Error on Google Cloud Platform: Failed to evaluate 'gvcf_paths' in Joint Genotyping
I'm running gatk-workflows/gatk4-germline-snps-indels on the Google Cloud platform. I'm implementing the JointGenotyping.wdl on 50 exome GVCF files from a Sentieon DNAseq_DNAscope run. I edited the JointGenotyping.hg19.wgs.inputs.json with the location of my sample map file, which references the GVCF file locations. It's important to note that the GVCFs of these 50 samples are located in the same bucket but not the same folder as with the example sample map file that comes with the json file. I come across this error: Failed to evaluate 'gvcf_paths' (reason 1 of 1): Evaluating line[1] failed: Bad array access line[1]: Array size 1 does not have an index value '1'. The partial error log is below.
Command run:
$ gcloud alpha genomics pipelines run --pipeline-file wdl_pipeline.yaml --regions us-central1 --inputs-from-file WDL=${GATK_GOOGLE_DIR}/JointGenotyping.wdl,WORKFLOW_INPUTS=${GATK_GOOGLE_DIR}/JointGenotyping.hg19.wgs.inputs.json,WORKFLOW_OPTIONS=${GATK_GOOGLE_DIR}/generic.google-papi.options.json --env-vars WORKSPACE=${GATK_OUTPUT_DIR}/work,OUTPUTS=${GATK_OUTPUT_DIR}/output --logging ${GATK_OUTPUT_DIR}/logging/
Error log:
2020-05-13 05:37:22,035 INFO - changelog.xml: changesets/drop_workflow_uri_and_local_command.xml::drop_workflow_uri_and_local_command::kshakir: Column LOCAL_JOB.COMMAND dropped
2020-05-13 05:37:22,036 INFO - changelog.xml: changesets/drop_workflow_uri_and_local_command.xml::drop_workflow_uri_and_local_command::kshakir: ChangeSet changesets/drop_workflow_uri_and_local_command.xml::drop_workflow_uri_and_local_command::kshakir ran successfully in 7ms
2020-05-13 05:37:22,039 INFO - changelog.xml: changesets/local_job_allow_null.xml::local_job_allow_null::kshakir: Null constraint dropped from ...skipping...
2020-05-13 05:41:21,240 cromwell-system-akka.dispatchers.engine-dispatcher-30 ERROR - WorkflowManagerActor Workflow 0e3d6249-4eb7-4168-b966-f1f1cd5f0189 failed (during ExecutingWorkflowState): java.lang.RuntimeException: Failed to evaluate 'gvcf_paths' (reason 1 of 1): Evaluating line[1] failed: Bad array access line[1]: Array size 1 does not have an index value '1'
at cromwell.engine.workflow.lifecycle.execution.keys.ExpressionKey.processRunnable(ExpressionKey.scala:29)
at cromwell.engine.workflow.lifecycle.execution.WorkflowExecutionActor.$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$$anon$1.$anonfun$foldRight$2(list.scala:66)
at cats.Eval$.advance(Eval.scala:271)
at cats.Eval$.loop$1(Eval.scala:350)
at cats.Eval$.cats$Eval$$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$WorkQueue.runTask(ForkJoinPool.java:1339)
at akka.dispatch.forkjoin.ForkJoinPool.runWorker(ForkJoinPool.java:1979)
at akka.dispatch.forkjoin.ForkJoinWorkerThread.run(ForkJoinWorkerThread.java:107)
java.lang.RuntimeException: Failed to evaluate 'gvcf_paths' (reason 1 of 1): Evaluating line[1] failed: Bad array access line[1]: Array size 1 does not have an index value '1'
at cromwell.engine.workflow.lifecycle.execution.keys.ExpressionKey.processRunnable(ExpressionKey.scala:29)
at cromwell.engine.workflow.lifecycle.execution.WorkflowExecutionActor.$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)
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Hi ikeoluwao_o,
Happy to see if I can help here. Would you be able to provide your JointGenotyping.hg19.wgs.inputs.json for closer examination? A gs:// path for me to download from would work—you can provide access to jcerrato@broadinstitute.org.
Kind regards,
Jason -
Hi Jason Cerrato,
Thank you for willingness to help.
Here is the path: gs://55trios/JointGenotyping.hg19.wgs.inputs.json. I've provided access to you.
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Hi ikeoluwao_o,
It looks like the issue may be down to the sample_name_map. Can you also share gs://bipolar_exomes_200/50_exomes.sample_map?
Kind regards,
Jason
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I'm unable to provide access to this individual object given that this specific bucket access control is uniform and not fine-grained. I've copied the file to the same bucket as the json so you should have access now.
gs://55trios/50_exomes.sample_map
Thank you,
Ike
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Hi Ike,
Was this sample map created using the generate-sample-map workflow?
https://portal.firecloud.org/?return=terra#methods/gatk/generate-sample-map/1
Kind regards,
Jason
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It was not created using the generate-sample-map workflow. It was created by manually putting together the sample names and corresponding paths.
I don't have access to this workflow on the GitHub repository for the Google Cloud Platform (GCP) runs: https://github.com/gatk-workflows/gatk4-germline-snps-indels. I'm not using Terra and would need to sign up. Since my analysis is on GCP, is there a way to access this workflow without Terra?
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Hi ikeoluwao_o,
Apologies for the delay here—I believe I missed your reply during one of my OOO days. Do you still require assistance with this issue? If so, I am happy to help once again.
Kind regards,
Jason
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Hi Jason Cerrato,
No worries at all. I would very much appreciate your help with this as it's still not resolved.
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HI ikeoluwao_o,
Here is a viewable version of the generate-sample-map workflow: https://api.firecloud.org/ga4gh/v1/tools/gatk:generate-sample-map/versions/2/plain-WDL/descriptor
After generating your sample map using this workflow, can you let me know if using the output with the JointGenotyping workflow allows you to get a successful run? If not please provide the .log and error output messages once again.
Many thanks,
Jason
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