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additional observation of Unusually long submission delay

June 7, 2017, 10:39 am
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This post is related to : http://gatkforums.broadinstitute.org/firecloud/discussion/9675/unusually-long-submission-delay#latest

Today, I seem to be observing delays (like those from the previously-linked post) . For example the task below took about an hour but when no delays are observed takes 15 minutes.

CallingGroup_Workflow.Mutect1_TaskHide
Call #1:
Operation:operations/EM_OupnIKxiM_Ja1z8KslRIg3orbxIMcKg9wcm9kdWN0aW9uUXVldWU
Status:Done
Cache Result:Miss
Started:June 7, 2017, 10:58 AM (2 hours ago)
Ended:June 7, 2017, 12:05 PM (1 hour ago)
Inputs:Show
Outputs:Show
stdout:Mutect1_Task-0-stdout.log
stderr:Mutect1_Task-0-stderr.log
JES log:Mutect1_Task-0.log

Here is an example of a task without delay:

CallingGroup_Workflow.Mutect1_TaskHide
Call #1:
Operation:operations/EISuoPrHKxjTyYeOsfrlrJMBIN6K28SDHCoPcHJvZHVjdGlvblF1ZXVl
Status:Done
Cache Result:Miss
Started:June 6, 2017, 5:20 PM (20 hours ago)
Ended:June 6, 2017, 5:38 PM (19 hours ago)
Inputs:Show
Outputs:Show
stdout:Mutect1_Task-0-stdout.log
stderr:Mutect1_Task-0-stderr.log
JES log:Mutect1_Task-0.log

The operations descriptions for each are shown here. Once each is "created" (see "createTime") then the endTime is about 17-18 minutes later. For the first operation however, cromwell shows a time of closer to 1 hour (10:58-12:05).

wm8b1-75c:~ esalinas$ gcloud alpha genomics operations describe  operations/EM_OupnIKxiM_Ja1z8KslRIg3orbxIMcKg9wcm9kdWN0aW9uUXVldWU
done: true
metadata:
  '@type': type.googleapis.com/google.genomics.v1.OperationMetadata
  clientId: ''
  createTime: '2017-06-07T15:31:31Z'
  endTime: '2017-06-07T15:47:40Z'
  events:
  - description: start
    startTime: '2017-06-07T15:32:30.575789627Z'
  - description: pulling-image
    startTime: '2017-06-07T15:32:32.802412488Z'
  - description: localizing-files
    startTime: '2017-06-07T15:33:46.826171474Z'
  - description: running-docker
    startTime: '2017-06-07T15:36:11.041332740Z'
  - description: delocalizing-files
    startTime: '2017-06-07T15:47:33.418218436Z'
  - description: copied 1 file(s) to "gs://fc-bd7b9b59-7254-432a-860d-a4779571cebb/3791f6f9-5fba-495c-908a-9ea035c9ad26/CallingGroup_Workflow/9b7dc36e-e577-419b-9ace-93abaf3e8b52/call-Mutect1_Task/shard-0/Mutect1_Task-0-rc.txt"
    startTime: '2017-06-07T15:47:35.055168003Z'
  - description: copied 1 file(s) to "gs://fc-bd7b9b59-7254-432a-860d-a4779571cebb/3791f6f9-5fba-495c-908a-9ea035c9ad26/CallingGroup_Workflow/9b7dc36e-e577-419b-9ace-93abaf3e8b52/call-Mutect1_Task/shard-0/HCC1954_100_gene_pair.MuTect1.call_stats.txt"
    startTime: '2017-06-07T15:47:36.535007878Z'
  - description: copied 1 file(s) to "gs://fc-bd7b9b59-7254-432a-860d-a4779571cebb/3791f6f9-5fba-495c-908a-9ea035c9ad26/CallingGroup_Workflow/9b7dc36e-e577-419b-9ace-93abaf3e8b52/call-Mutect1_Task/shard-0/HCC1954_100_gene_pair.MuTect1.power.wig.txt"
    startTime: '2017-06-07T15:47:37.895861890Z'
  - description: copied 1 file(s) to "gs://fc-bd7b9b59-7254-432a-860d-a4779571cebb/3791f6f9-5fba-495c-908a-9ea035c9ad26/CallingGroup_Workflow/9b7dc36e-e577-419b-9ace-93abaf3e8b52/call-Mutect1_Task/shard-0/HCC1954_100_gene_pair.MuTect1.coverage.wig.txt"
    startTime: '2017-06-07T15:47:39.271279483Z'
  - description: ok
    startTime: '2017-06-07T15:47:40.594967031Z'
  labels:
    cromwell-workflow-id: cromwell-9b7dc36e-e577-419b-9ace-93abaf3e8b52
    cromwell-workflow-name: callinggroup-workflow
    wdl-task-name: mutect1-task
  projectId: broad-firecloud-benchmark
  request:
    '@type': type.googleapis.com/google.genomics.v1alpha2.RunPipelineRequest
    ephemeralPipeline:
      description: ''
      docker:
        cmd: /bin/bash /cromwell_root/exec.sh
        imageName: broadinstitute/broadmutationcalling_beta@sha256:2285809244dabf3aefe11f4e16e91fe3d541b894f8325e4f6c9c98a8dfc81deb
      inputParameters:
      - defaultValue: ''
        description: ''
        name: __extra_config_gcs_path
      - defaultValue: ''
        description: ''
        localCopy:
          disk: local-disk
          path: firecloud-tcga-open-access/tutorial/bams/HCC1954_BL.100_gene_250bp_pad.bam
        name: Mutect1_Task.normalBam-0
      - defaultValue: ''
        description: ''
        localCopy:
          disk: local-disk
          path: firecloud-tcga-open-access/tutorial/reference/Homo_sapiens_assembly19.dict
        name: Mutect1_Task.refFastaDict-0
      - defaultValue: ''
        description: ''
        localCopy:
          disk: local-disk
          path: firecloud-tcga-open-access/tutorial/bams/HCC1954_BL.100_gene_250bp_pad.bai
        name: Mutect1_Task.normalBamIdx-0
      - defaultValue: ''
        description: ''
        localCopy:
          disk: local-disk
          path: firecloud-tcga-open-access/tutorial/reference/dbsnp_134_b37.leftAligned.vcf
        name: Mutect1_Task.dbSNPVCF-0
      - defaultValue: ''
        description: ''
        localCopy:
          disk: local-disk
          path: firecloud-tcga-open-access/tutorial/reference/Homo_sapiens_assembly19.fasta
        name: Mutect1_Task.refFasta-0
      - defaultValue: ''
        description: ''
        localCopy:
          disk: local-disk
          path: firecloud-tcga-open-access/tutorial/bams/HCC1954.100_gene_250bp_pad.bai
        name: Mutect1_Task.tumorBamIdx-0
      - defaultValue: ''
        description: ''
        localCopy:
          disk: local-disk
          path: firecloud-tcga-open-access/tutorial/bams/HCC1954.100_gene_250bp_pad.bam
        name: Mutect1_Task.tumorBam-0
      - defaultValue: ''
        description: ''
        localCopy:
          disk: local-disk
          path: fc-bd7b9b59-7254-432a-860d-a4779571cebb/3791f6f9-5fba-495c-908a-9ea035c9ad26/CallingGroup_Workflow/9b7dc36e-e577-419b-9ace-93abaf3e8b52/call-CallSomaticMutations_131_Prepare_Task/glob-bcd274f6f6e2bd6e474e81d4a4949f55/split_base.01.interval_list
        name: Mutect1_Task.mutectIntervals-0
      - defaultValue: ''
        description: ''
        localCopy:
          disk: local-disk
          path: firecloud-tcga-open-access/tutorial/reference/read_group_blacklist.v1.txt
        name: Mutect1_Task.readGroupBlackList-0
      - defaultValue: ''
        description: ''
        localCopy:
          disk: local-disk
          path: exec.sh
        name: exec
      - defaultValue: ''
        description: ''
        localCopy:
          disk: local-disk
          path: firecloud-tcga-open-access/tutorial/reference/Homo_sapiens_assembly19.fasta.fai
        name: Mutect1_Task.refFastaIdx-0
      - defaultValue: ''
        description: ''
        localCopy:
          disk: local-disk
          path: firecloud-tcga-open-access/tutorial/reference/refseq_exome_10bp_hg19_300_1kg_normal_panel.vcf
        name: Mutect1_Task.normalPanel-0
      - defaultValue: ''
        description: ''
        localCopy:
          disk: local-disk
          path: firecloud-tcga-open-access/tutorial/reference/hg19_cosmic_v54_120711.vcf
        name: Mutect1_Task.cosmicVCF-0
      name: CallingGroup_Workflow
      outputParameters:
      - defaultValue: ''
        description: ''
        localCopy:
          disk: local-disk
          path: Mutect1_Task-0-rc.txt
        name: Mutect1_Task-0-rc.txt
      - defaultValue: ''
        description: ''
        localCopy:
          disk: local-disk
          path: HCC1954_100_gene_pair.MuTect1.call_stats.txt
        name: HCC1954_100_gene_pair.MuTect1.call_stats.txt
      - defaultValue: ''
        description: ''
        localCopy:
          disk: local-disk
          path: HCC1954_100_gene_pair.MuTect1.power.wig.txt
        name: HCC1954_100_gene_pair.MuTect1.power.wig.txt
      - defaultValue: ''
        description: ''
        localCopy:
          disk: local-disk
          path: HCC1954_100_gene_pair.MuTect1.coverage.wig.txt
        name: HCC1954_100_gene_pair.MuTect1.coverage.wig.txt
      pipelineId: ''
      projectId: broad-firecloud-benchmark
      resources:
        bootDiskSizeGb: 10
        disks:
        - autoDelete: false
          mountPoint: /cromwell_root
          name: local-disk
          readOnly: false
          sizeGb: 19
          source: ''
          type: PERSISTENT_HDD
        minimumCpuCores: 1
        minimumRamGb: 3
        noAddress: false
        preemptible: true
        zones:
        - us-central1-b
        - us-central1-c
        - us-central1-f
    pipelineArgs:
      clientId: ''
      inputs:
        Mutect1_Task.cosmicVCF-0: gs://firecloud-tcga-open-access/tutorial/reference/hg19_cosmic_v54_120711.vcf
        Mutect1_Task.dbSNPVCF-0: gs://firecloud-tcga-open-access/tutorial/reference/dbsnp_134_b37.leftAligned.vcf
        Mutect1_Task.mutectIntervals-0: gs://fc-bd7b9b59-7254-432a-860d-a4779571cebb/3791f6f9-5fba-495c-908a-9ea035c9ad26/CallingGroup_Workflow/9b7dc36e-e577-419b-9ace-93abaf3e8b52/call-CallSomaticMutations_131_Prepare_Task/glob-bcd274f6f6e2bd6e474e81d4a4949f55/split_base.01.interval_list
        Mutect1_Task.normalBam-0: gs://firecloud-tcga-open-access/tutorial/bams/HCC1954_BL.100_gene_250bp_pad.bam
        Mutect1_Task.normalBamIdx-0: gs://firecloud-tcga-open-access/tutorial/bams/HCC1954_BL.100_gene_250bp_pad.bai
        Mutect1_Task.normalPanel-0: gs://firecloud-tcga-open-access/tutorial/reference/refseq_exome_10bp_hg19_300_1kg_normal_panel.vcf
        Mutect1_Task.readGroupBlackList-0: gs://firecloud-tcga-open-access/tutorial/reference/read_group_blacklist.v1.txt
        Mutect1_Task.refFasta-0: gs://firecloud-tcga-open-access/tutorial/reference/Homo_sapiens_assembly19.fasta
        Mutect1_Task.refFastaDict-0: gs://firecloud-tcga-open-access/tutorial/reference/Homo_sapiens_assembly19.dict
        Mutect1_Task.refFastaIdx-0: gs://firecloud-tcga-open-access/tutorial/reference/Homo_sapiens_assembly19.fasta.fai
        Mutect1_Task.tumorBam-0: gs://firecloud-tcga-open-access/tutorial/bams/HCC1954.100_gene_250bp_pad.bam
        Mutect1_Task.tumorBamIdx-0: gs://firecloud-tcga-open-access/tutorial/bams/HCC1954.100_gene_250bp_pad.bai
        __extra_config_gcs_path: gs://cromwell-auth-broad-firecloud-benchmark/9b7dc36e-e577-419b-9ace-93abaf3e8b52_auth.json
        exec: gs://fc-bd7b9b59-7254-432a-860d-a4779571cebb/3791f6f9-5fba-495c-908a-9ea035c9ad26/CallingGroup_Workflow/9b7dc36e-e577-419b-9ace-93abaf3e8b52/call-Mutect1_Task/shard-0/exec.sh
      labels:
        cromwell-workflow-id: cromwell-9b7dc36e-e577-419b-9ace-93abaf3e8b52
        cromwell-workflow-name: callinggroup-workflow
        wdl-task-name: mutect1-task
      logging:
        gcsPath: gs://fc-bd7b9b59-7254-432a-860d-a4779571cebb/3791f6f9-5fba-495c-908a-9ea035c9ad26/CallingGroup_Workflow/9b7dc36e-e577-419b-9ace-93abaf3e8b52/call-Mutect1_Task/shard-0/Mutect1_Task-0.log
      outputs:
        HCC1954_100_gene_pair.MuTect1.call_stats.txt: gs://fc-bd7b9b59-7254-432a-860d-a4779571cebb/3791f6f9-5fba-495c-908a-9ea035c9ad26/CallingGroup_Workflow/9b7dc36e-e577-419b-9ace-93abaf3e8b52/call-Mutect1_Task/shard-0/HCC1954_100_gene_pair.MuTect1.call_stats.txt
        HCC1954_100_gene_pair.MuTect1.coverage.wig.txt: gs://fc-bd7b9b59-7254-432a-860d-a4779571cebb/3791f6f9-5fba-495c-908a-9ea035c9ad26/CallingGroup_Workflow/9b7dc36e-e577-419b-9ace-93abaf3e8b52/call-Mutect1_Task/shard-0/HCC1954_100_gene_pair.MuTect1.coverage.wig.txt
        HCC1954_100_gene_pair.MuTect1.power.wig.txt: gs://fc-bd7b9b59-7254-432a-860d-a4779571cebb/3791f6f9-5fba-495c-908a-9ea035c9ad26/CallingGroup_Workflow/9b7dc36e-e577-419b-9ace-93abaf3e8b52/call-Mutect1_Task/shard-0/HCC1954_100_gene_pair.MuTect1.power.wig.txt
        Mutect1_Task-0-rc.txt: gs://fc-bd7b9b59-7254-432a-860d-a4779571cebb/3791f6f9-5fba-495c-908a-9ea035c9ad26/CallingGroup_Workflow/9b7dc36e-e577-419b-9ace-93abaf3e8b52/call-Mutect1_Task/shard-0/Mutect1_Task-0-rc.txt
      projectId: broad-firecloud-benchmark
      resources:
        bootDiskSizeGb: 10
        disks:
        - autoDelete: false
          mountPoint: ''
          name: local-disk
          readOnly: false
          sizeGb: 19
          source: ''
          type: PERSISTENT_HDD
        minimumCpuCores: 1
        minimumRamGb: 3
        noAddress: false
        preemptible: true
        zones:
        - us-central1-b
        - us-central1-c
        - us-central1-f
      serviceAccount:
        email: default
        scopes:
        - https://www.googleapis.com/auth/genomics
        - https://www.googleapis.com/auth/compute
  runtimeMetadata:
    '@type': type.googleapis.com/google.genomics.v1alpha2.RuntimeMetadata
    computeEngine:
      diskNames:
      - local-disk-1309054444811697676
      instanceName: ggp-1309054444811697676
      machineType: us-central1-c/n1-standard-1
      zone: us-central1-c
  startTime: '2017-06-07T15:31:38Z'
name: operations/EM_OupnIKxiM_Ja1z8KslRIg3orbxIMcKg9wcm9kdWN0aW9uUXVldWU
wm8b1-75c:~ esalinas$ gcloud alpha genomics operations describe operations/EISuoPrHKxjTyYeOsfrlrJMBIN6K28SDHCoPcHJvZHVjdGlvblF1ZXVl
done: true
metadata:
  '@type': type.googleapis.com/google.genomics.v1.OperationMetadata
  clientId: ''
  createTime: '2017-06-06T21:20:49Z'
  endTime: '2017-06-06T21:38:16Z'
  events:
  - description: start
    startTime: '2017-06-06T21:22:09.204113273Z'
  - description: pulling-image
    startTime: '2017-06-06T21:22:11.618630382Z'
  - description: localizing-files
    startTime: '2017-06-06T21:23:32.952560276Z'
  - description: running-docker
    startTime: '2017-06-06T21:25:52.819738503Z'
  - description: delocalizing-files
    startTime: '2017-06-06T21:38:07.995202628Z'
  - description: copied 1 file(s) to "gs://fc-bd7b9b59-7254-432a-860d-a4779571cebb/72eea5be-ec36-4632-a962-d73c3723b2a4/CallingGroup_Workflow/418a4c92-0821-4695-acc8-291472136fb9/call-Mutect1_Task/shard-0/HCC1954_100_gene_pair.MuTect1.coverage.wig.txt"
    startTime: '2017-06-06T21:38:09.698515389Z'
  - description: copied 1 file(s) to "gs://fc-bd7b9b59-7254-432a-860d-a4779571cebb/72eea5be-ec36-4632-a962-d73c3723b2a4/CallingGroup_Workflow/418a4c92-0821-4695-acc8-291472136fb9/call-Mutect1_Task/shard-0/Mutect1_Task-0-rc.txt"
    startTime: '2017-06-06T21:38:11.524526146Z'
  - description: copied 1 file(s) to "gs://fc-bd7b9b59-7254-432a-860d-a4779571cebb/72eea5be-ec36-4632-a962-d73c3723b2a4/CallingGroup_Workflow/418a4c92-0821-4695-acc8-291472136fb9/call-Mutect1_Task/shard-0/HCC1954_100_gene_pair.MuTect1.call_stats.txt"
    startTime: '2017-06-06T21:38:12.964677052Z'
  - description: copied 1 file(s) to "gs://fc-bd7b9b59-7254-432a-860d-a4779571cebb/72eea5be-ec36-4632-a962-d73c3723b2a4/CallingGroup_Workflow/418a4c92-0821-4695-acc8-291472136fb9/call-Mutect1_Task/shard-0/HCC1954_100_gene_pair.MuTect1.power.wig.txt"
    startTime: '2017-06-06T21:38:14.384774842Z'
  - description: ok
    startTime: '2017-06-06T21:38:15.834811124Z'
  labels:
    cromwell-workflow-id: cromwell-418a4c92-0821-4695-acc8-291472136fb9
    cromwell-workflow-name: callinggroup-workflow
    wdl-task-name: mutect1-task
  projectId: broad-firecloud-benchmark
  request:
    '@type': type.googleapis.com/google.genomics.v1alpha2.RunPipelineRequest
    ephemeralPipeline:
      description: ''
      docker:
        cmd: /bin/bash /cromwell_root/exec.sh
        imageName: broadinstitute/broadmutationcalling_beta@sha256:2285809244dabf3aefe11f4e16e91fe3d541b894f8325e4f6c9c98a8dfc81deb
      inputParameters:
      - defaultValue: ''
        description: ''
        name: __extra_config_gcs_path
      - defaultValue: ''
        description: ''
        localCopy:
          disk: local-disk
          path: firecloud-tcga-open-access/tutorial/bams/HCC1954_BL.100_gene_250bp_pad.bam
        name: Mutect1_Task.normalBam-0
      - defaultValue: ''
        description: ''
        localCopy:
          disk: local-disk
          path: firecloud-tcga-open-access/tutorial/reference/Homo_sapiens_assembly19.dict
        name: Mutect1_Task.refFastaDict-0
      - defaultValue: ''
        description: ''
        localCopy:
          disk: local-disk
          path: firecloud-tcga-open-access/tutorial/bams/HCC1954_BL.100_gene_250bp_pad.bai
        name: Mutect1_Task.normalBamIdx-0
      - defaultValue: ''
        description: ''
        localCopy:
          disk: local-disk
          path: firecloud-tcga-open-access/tutorial/reference/dbsnp_134_b37.leftAligned.vcf
        name: Mutect1_Task.dbSNPVCF-0
      - defaultValue: ''
        description: ''
        localCopy:
          disk: local-disk
          path: fc-bd7b9b59-7254-432a-860d-a4779571cebb/72eea5be-ec36-4632-a962-d73c3723b2a4/CallingGroup_Workflow/418a4c92-0821-4695-acc8-291472136fb9/call-CallSomaticMutations_131_Prepare_Task/glob-bcd274f6f6e2bd6e474e81d4a4949f55/split_base.01.interval_list
        name: Mutect1_Task.mutectIntervals-0
      - defaultValue: ''
        description: ''
        localCopy:
          disk: local-disk
          path: firecloud-tcga-open-access/tutorial/reference/Homo_sapiens_assembly19.fasta
        name: Mutect1_Task.refFasta-0
      - defaultValue: ''
        description: ''
        localCopy:
          disk: local-disk
          path: firecloud-tcga-open-access/tutorial/bams/HCC1954.100_gene_250bp_pad.bai
        name: Mutect1_Task.tumorBamIdx-0
      - defaultValue: ''
        description: ''
        localCopy:
          disk: local-disk
          path: firecloud-tcga-open-access/tutorial/bams/HCC1954.100_gene_250bp_pad.bam
        name: Mutect1_Task.tumorBam-0
      - defaultValue: ''
        description: ''
        localCopy:
          disk: local-disk
          path: firecloud-tcga-open-access/tutorial/reference/read_group_blacklist.v1.txt
        name: Mutect1_Task.readGroupBlackList-0
      - defaultValue: ''
        description: ''
        localCopy:
          disk: local-disk
          path: exec.sh
        name: exec
      - defaultValue: ''
        description: ''
        localCopy:
          disk: local-disk
          path: firecloud-tcga-open-access/tutorial/reference/Homo_sapiens_assembly19.fasta.fai
        name: Mutect1_Task.refFastaIdx-0
      - defaultValue: ''
        description: ''
        localCopy:
          disk: local-disk
          path: firecloud-tcga-open-access/tutorial/reference/refseq_exome_10bp_hg19_300_1kg_normal_panel.vcf
        name: Mutect1_Task.normalPanel-0
      - defaultValue: ''
        description: ''
        localCopy:
          disk: local-disk
          path: firecloud-tcga-open-access/tutorial/reference/hg19_cosmic_v54_120711.vcf
        name: Mutect1_Task.cosmicVCF-0
      name: CallingGroup_Workflow
      outputParameters:
      - defaultValue: ''
        description: ''
        localCopy:
          disk: local-disk
          path: Mutect1_Task-0-rc.txt
        name: Mutect1_Task-0-rc.txt
      - defaultValue: ''
        description: ''
        localCopy:
          disk: local-disk
          path: HCC1954_100_gene_pair.MuTect1.call_stats.txt
        name: HCC1954_100_gene_pair.MuTect1.call_stats.txt
      - defaultValue: ''
        description: ''
        localCopy:
          disk: local-disk
          path: HCC1954_100_gene_pair.MuTect1.power.wig.txt
        name: HCC1954_100_gene_pair.MuTect1.power.wig.txt
      - defaultValue: ''
        description: ''
        localCopy:
          disk: local-disk
          path: HCC1954_100_gene_pair.MuTect1.coverage.wig.txt
        name: HCC1954_100_gene_pair.MuTect1.coverage.wig.txt
      pipelineId: ''
      projectId: broad-firecloud-benchmark
      resources:
        bootDiskSizeGb: 10
        disks:
        - autoDelete: false
          mountPoint: /cromwell_root
          name: local-disk
          readOnly: false
          sizeGb: 19
          source: ''
          type: PERSISTENT_HDD
        minimumCpuCores: 1
        minimumRamGb: 3
        noAddress: false
        preemptible: true
        zones:
        - us-central1-b
        - us-central1-c
        - us-central1-f
    pipelineArgs:
      clientId: ''
      inputs:
        Mutect1_Task.cosmicVCF-0: gs://firecloud-tcga-open-access/tutorial/reference/hg19_cosmic_v54_120711.vcf
        Mutect1_Task.dbSNPVCF-0: gs://firecloud-tcga-open-access/tutorial/reference/dbsnp_134_b37.leftAligned.vcf
        Mutect1_Task.mutectIntervals-0: gs://fc-bd7b9b59-7254-432a-860d-a4779571cebb/72eea5be-ec36-4632-a962-d73c3723b2a4/CallingGroup_Workflow/418a4c92-0821-4695-acc8-291472136fb9/call-CallSomaticMutations_131_Prepare_Task/glob-bcd274f6f6e2bd6e474e81d4a4949f55/split_base.01.interval_list
        Mutect1_Task.normalBam-0: gs://firecloud-tcga-open-access/tutorial/bams/HCC1954_BL.100_gene_250bp_pad.bam
        Mutect1_Task.normalBamIdx-0: gs://firecloud-tcga-open-access/tutorial/bams/HCC1954_BL.100_gene_250bp_pad.bai
        Mutect1_Task.normalPanel-0: gs://firecloud-tcga-open-access/tutorial/reference/refseq_exome_10bp_hg19_300_1kg_normal_panel.vcf
        Mutect1_Task.readGroupBlackList-0: gs://firecloud-tcga-open-access/tutorial/reference/read_group_blacklist.v1.txt
        Mutect1_Task.refFasta-0: gs://firecloud-tcga-open-access/tutorial/reference/Homo_sapiens_assembly19.fasta
        Mutect1_Task.refFastaDict-0: gs://firecloud-tcga-open-access/tutorial/reference/Homo_sapiens_assembly19.dict
        Mutect1_Task.refFastaIdx-0: gs://firecloud-tcga-open-access/tutorial/reference/Homo_sapiens_assembly19.fasta.fai
        Mutect1_Task.tumorBam-0: gs://firecloud-tcga-open-access/tutorial/bams/HCC1954.100_gene_250bp_pad.bam
        Mutect1_Task.tumorBamIdx-0: gs://firecloud-tcga-open-access/tutorial/bams/HCC1954.100_gene_250bp_pad.bai
        __extra_config_gcs_path: gs://cromwell-auth-broad-firecloud-benchmark/418a4c92-0821-4695-acc8-291472136fb9_auth.json
        exec: gs://fc-bd7b9b59-7254-432a-860d-a4779571cebb/72eea5be-ec36-4632-a962-d73c3723b2a4/CallingGroup_Workflow/418a4c92-0821-4695-acc8-291472136fb9/call-Mutect1_Task/shard-0/exec.sh
      labels:
        cromwell-workflow-id: cromwell-418a4c92-0821-4695-acc8-291472136fb9
        cromwell-workflow-name: callinggroup-workflow
        wdl-task-name: mutect1-task
      logging:
        gcsPath: gs://fc-bd7b9b59-7254-432a-860d-a4779571cebb/72eea5be-ec36-4632-a962-d73c3723b2a4/CallingGroup_Workflow/418a4c92-0821-4695-acc8-291472136fb9/call-Mutect1_Task/shard-0/Mutect1_Task-0.log
      outputs:
        HCC1954_100_gene_pair.MuTect1.call_stats.txt: gs://fc-bd7b9b59-7254-432a-860d-a4779571cebb/72eea5be-ec36-4632-a962-d73c3723b2a4/CallingGroup_Workflow/418a4c92-0821-4695-acc8-291472136fb9/call-Mutect1_Task/shard-0/HCC1954_100_gene_pair.MuTect1.call_stats.txt
        HCC1954_100_gene_pair.MuTect1.coverage.wig.txt: gs://fc-bd7b9b59-7254-432a-860d-a4779571cebb/72eea5be-ec36-4632-a962-d73c3723b2a4/CallingGroup_Workflow/418a4c92-0821-4695-acc8-291472136fb9/call-Mutect1_Task/shard-0/HCC1954_100_gene_pair.MuTect1.coverage.wig.txt
        HCC1954_100_gene_pair.MuTect1.power.wig.txt: gs://fc-bd7b9b59-7254-432a-860d-a4779571cebb/72eea5be-ec36-4632-a962-d73c3723b2a4/CallingGroup_Workflow/418a4c92-0821-4695-acc8-291472136fb9/call-Mutect1_Task/shard-0/HCC1954_100_gene_pair.MuTect1.power.wig.txt
        Mutect1_Task-0-rc.txt: gs://fc-bd7b9b59-7254-432a-860d-a4779571cebb/72eea5be-ec36-4632-a962-d73c3723b2a4/CallingGroup_Workflow/418a4c92-0821-4695-acc8-291472136fb9/call-Mutect1_Task/shard-0/Mutect1_Task-0-rc.txt
      projectId: broad-firecloud-benchmark
      resources:
        bootDiskSizeGb: 10
        disks:
        - autoDelete: false
          mountPoint: ''
          name: local-disk
          readOnly: false
          sizeGb: 19
          source: ''
          type: PERSISTENT_HDD
        minimumCpuCores: 1
        minimumRamGb: 3
        noAddress: false
        preemptible: true
        zones:
        - us-central1-b
        - us-central1-c
        - us-central1-f
      serviceAccount:
        email: default
        scopes:
        - https://www.googleapis.com/auth/genomics
        - https://www.googleapis.com/auth/compute
  runtimeMetadata:
    '@type': type.googleapis.com/google.genomics.v1alpha2.RuntimeMetadata
    computeEngine:
      diskNames:
      - local-disk-10617684529294468307
      instanceName: ggp-10617684529294468307
      machineType: us-central1-f/n1-standard-1
      zone: us-central1-f
  startTime: '2017-06-06T21:20:57Z'
name: operations/EISuoPrHKxjTyYeOsfrlrJMBIN6K28SDHCoPcHJvZHVjdGlvblF1ZXVl
wm8b1-75c:~ esalinas$
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