence$Equals.doHash(Equivalence.java:348)
    at com.google.common.base.Equivalence.hash(Equivalence.java:112)
    at com.google.common.cache.LocalCache.hash(LocalCache.java:1696)
    at com.google.common.cache.LocalCache.getIfPresent(LocalCache.java:3956)
    at com.google.common.cache.LocalCache$LocalManualCache.getIfPresent(LocalCache.java:4865)
    at cromwell.engine.io.IoActorProxy$$anonfun$receive$1.applyOrElse(IoActorProxy.scala:25)
    at akka.actor.Actor.aroundReceive(Actor.scala:539)
    at akka.actor.Actor.aroundReceive$(Actor.scala:537)
    at cromwell.engine.io.IoActorProxy.aroundReceive(IoActorProxy.scala:16)
    at akka.actor.ActorCell.receiveMessage(ActorCell.scala:612)
    at akka.actor.ActorCell.invoke(ActorCell.scala:581)
    at akka.dispatch.Mailbox.processMailbox(Mailbox.scala:268)
    at akka.dispatch.Mailbox.run(Mailbox.scala:229)
    at akka.dispatch.Mailbox.exec(Mailbox.scala:241)
    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)

I tried reading the code but I don't know scala so did not get very far: https://github.com/broadinstitute/cromwell/blob/f1cce2cd2723b849c4d8f285510f30913ec188a0/filesystems/sra/src/main/scala/cromwell/filesystems/sra/SraPathBuilder.scala

The input I feed in the following:

  "Mutect2.tumor_reads": "sra://SRR9247315/NWD751606.b38.irc.v1.cram",

The whole json input looks like this:

{
  "Mutect2.gatk_docker": "broadinstitute/gatk:4.1.4.1",

  "Mutect2.intervals": "gs://gatk-best-practices/somatic-b37/whole_exome_agilent_1.1_refseq_plus_3_boosters.Homo_sapiens_assembly19.baits.interval_list",
  "Mutect2.scatter_count": 50,
  "Mutect2.m2_extra_args": "--downsampling-stride 20 --max-reads-per-alignment-start 6 --max-suspicious-reads-per-alignment-start 6",
  "Mutect2.filter_funcotations": "True",
  "Mutect2.funco_reference_version": "hg19",
  "Mutect2.funco_data_sources_tar_gz": "gs://broad-public-datasets/funcotator/funcotator_dataSources.v1.6.20190124s.tar.gz",
  "Mutect2.funco_transcript_selection_list": "gs://broad-public-datasets/funcotator/transcriptList.exact_uniprot_matches.AKT1_CRLF2_FGFR1.txt",

  "Mutect2.ref_fasta": "gs://gatk-best-practices/somatic-b37/Homo_sapiens_assembly19.fasta",
  "Mutect2.ref_dict": "gs://gatk-best-practices/somatic-b37/Homo_sapiens_assembly19.dict",
  "Mutect2.ref_fai": "gs://gatk-best-practices/somatic-b37/Homo_sapiens_assembly19.fasta.fai",
  "Mutect2.tumor_reads": "sra://SRR9247315/NWD751606.b38.irc.v1.cram",
  "Mutect2.tumor_reads_index": "sra://SRR9247315/NWD751606NWD751606.b38.irc.v1.cram.crai",

  "Mutect2.pon": "gs://gatk-best-practices/somatic-b37/Mutect2-exome-panel.vcf",
  "Mutect2.pon_idx": "gs://gatk-best-practices/somatic-b37/Mutect2-exome-panel.vcf.idx",
  "Mutect2.gnomad": "gs://gatk-best-practices/somatic-b37/af-only-gnomad.raw.sites.vcf",
  "Mutect2.gnomad_idx": "gs://gatk-best-practices/somatic-b37/af-only-gnomad.raw.sites.vcf.idx",
  "Mutect2.variants_for_contamination": "gs://gatk-best-practices/somatic-b37/small_exac_common_3.vcf",
  "Mutect2.variants_for_contamination_idx": "gs://gatk-best-practices/somatic-b37/small_exac_common_3.vcf.idx",
  "Mutect2.realignment_index_bundle": "gs://gatk-test-data/mutect2/Homo_sapiens_assembly38.index_bundle"
}
njbernstein commented 4 years ago

The path seems like it should be fine according to: https://github.com/broadinstitute/cromwell/blob/f1cce2cd2723b849c4d8f285510f30913ec188a0/filesystems/sra/src/test/scala/cromwell/filesystems/sra/SraPathBuilderSpec.scala

njbernstein commented 4 years ago

Alright so if I have a sra stanza in the engine portion of the config I get the error from above.

If I remove it and only keep the sra stanza in the top level filesystems part of the config and an sra stanza in the backend filesystems portion of the config I then get the following error:

[2020-08-24 17:31:17,07] [info] WorkflowManagerActor Workflow fbc40d55-a668-4fd8-982c-e53333ad04f5 failed (during ExecutingWorkflowState): java.lang.RuntimeException: Failed to evaluate 'tumor_only_reads_size' (reason 1 of 1): Evaluating ceil(size(tumor_reads, "GB")) failed: java.lang.IllegalArgumentException: Could not build the path "sra://SRR2841273/SRR2841273". It may refer to a filesystem not supported by this instance of Cromwell. Supported filesystems are: Google Cloud Storage, HTTP, LinuxFileSystem. Failures: 
Google Cloud Storage: Cloud Storage URIs must have 'gs' scheme: sra://SRR2841273/SRR2841273 (IllegalArgumentException)
HTTP: sra://SRR2841273/SRR2841273 does not have an http or https scheme (IllegalArgumentException)
LinuxFileSystem: Cannot build a local path from sra://SRR2841273/SRR2841273 (RuntimeException)
 Please refer to the documentation for more information on how to configure filesystems: http://cromwell.readthedocs.io/en/develop/backends/HPC/#filesystems
    at cromwell.engine.workflow.lifecycle.execution.keys.ExpressionKey.processRunnable(ExpressionKey.scala:29)
    at cromwell.engine.workflow.lifecycle.execution.WorkflowExecutionActor.$anonfun$startRunnableNodes$7(WorkflowExecutionActor.scala:538)
    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$$anon$1.$anonfun$foldRight$1(list.scala:64)
    at cats.Eval$.loop$1(Eval.scala:338)
    at cats.Eval$.cats$Eval$$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$$anon$2.traverse(Traverse.scala:19)
    at cromwell.engine.workflow.lifecycle.execution.WorkflowExecutionActor.cromwell$engine$workflow$lifecycle$execution$WorkflowExecutionActor$$startRunnableNodes(WorkflowExecutionActor.scala:532)
    at cromwell.engine.workflow.lifecycle.execution.WorkflowExecutionActor$$anonfun$5.applyOrElse(WorkflowExecutionActor.scala:191)
    at cromwell.engine.workflow.lifecycle.execution.WorkflowExecutionActor$$anonfun$5.applyOrElse(WorkflowExecutionActor.scala:189)
    at scala.PartialFunction$OrElse.apply(PartialFunction.scala:172)
    at akka.actor.FSM.processEvent(FSM.scala:710)
    at akka.actor.FSM.processEvent$(FSM.scala:704)
    at cromwell.engine.workflow.lifecycle.execution.WorkflowExecutionActor.akka$actor$LoggingFSM$$super$processEvent(WorkflowExecutionActor.scala:52)
    at akka.actor.LoggingFSM.processEvent(FSM.scala:847)
    at akka.actor.LoggingFSM.processEvent$(FSM.scala:829)
    at cromwell.engine.workflow.lifecycle.execution.WorkflowExecutionActor.processEvent(WorkflowExecutionActor.scala:52)
    at akka.actor.FSM.akka$actor$FSM$$processMsg(FSM.scala:701)
    at akka.actor.FSM$$anonfun$receive$1.applyOrElse(FSM.scala:695)
    at akka.actor.Actor.aroundReceive(Actor.scala:539)
    at akka.actor.Actor.aroundReceive$(Actor.scala:537)
    at cromwell.engine.workflow.lifecycle.execution.WorkflowExecutionActor.akka$actor$Timers$$super$aroundReceive(WorkflowExecutionActor.scala:52)
    at akka.actor.Timers.aroundReceive(Timers.scala:51)
    at akka.actor.Timers.aroundReceive$(Timers.scala:40)
    at cromwell.engine.workflow.lifecycle.execution.WorkflowExecutionActor.aroundReceive(WorkflowExecutionActor.scala:52)
    at akka.actor.ActorCell.receiveMessage(ActorCell.scala:612)
    at akka.actor.ActorCell.invoke(ActorCell.scala:581)
    at akka.dispatch.Mailbox.processMailbox(Mailbox.scala:268)
    at akka.dispatch.Mailbox.run(Mailbox.scala:229)
    at akka.dispatch.Mailbox.exec(Mailbox.scala:241)
    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)

This leads me to believe I need somehow enable the sra filesystem

When I've tried enabled = True in both stanza that hasn't helped though. Thoughts?

njbernstein commented 4 years ago

Okay, I've made more progress. But more issues are popping up. @cjllanwarne

You cannot ask for the filesize of an sra file to configure the disk space you'd like at runtime thats what causes the [2020-08-24 15:28:47,48] [error] 'nioPath' not implemented for SraPath issue mentioned above. When I remove that line from my wdl things get better, but I'm running into two new separate issues.

  1. Cromwell tries to chmod the mounted sra directory which is not allowed. code: https://github.com/broadinstitute/cromwell/blob/5c8f932b6e1a5706286913e21c78dc296dd5c79c/supportedBackends/google/pipelines/v2alpha1/src/main/scala/cromwell/backend/google/pipelines/v2alpha1/api/ContainerSetup.scala error:

    
[2020-08-25 10:40:46,26] [info] WorkflowManagerActor Workflow 282f5595-171e-4296-a7fa-9bd9f7a2f33b failed (during ExecutingWorkflowState): java.lang.Exception: Task Mutect2.renameBamIndex:NA:1 failed. The job was stopped before the command finished. PAPI error code 9. Execution failed: generic::failed_precondition: while running "/bin/bash -c mkdir -p /cromwell_root && chmod -R a+rwx /cromwell_root": unexpected exit status 1 was not ignored
[ContainerSetup] Unexpected exit status 1 while running "/bin/bash -c mkdir -p /cromwell_root && chmod -R a+rwx /cromwell_root": chmod: changing permissions of '/cromwell_root/sra-SRR2806786': Function not implemented
chmod: changing permissions of '/cromwell_root/sra-SRR2806786/.initialized': Function not implemented

at cromwell.backend.google.pipelines.common.PipelinesApiAsyncBackendJobExecutionActor$.StandardException(PipelinesApiAsyncBackendJobExecutionActor.scala:88)
at cromwell.backend.google.pipelines.common.PipelinesApiAsyncBackendJobExecutionActor.handleFailedRunStatus$1(PipelinesApiAsyncBackendJobExecutionActor.scala:695)
at cromwell.backend.google.pipelines.common.PipelinesApiAsyncBackendJobExecutionActor.$anonfun$handleExecutionFailure$1(PipelinesApiAsyncBackendJobExecutionActor.scala:707)
at scala.util.Try$.apply(Try.scala:213)
at cromwell.backend.google.pipelines.common.PipelinesApiAsyncBackendJobExecutionActor.handleExecutionFailure(PipelinesApiAsyncBackendJobExecutionActor.scala:704)
at cromwell.backend.google.pipelines.common.PipelinesApiAsyncBackendJobExecutionActor.handleExecutionFailure(PipelinesApiAsyncBackendJobExecutionActor.scala:92)
at cromwell.backend.standard.StandardAsyncExecutionActor$$anonfun$handleExecutionResult$11.applyOrElse(StandardAsyncExecutionActor.scala:1258)
at cromwell.backend.standard.StandardAsyncExecutionActor$$anonfun$handleExecutionResult$11.applyOrElse(StandardAsyncExecutionActor.scala:1254)
at scala.concurrent.Future.$anonfun$recoverWith$1(Future.scala:417)
at scala.concurrent.impl.Promise.$anonfun$transformWith$1(Promise.scala:41)
at scala.concurrent.impl.CallbackRunnable.run(Promise.scala:64)
at akka.dispatch.BatchingExecutor$AbstractBatch.processBatch(BatchingExecutor.scala:55)
at akka.dispatch.BatchingExecutor$BlockableBatch.$anonfun$run$1(BatchingExecutor.scala:92)
at scala.runtime.java8.JFunction0$mcV$sp.apply(JFunction0$mcV$sp.java:23)
at scala.concurrent.BlockContext$.withBlockContext(BlockContext.scala:85)
at akka.dispatch.BatchingExecutor$BlockableBatch.run(BatchingExecutor.scala:92)
at akka.dispatch.TaskInvocation.run(AbstractDispatcher.scala:41)
at akka.dispatch.ForkJoinExecutorConfigurator$AkkaForkJoinTask.exec(ForkJoinExecutorConfigurator.scala:49)
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)

[2020-08-25 10:40:46,27] [info] WorkflowManagerActor WorkflowActor-282f5595-171e-4296-a7fa-9bd9f7a2f33b is in a terminal state: WorkflowFailedState

However, this error occurs only about 80 percent of the time when I'm trying to run a job.

2. Cromwell doesn't localize sra files to the right level
You can see below 
`2020/08/25 17:32:56 Localizing input sra://SRR2806786/SRR2806786 -> /cromwell_root/SRR2806786/SRR2806786`
but the workflow calls the file in my script
`mv: cannot stat ‘/cromwell_root/sra-SRR2806786/SRR2806786/SRR2806786’: No such file or directory`

Full log:

2020/08/25 17:32:38 Starting container setup. 2020/08/25 17:32:43 Done container setup. 2020/08/25 17:32:44 Starting localization. 2020/08/25 17:32:51 Localization script execution started... 2020/08/25 17:32:51 Localizing input gs://chip_dbgap/Mutect2/b749ec2f-c549-4d26-8fec-2fe271a37b75/call-renameBamIndex/script -> /cromwell_root/script 2020/08/25 17:32:52 Localization script execution complete. 2020/08/25 17:32:56 Localizing input sra://SRR2806786/SRR2806786 -> /cromwell_root/SRR2806786/SRR2806786 2020/08/25 17:32:58 Done localization. 2020/08/25 17:33:00 Running user action: docker run -v /mnt/local-disk:/cromwell_root --entrypoint= us.gcr.io/broad-gotc-prod/genomes-in-the-cloud@sha256:4fca8ca945c17fd86e31eeef1c02983e091d4f2cb437199e74b164d177d5b2d1 /bin/bash /cromwell_root/script mv: cannot stat ‘/cromwell_root/sra-SRR2806786/SRR2806786/SRR2806786’: No such file or directory 2020/08/25 17:33:02 Starting delocalization. 2020/08/25 17:33:03 Delocalization script execution started... 2020/08/25 17:33:03 Delocalizing output /cromwell_root/memory_retry_rc -> gs://chip_dbgap/Mutect2/b749ec2f-c549-4d26-8fec-2fe271a37b75/call-renameBamIndex/memory_retry_rc 2020/08/25 17:33:03 Delocalizing output /cromwell_root/rc -> gs://chip_dbgap/Mutect2/b749ec2f-c549-4d26-8fec-2fe271a37b75/call-renameBamIndex/rc 2020/08/25 17:33:04 Delocalizing output /cromwell_root/stdout -> gs://chip_dbgap/Mutect2/b749ec2f-c549-4d26-8fec-2fe271a37b75/call-renameBamIndex/stdout 2020/08/25 17:33:05 Delocalizing output /cromwell_root/stderr -> gs://chip_dbgap/Mutect2/b749ec2f-c549-4d26-8fec-2fe271a37b75/call-renameBamIndex/stderr 2020/08/25 17:33:06 Delocalizing output /cromwell_root/SRR2806786.bam -> gs://chip_dbgap/Mutect2/b749ec2f-c549-4d26-8fec-2fe271a37b75/call-renameBamIndex/SRR2806786.bam Required file output '/cromwell_root/SRR2806786.bam' does not exist.

njbernstein commented 4 years ago

Closing this issue as its been resolved and will create a new one for the issues above