gistfile1.txt

16-02-19 22:52:31,493 cromwell-system-akka.actor.default-dispatcher-7 INFO  - WorkflowActor [UUID(60d1afe2)]: ExecutionStoreCreated(Start(Some(Actor[akka://cromwell-system/user/cromwell-service/Endpoint-endpointActorName2416685706549335/Endpoint-endpointActorName2416685706549335#-1982900038]))) message received
16-02-19 22:55:38,085 cromwell-system-akka.actor.default-dispatcher-5 INFO  - JES Run [UUID(60d1afe2):StripUnmappedBamSuffix:2]: Status change from Initializing to Running
16-02-19 22:56:02,356 cromwell-system-akka.actor.default-dispatcher-26 INFO  - JES Run [UUID(60d1afe2):StripUnmappedBamSuffix:4]: Status change from Initializing to Running
16-02-19 23:02:41,207 cromwell-system-akka.actor.default-dispatcher-7 INFO  - JES Run [UUID(60d1afe2):StripUnmappedBamSuffix:3]: Status change from Initializing to Running
16-02-19 23:03:53,065 cromwell-system-akka.actor.default-dispatcher-7 INFO  - JES Run [UUID(60d1afe2):StripUnmappedBamSuffix:2]: Status change from Running to Success
16-02-19 23:03:53,778 cromwell-system-akka.actor.default-dispatcher-20 INFO  - WorkflowActor [UUID(60d1afe2)]: persisting status of StripUnmappedBamSuffix:2 to Done.
16-02-19 23:03:53,883 cromwell-system-akka.actor.default-dispatcher-21 INFO  - WorkflowActor [UUID(60d1afe2)]: starting calls: PairedEndSingleSampleWorkflow.SamToFastqAndBwaMem
16-02-19 23:03:53,883 cromwell-system-akka.actor.default-dispatcher-21 INFO  - WorkflowActor [UUID(60d1afe2)]: persisting status of SamToFastqAndBwaMem:2 to Starting.
16-02-19 23:03:54,002 cromwell-system-akka.actor.default-dispatcher-4 INFO  - WorkflowActor [UUID(60d1afe2)]: inputs for call 'SamToFastqAndBwaMem:2':
16-02-19 23:03:54,002 cromwell-system-akka.actor.default-dispatcher-4 INFO  - WorkflowActor [UUID(60d1afe2)]: created call actor for SamToFastqAndBwaMem:2.
16-02-19 23:03:54,002 cromwell-system-akka.actor.default-dispatcher-4 INFO  - WorkflowActor [UUID(60d1afe2)]: persisting status of SamToFastqAndBwaMem:2 to Running.
16-02-19 23:03:54,002 cromwell-system-akka.actor.default-dispatcher-26 INFO  - JesBackend [UUID(60d1afe2):SamToFastqAndBwaMem:2]: Call GCS path: gs://broad-gp-gotc-pilot/cromwell_execution/PairedEndSingleSampleWorkflow/60d1afe2-dbd4-47e5-9cf5-e2a76d7947cd/call-SamToFastqAndBwaMem/shard-2
16-02-19 23:03:54,003 cromwell-system-akka.actor.default-dispatcher-26 INFO  - JesBackend [UUID(60d1afe2):SamToFastqAndBwaMem:2]: `set -o pipefail
16-02-19 23:03:54,166 cromwell-system-akka.actor.default-dispatcher-26 INFO  - JesBackend [UUID(60d1afe2):SamToFastqAndBwaMem:2]: Starting call with pre-emptible VM
16-02-19 23:03:54,166 cromwell-system-akka.actor.default-dispatcher-26 INFO  - JES Pipeline [UUID(60d1afe2):SamToFastqAndBwaMem:2]: Pipeline parameters are:
16-02-19 23:03:54,213 cromwell-system-akka.actor.default-dispatcher-26 INFO  - JES Pipeline [UUID(60d1afe2):SamToFastqAndBwaMem:2]: Pipeline ID is 9762258500625582785
16-02-19 23:03:54,213 cromwell-system-akka.actor.default-dispatcher-26 INFO  - JES Pipeline [UUID(60d1afe2):SamToFastqAndBwaMem:2]: Project ID: broad-gp-gotc-pilot
16-02-19 23:03:54,213 cromwell-system-akka.actor.default-dispatcher-26 INFO  - JES Run [UUID(60d1afe2):SamToFastqAndBwaMem:2]: Inputs:
xec -> gs://broad-gp-gotc-pilot/cromwell_execution/PairedEndSingleSampleWorkflow/60d1afe2-dbd4-47e5-9cf5-e2a76d7947cd/call-SamToFastqAndBwaMem/shard-2/exec.sh
16-02-19 23:03:54,213 cromwell-system-akka.actor.default-dispatcher-26 INFO  - JES Run [UUID(60d1afe2):SamToFastqAndBwaMem:2]: Outputs:
amToFastqAndBwaMem-2-rc.txt -> gs://broad-gp-gotc-pilot/cromwell_execution/PairedEndSingleSampleWorkflow/60d1afe2-dbd4-47e5-9cf5-e2a76d7947cd/call-SamToFastqAndBwaMem/shard-2/SamToFastqAndBwaMem-2-rc.txt
H7LLCCXX.3.CCTACCAT-GCTTCCTA.unmerged.bam -> gs://broad-gp-gotc-pilot/cromwell_execution/PairedEndSingleSampleWorkflow/60d1afe2-dbd4-47e5-9cf5-e2a76d7947cd/call-SamToFastqAndBwaMem/shard-2/HH7LLCCXX.3.CCTACCAT-GCTTCCTA.unmerged.bam
onitoring -> gs://broad-gp-gotc-pilot/cromwell_execution/PairedEndSingleSampleWorkflow/60d1afe2-dbd4-47e5-9cf5-e2a76d7947cd/call-SamToFastqAndBwaMem/shard-2/monitoring.log
16-02-19 23:03:54,373 cromwell-system-akka.actor.default-dispatcher-26 INFO  - JES Run [UUID(60d1afe2):SamToFastqAndBwaMem:2]: JES Run ID is operations/EKXxmd6vKhjf472KvOvd1l8g6a343KwYKg9wcm9kdWN0aW9uUXVldWU
16-02-19 23:03:54,406 cromwell-system-akka.actor.default-dispatcher-26 INFO  - JES Run [UUID(60d1afe2):SamToFastqAndBwaMem:2]: Status change from - to Initializing
16-02-19 23:06:25,691 cromwell-system-akka.actor.default-dispatcher-19 INFO  - JES Run [UUID(60d1afe2):StripUnmappedBamSuffix:5]: Status change from Initializing to Running
16-02-19 23:08:23,170 cromwell-system-akka.actor.default-dispatcher-14 INFO  - JES Run [UUID(60d1afe2):StripUnmappedBamSuffix:7]: Status change from Initializing to Running
16-02-19 23:08:49,570 cromwell-system-akka.actor.default-dispatcher-17 INFO  - JES Run [UUID(60d1afe2):StripBamExtension:1]: Status change from Initializing to Running
16-02-19 23:09:49,986 cromwell-system-akka.actor.default-dispatcher-18 INFO  - JES Run [UUID(60d1afe2):SamToFastqAndBwaMem:2]: Status change from Initializing to Running
16-02-19 23:10:20,652 cromwell-system-akka.actor.default-dispatcher-19 INFO  - JES Run [UUID(60d1afe2):StripUnmappedBamSuffix:1]: Status change from Initializing to Running
16-02-19 23:11:34,958 cromwell-system-akka.actor.default-dispatcher-13 INFO  - JES Run [UUID(60d1afe2):CreateSequenceGroupingTSV]: Status change from Initializing to Running
16-02-19 23:12:23,152 cromwell-system-akka.actor.default-dispatcher-2 INFO  - JES Run [UUID(60d1afe2):StripUnmappedBamSuffix:5]: Status change from Running to Success
16-02-19 23:12:23,703 cromwell-system-akka.actor.default-dispatcher-19 INFO  - WorkflowActor [UUID(60d1afe2)]: persisting status of StripUnmappedBamSuffix:5 to Done.
16-02-19 23:12:23,801 cromwell-system-akka.actor.default-dispatcher-21 INFO  - WorkflowActor [UUID(60d1afe2)]: starting calls: PairedEndSingleSampleWorkflow.SamToFastqAndBwaMem
16-02-19 23:12:23,801 cromwell-system-akka.actor.default-dispatcher-21 INFO  - WorkflowActor [UUID(60d1afe2)]: persisting status of SamToFastqAndBwaMem:5 to Starting.
16-02-19 23:12:23,921 cromwell-system-akka.actor.default-dispatcher-22 INFO  - WorkflowActor [UUID(60d1afe2)]: inputs for call 'SamToFastqAndBwaMem:5':
16-02-19 23:12:23,921 cromwell-system-akka.actor.default-dispatcher-22 INFO  - WorkflowActor [UUID(60d1afe2)]: created call actor for SamToFastqAndBwaMem:5.
16-02-19 23:12:23,921 cromwell-system-akka.actor.default-dispatcher-15 INFO  - WorkflowActor [UUID(60d1afe2)]: persisting status of SamToFastqAndBwaMem:5 to Running.
16-02-19 23:12:23,921 cromwell-system-akka.actor.default-dispatcher-15 INFO  - JesBackend [UUID(60d1afe2):SamToFastqAndBwaMem:5]: Call GCS path: gs://broad-gp-gotc-pilot/cromwell_execution/PairedEndSingleSampleWorkflow/60d1afe2-dbd4-47e5-9cf5-e2a76d7947cd/call-SamToFastqAndBwaMem/shard-5
16-02-19 23:12:23,922 cromwell-system-akka.actor.default-dispatcher-15 INFO  - JesBackend [UUID(60d1afe2):SamToFastqAndBwaMem:5]: `set -o pipefail
16-02-19 23:12:24,088 cromwell-system-akka.actor.default-dispatcher-15 INFO  - JesBackend [UUID(60d1afe2):SamToFastqAndBwaMem:5]: Starting call with pre-emptible VM
16-02-19 23:12:24,088 cromwell-system-akka.actor.default-dispatcher-15 INFO  - JES Pipeline [UUID(60d1afe2):SamToFastqAndBwaMem:5]: Pipeline parameters are:
16-02-19 23:12:24,141 cromwell-system-akka.actor.default-dispatcher-15 INFO  - JES Pipeline [UUID(60d1afe2):SamToFastqAndBwaMem:5]: Pipeline ID is 7517741029305967950
16-02-19 23:12:24,141 cromwell-system-akka.actor.default-dispatcher-15 INFO  - JES Pipeline [UUID(60d1afe2):SamToFastqAndBwaMem:5]: Project ID: broad-gp-gotc-pilot
16-02-19 23:12:24,141 cromwell-system-akka.actor.default-dispatcher-15 INFO  - JES Run [UUID(60d1afe2):SamToFastqAndBwaMem:5]: Inputs:
xec -> gs://broad-gp-gotc-pilot/cromwell_execution/PairedEndSingleSampleWorkflow/60d1afe2-dbd4-47e5-9cf5-e2a76d7947cd/call-SamToFastqAndBwaMem/shard-5/exec.sh
16-02-19 23:12:24,141 cromwell-system-akka.actor.default-dispatcher-15 INFO  - JES Run [UUID(60d1afe2):SamToFastqAndBwaMem:5]: Outputs:
amToFastqAndBwaMem-5-rc.txt -> gs://broad-gp-gotc-pilot/cromwell_execution/PairedEndSingleSampleWorkflow/60d1afe2-dbd4-47e5-9cf5-e2a76d7947cd/call-SamToFastqAndBwaMem/shard-5/SamToFastqAndBwaMem-5-rc.txt
H7LLCCXX.6.CCTACCAT-GCTTCCTA.unmerged.bam -> gs://broad-gp-gotc-pilot/cromwell_execution/PairedEndSingleSampleWorkflow/60d1afe2-dbd4-47e5-9cf5-e2a76d7947cd/call-SamToFastqAndBwaMem/shard-5/HH7LLCCXX.6.CCTACCAT-GCTTCCTA.unmerged.bam
onitoring -> gs://broad-gp-gotc-pilot/cromwell_execution/PairedEndSingleSampleWorkflow/60d1afe2-dbd4-47e5-9cf5-e2a76d7947cd/call-SamToFastqAndBwaMem/shard-5/monitoring.log
16-02-19 23:12:24,232 cromwell-system-akka.actor.default-dispatcher-15 INFO  - JES Run [UUID(60d1afe2):SamToFastqAndBwaMem:5]: JES Run ID is operations/EN6Aud6vKhjKjOW7l4D95uIBIOmt-NysGCoPcHJvZHVjdGlvblF1ZXVl
16-02-19 23:12:24,253 cromwell-system-akka.actor.default-dispatcher-15 INFO  - JES Run [UUID(60d1afe2):SamToFastqAndBwaMem:5]: Status change from - to Initializing
16-02-19 23:13:25,356 cromwell-system-akka.actor.default-dispatcher-10 INFO  - JES Run [UUID(60d1afe2):StripBamExtension:3]: Status change from Initializing to Running
16-02-19 23:14:05,671 cromwell-system-akka.actor.default-dispatcher-6 INFO  - JES Run [UUID(60d1afe2):StripBamExtension:1]: Status change from Running to Success
16-02-19 23:14:06,352 cromwell-system-akka.actor.default-dispatcher-22 INFO  - WorkflowActor [UUID(60d1afe2)]: persisting status of StripBamExtension:1 to Done.
16-02-19 23:14:06,445 cromwell-system-akka.actor.default-dispatcher-12 INFO  - WorkflowActor [UUID(60d1afe2)]: starting calls: PairedEndSingleSampleWorkflow.CollectQualityYieldMetrics
16-02-19 23:14:06,445 cromwell-system-akka.actor.default-dispatcher-12 INFO  - WorkflowActor [UUID(60d1afe2)]: persisting status of CollectQualityYieldMetrics:1 to Starting.
16-02-19 23:14:06,561 cromwell-system-akka.actor.default-dispatcher-16 INFO  - WorkflowActor [UUID(60d1afe2)]: inputs for call 'CollectQualityYieldMetrics:1':
16-02-19 23:14:06,561 cromwell-system-akka.actor.default-dispatcher-18 INFO  - WorkflowActor [UUID(60d1afe2)]: created call actor for CollectQualityYieldMetrics:1.
16-02-19 23:14:06,562 cromwell-system-akka.actor.default-dispatcher-22 INFO  - WorkflowActor [UUID(60d1afe2)]: persisting status of CollectQualityYieldMetrics:1 to Running.
16-02-19 23:14:06,562 cromwell-system-akka.actor.default-dispatcher-6 INFO  - JesBackend [UUID(60d1afe2):CollectQualityYieldMetrics:1]: Call GCS path: gs://broad-gp-gotc-pilot/cromwell_execution/PairedEndSingleSampleWorkflow/60d1afe2-dbd4-47e5-9cf5-e2a76d7947cd/call-CollectQualityYieldMetrics/shard-1
16-02-19 23:14:06,562 cromwell-system-akka.actor.default-dispatcher-6 INFO  - JesBackend [UUID(60d1afe2):CollectQualityYieldMetrics:1]: `java -Xmx128m -jar /usr/gitc/picard.jar \
16-02-19 23:14:06,742 cromwell-system-akka.actor.default-dispatcher-6 INFO  - JesBackend [UUID(60d1afe2):CollectQualityYieldMetrics:1]: Starting call with pre-emptible VM
16-02-19 23:14:06,742 cromwell-system-akka.actor.default-dispatcher-6 INFO  - JES Pipeline [UUID(60d1afe2):CollectQualityYieldMetrics:1]: Pipeline parameters are:
16-02-19 23:14:07,015 cromwell-system-akka.actor.default-dispatcher-6 INFO  - JES Pipeline [UUID(60d1afe2):CollectQualityYieldMetrics:1]: Pipeline ID is 4840821941010260279
16-02-19 23:14:07,015 cromwell-system-akka.actor.default-dispatcher-6 INFO  - JES Pipeline [UUID(60d1afe2):CollectQualityYieldMetrics:1]: Project ID: broad-gp-gotc-pilot
16-02-19 23:14:07,015 cromwell-system-akka.actor.default-dispatcher-6 INFO  - JES Run [UUID(60d1afe2):CollectQualityYieldMetrics:1]: Inputs:
xec -> gs://broad-gp-gotc-pilot/cromwell_execution/PairedEndSingleSampleWorkflow/60d1afe2-dbd4-47e5-9cf5-e2a76d7947cd/call-CollectQualityYieldMetrics/shard-1/exec.sh
16-02-19 23:14:07,015 cromwell-system-akka.actor.default-dispatcher-6 INFO  - JES Run [UUID(60d1afe2):CollectQualityYieldMetrics:1]: Outputs:
ollectQualityYieldMetrics-1-rc.txt -> gs://broad-gp-gotc-pilot/cromwell_execution/PairedEndSingleSampleWorkflow/60d1afe2-dbd4-47e5-9cf5-e2a76d7947cd/call-CollectQualityYieldMetrics/shard-1/CollectQualityYieldMetrics-1-rc.txt
H7LLCCXX.2.CCTACCAT-GCTTCCTA.unmapped.quality_yield_metrics -> gs://broad-gp-gotc-pilot/cromwell_execution/PairedEndSingleSampleWorkflow/60d1afe2-dbd4-47e5-9cf5-e2a76d7947cd/call-CollectQualityYieldMetrics/shard-1/HH7LLCCXX.2.CCTACCAT-GCTTCCTA.unmapped.quality_yield_metrics
onitoring -> gs://broad-gp-gotc-pilot/cromwell_execution/PairedEndSingleSampleWorkflow/60d1afe2-dbd4-47e5-9cf5-e2a76d7947cd/call-CollectQualityYieldMetrics/shard-1/monitoring.log
16-02-19 23:14:07,252 cromwell-system-akka.actor.default-dispatcher-6 INFO  - JES Run [UUID(60d1afe2):CollectQualityYieldMetrics:1]: JES Run ID is operations/ENykv96vKhin3ImN3LPM-JYBIOmt-NysGCoPcHJvZHVjdGlvblF1ZXVl
16-02-19 23:14:07,361 cromwell-system-akka.actor.default-dispatcher-25 INFO  - JES Run [UUID(60d1afe2):CollectQualityYieldMetrics:1]: Status change from - to Initializing
16-02-19 23:14:14,667 cromwell-system-akka.actor.default-dispatcher-3 INFO  - WorkflowActor [UUID(60d1afe2)]: persisting status of StripUnmappedBamSuffix:7 to Done.
16-02-19 23:14:14,794 cromwell-system-akka.actor.default-dispatcher-5 INFO  - WorkflowActor [UUID(60d1afe2)]: starting calls: PairedEndSingleSampleWorkflow.SamToFastqAndBwaMem
16-02-19 23:14:14,794 cromwell-system-akka.actor.default-dispatcher-5 INFO  - WorkflowActor [UUID(60d1afe2)]: persisting status of SamToFastqAndBwaMem:7 to Starting.
16-02-19 23:14:14,912 cromwell-system-akka.actor.default-dispatcher-22 INFO  - WorkflowActor [UUID(60d1afe2)]: inputs for call 'SamToFastqAndBwaMem:7':
16-02-19 23:14:14,912 cromwell-system-akka.actor.default-dispatcher-22 INFO  - WorkflowActor [UUID(60d1afe2)]: created call actor for SamToFastqAndBwaMem:7.
16-02-19 23:14:14,912 cromwell-system-akka.actor.default-dispatcher-22 INFO  - WorkflowActor [UUID(60d1afe2)]: persisting status of SamToFastqAndBwaMem:7 to Running.
16-02-19 23:14:14,912 cromwell-system-akka.actor.default-dispatcher-24 INFO  - JesBackend [UUID(60d1afe2):SamToFastqAndBwaMem:7]: Call GCS path: gs://broad-gp-gotc-pilot/cromwell_execution/PairedEndSingleSampleWorkflow/60d1afe2-dbd4-47e5-9cf5-e2a76d7947cd/call-SamToFastqAndBwaMem/shard-7
16-02-19 23:14:14,912 cromwell-system-akka.actor.default-dispatcher-24 INFO  - JesBackend [UUID(60d1afe2):SamToFastqAndBwaMem:7]: `set -o pipefail
16-02-19 23:14:15,119 cromwell-system-akka.actor.default-dispatcher-24 INFO  - JesBackend [UUID(60d1afe2):SamToFastqAndBwaMem:7]: Starting call with pre-emptible VM
16-02-19 23:14:15,119 cromwell-system-akka.actor.default-dispatcher-24 INFO  - JES Pipeline [UUID(60d1afe2):SamToFastqAndBwaMem:7]: Pipeline parameters are:
16-02-19 23:14:15,208 cromwell-system-akka.actor.default-dispatcher-24 INFO  - JES Pipeline [UUID(60d1afe2):SamToFastqAndBwaMem:7]: Pipeline ID is 17095598234441831593
16-02-19 23:14:15,208 cromwell-system-akka.actor.default-dispatcher-24 INFO  - JES Pipeline [UUID(60d1afe2):SamToFastqAndBwaMem:7]: Project ID: broad-gp-gotc-pilot
16-02-19 23:14:15,208 cromwell-system-akka.actor.default-dispatcher-24 INFO  - JES Run [UUID(60d1afe2):SamToFastqAndBwaMem:7]: Inputs:
xec -> gs://broad-gp-gotc-pilot/cromwell_execution/PairedEndSingleSampleWorkflow/60d1afe2-dbd4-47e5-9cf5-e2a76d7947cd/call-SamToFastqAndBwaMem/shard-7/exec.sh
16-02-19 23:14:15,208 cromwell-system-akka.actor.default-dispatcher-24 INFO  - JES Run [UUID(60d1afe2):SamToFastqAndBwaMem:7]: Outputs:
amToFastqAndBwaMem-7-rc.txt -> gs://broad-gp-gotc-pilot/cromwell_execution/PairedEndSingleSampleWorkflow/60d1afe2-dbd4-47e5-9cf5-e2a76d7947cd/call-SamToFastqAndBwaMem/shard-7/SamToFastqAndBwaMem-7-rc.txt
H7LLCCXX.8.CCTACCAT-GCTTCCTA.unmerged.bam -> gs://broad-gp-gotc-pilot/cromwell_execution/PairedEndSingleSampleWorkflow/60d1afe2-dbd4-47e5-9cf5-e2a76d7947cd/call-SamToFastqAndBwaMem/shard-7/HH7LLCCXX.8.CCTACCAT-GCTTCCTA.unmerged.bam
onitoring -> gs://broad-gp-gotc-pilot/cromwell_execution/PairedEndSingleSampleWorkflow/60d1afe2-dbd4-47e5-9cf5-e2a76d7947cd/call-SamToFastqAndBwaMem/shard-7/monitoring.log
16-02-19 23:14:15,551 cromwell-system-akka.actor.default-dispatcher-24 INFO  - JES Run [UUID(60d1afe2):SamToFastqAndBwaMem:7]: JES Run ID is operations/EMTlv96vKhicn9uGztuivG8g6a343KwYKg9wcm9kdWN0aW9uUXVldWU
16-02-19 23:14:15,621 cromwell-system-akka.actor.default-dispatcher-10 INFO  - JES Run [UUID(60d1afe2):SamToFastqAndBwaMem:7]: Status change from - to Initializing
16-02-19 23:16:46,380 cromwell-system-akka.actor.default-dispatcher-17 INFO  - JES Run [UUID(60d1afe2):StripBamExtension:5]: Status change from Initializing to Running
16-02-19 23:20:22,771 cromwell-system-akka.actor.default-dispatcher-2 INFO  - JES Run [UUID(60d1afe2):StripBamExtension:4]: Status change from Initializing to Running
16-02-19 23:20:27,099 cromwell-system-akka.actor.default-dispatcher-21 INFO  - JES Run [UUID(60d1afe2):StripUnmappedBamSuffix:6]: Status change from Running to Success
16-02-19 23:20:27,772 cromwell-system-akka.actor.default-dispatcher-8 INFO  - WorkflowActor [UUID(60d1afe2)]: persisting status of StripUnmappedBamSuffix:6 to Done.
16-02-19 23:20:27,872 cromwell-system-akka.actor.default-dispatcher-5 INFO  - WorkflowActor [UUID(60d1afe2)]: starting calls: PairedEndSingleSampleWorkflow.SamToFastqAndBwaMem
16-02-19 23:20:27,873 cromwell-system-akka.actor.default-dispatcher-5 INFO  - WorkflowActor [UUID(60d1afe2)]: persisting status of SamToFastqAndBwaMem:6 to Starting.
16-02-19 23:20:27,991 cromwell-system-akka.actor.default-dispatcher-13 INFO  - WorkflowActor [UUID(60d1afe2)]: inputs for call 'SamToFastqAndBwaMem:6':
16-02-19 23:20:27,991 cromwell-system-akka.actor.default-dispatcher-10 INFO  - WorkflowActor [UUID(60d1afe2)]: created call actor for SamToFastqAndBwaMem:6.
16-02-19 23:20:27,992 cromwell-system-akka.actor.default-dispatcher-10 INFO  - WorkflowActor [UUID(60d1afe2)]: persisting status of SamToFastqAndBwaMem:6 to Running.
16-02-19 23:20:27,992 cromwell-system-akka.actor.default-dispatcher-10 INFO  - JesBackend [UUID(60d1afe2):SamToFastqAndBwaMem:6]: Call GCS path: gs://broad-gp-gotc-pilot/cromwell_execution/PairedEndSingleSampleWorkflow/60d1afe2-dbd4-47e5-9cf5-e2a76d7947cd/call-SamToFastqAndBwaMem/shard-6
16-02-19 23:20:27,992 cromwell-system-akka.actor.default-dispatcher-10 INFO  - JesBackend [UUID(60d1afe2):SamToFastqAndBwaMem:6]: `set -o pipefail
16-02-19 23:20:28,198 cromwell-system-akka.actor.default-dispatcher-10 INFO  - JesBackend [UUID(60d1afe2):SamToFastqAndBwaMem:6]: Starting call with pre-emptible VM
16-02-19 23:20:28,198 cromwell-system-akka.actor.default-dispatcher-10 INFO  - JES Pipeline [UUID(60d1afe2):SamToFastqAndBwaMem:6]: Pipeline parameters are:
16-02-19 23:20:28,241 cromwell-system-akka.actor.default-dispatcher-10 INFO  - JES Pipeline [UUID(60d1afe2):SamToFastqAndBwaMem:6]: Pipeline ID is 2998452744190811110
16-02-19 23:20:28,241 cromwell-system-akka.actor.default-dispatcher-10 INFO  - JES Pipeline [UUID(60d1afe2):SamToFastqAndBwaMem:6]: Project ID: broad-gp-gotc-pilot
16-02-19 23:20:28,241 cromwell-system-akka.actor.default-dispatcher-10 INFO  - JES Run [UUID(60d1afe2):SamToFastqAndBwaMem:6]: Inputs:
xec -> gs://broad-gp-gotc-pilot/cromwell_execution/PairedEndSingleSampleWorkflow/60d1afe2-dbd4-47e5-9cf5-e2a76d7947cd/call-SamToFastqAndBwaMem/shard-6/exec.sh
16-02-19 23:20:28,241 cromwell-system-akka.actor.default-dispatcher-10 INFO  - JES Run [UUID(60d1afe2):SamToFastqAndBwaMem:6]: Outputs:
amToFastqAndBwaMem-6-rc.txt -> gs://broad-gp-gotc-pilot/cromwell_execution/PairedEndSingleSampleWorkflow/60d1afe2-dbd4-47e5-9cf5-e2a76d7947cd/call-SamToFastqAndBwaMem/shard-6/SamToFastqAndBwaMem-6-rc.txt
H7LLCCXX.7.CCTACCAT-GCTTCCTA.unmerged.bam -> gs://broad-gp-gotc-pilot/cromwell_execution/PairedEndSingleSampleWorkflow/60d1afe2-dbd4-47e5-9cf5-e2a76d7947cd/call-SamToFastqAndBwaMem/shard-6/HH7LLCCXX.7.CCTACCAT-GCTTCCTA.unmerged.bam
onitoring -> gs://broad-gp-gotc-pilot/cromwell_execution/PairedEndSingleSampleWorkflow/60d1afe2-dbd4-47e5-9cf5-e2a76d7947cd/call-SamToFastqAndBwaMem/shard-6/monitoring.log
16-02-19 23:20:28,407 cromwell-system-akka.actor.default-dispatcher-10 INFO  - JES Run [UUID(60d1afe2):SamToFastqAndBwaMem:6]: JES Run ID is operations/EP3G1t6vKhjgoqbBlszcvigg6a343KwYKg9wcm9kdWN0aW9uUXVldWU
16-02-19 23:20:28,430 cromwell-system-akka.actor.default-dispatcher-6 INFO  - JES Run [UUID(60d1afe2):SamToFastqAndBwaMem:6]: Status change from - to Initializing
16-02-19 23:26:52,709 cromwell-system-akka.actor.default-dispatcher-13 INFO  - JES Run [UUID(60d1afe2):StripBamExtension:3]: Status change from Running to Success
16-02-19 23:26:53,361 cromwell-system-akka.actor.default-dispatcher-5 INFO  - WorkflowActor [UUID(60d1afe2)]: persisting status of StripBamExtension:3 to Done.
16-02-19 23:31:22,350 cromwell-system-akka.actor.default-dispatcher-23 INFO  - JES Run [UUID(60d1afe2):CreateSequenceGroupingTSV]: Status change from Running to Success
16-02-19 23:31:23,037 cromwell-system-akka.actor.default-dispatcher-26 INFO  - WorkflowActor [UUID(60d1afe2)]: persisting status of CreateSequenceGroupingTSV to Done.
16-02-19 23:31:23,133 cromwell-system-akka.actor.default-dispatcher-14 INFO  - WorkflowActor [UUID(60d1afe2)]: persisting status of $scatter_1 to Starting.
16-02-19 23:47:00,272 cromwell-system-akka.actor.default-dispatcher-13 INFO  - JES Run [UUID(60d1afe2):StripUnmappedBamSuffix:1]: Status change from Running to Success
16-02-19 23:47:01,022 cromwell-system-akka.actor.default-dispatcher-18 INFO  - WorkflowActor [UUID(60d1afe2)]: persisting status of StripUnmappedBamSuffix:1 to Done.
16-02-19 23:47:01,117 cromwell-system-akka.actor.default-dispatcher-17 INFO  - WorkflowActor [UUID(60d1afe2)]: starting calls: PairedEndSingleSampleWorkflow.SamToFastqAndBwaMem
16-02-19 23:47:01,117 cromwell-system-akka.actor.default-dispatcher-17 INFO  - WorkflowActor [UUID(60d1afe2)]: persisting status of SamToFastqAndBwaMem:1 to Starting.
16-02-19 23:47:01,118 cromwell-system-akka.actor.default-dispatcher-17 INFO  - WorkflowActor [UUID(60d1afe2)]: persisting status of StripUnmappedBamSuffix to Starting.
16-02-19 23:47:01,119 cromwell-system-akka.actor.default-dispatcher-17 INFO  - WorkflowActor [UUID(60d1afe2)]: Collection complete for Scattered Call StripUnmappedBamSuffix.
16-02-19 23:47:01,352 cromwell-system-akka.actor.default-dispatcher-23 INFO  - WorkflowActor [UUID(60d1afe2)]: inputs for call 'SamToFastqAndBwaMem:1':
16-02-19 23:47:01,352 cromwell-system-akka.actor.default-dispatcher-23 INFO  - WorkflowActor [UUID(60d1afe2)]: created call actor for SamToFastqAndBwaMem:1.
16-02-19 23:47:01,352 cromwell-system-akka.actor.default-dispatcher-17 INFO  - WorkflowActor [UUID(60d1afe2)]: persisting status of SamToFastqAndBwaMem:1 to Running.
16-02-19 23:47:01,352 cromwell-system-akka.actor.default-dispatcher-25 INFO  - JesBackend [UUID(60d1afe2):SamToFastqAndBwaMem:1]: Call GCS path: gs://broad-gp-gotc-pilot/cromwell_execution/PairedEndSingleSampleWorkflow/60d1afe2-dbd4-47e5-9cf5-e2a76d7947cd/call-SamToFastqAndBwaMem/shard-1
16-02-19 23:47:01,352 cromwell-system-akka.actor.default-dispatcher-25 INFO  - JesBackend [UUID(60d1afe2):SamToFastqAndBwaMem:1]: `set -o pipefail
16-02-19 23:47:01,551 cromwell-system-akka.actor.default-dispatcher-25 INFO  - JesBackend [UUID(60d1afe2):SamToFastqAndBwaMem:1]: Starting call with pre-emptible VM
16-02-19 23:47:01,551 cromwell-system-akka.actor.default-dispatcher-25 INFO  - JES Pipeline [UUID(60d1afe2):SamToFastqAndBwaMem:1]: Pipeline parameters are:
16-02-19 23:47:01,639 cromwell-system-akka.actor.default-dispatcher-25 INFO  - JES Pipeline [UUID(60d1afe2):SamToFastqAndBwaMem:1]: Pipeline ID is 14952001705732422143
16-02-19 23:47:01,639 cromwell-system-akka.actor.default-dispatcher-25 INFO  - JES Pipeline [UUID(60d1afe2):SamToFastqAndBwaMem:1]: Project ID: broad-gp-gotc-pilot
16-02-19 23:47:01,639 cromwell-system-akka.actor.default-dispatcher-25 INFO  - JES Run [UUID(60d1afe2):SamToFastqAndBwaMem:1]: Inputs:
xec -> gs://broad-gp-gotc-pilot/cromwell_execution/PairedEndSingleSampleWorkflow/60d1afe2-dbd4-47e5-9cf5-e2a76d7947cd/call-SamToFastqAndBwaMem/shard-1/exec.sh
16-02-19 23:47:01,639 cromwell-system-akka.actor.default-dispatcher-25 INFO  - JES Run [UUID(60d1afe2):SamToFastqAndBwaMem:1]: Outputs:
amToFastqAndBwaMem-1-rc.txt -> gs://broad-gp-gotc-pilot/cromwell_execution/PairedEndSingleSampleWorkflow/60d1afe2-dbd4-47e5-9cf5-e2a76d7947cd/call-SamToFastqAndBwaMem/shard-1/SamToFastqAndBwaMem-1-rc.txt
H7LLCCXX.2.CCTACCAT-GCTTCCTA.unmerged.bam -> gs://broad-gp-gotc-pilot/cromwell_execution/PairedEndSingleSampleWorkflow/60d1afe2-dbd4-47e5-9cf5-e2a76d7947cd/call-SamToFastqAndBwaMem/shard-1/HH7LLCCXX.2.CCTACCAT-GCTTCCTA.unmerged.bam
onitoring -> gs://broad-gp-gotc-pilot/cromwell_execution/PairedEndSingleSampleWorkflow/60d1afe2-dbd4-47e5-9cf5-e2a76d7947cd/call-SamToFastqAndBwaMem/shard-1/monitoring.log
16-02-19 23:47:01,716 cromwell-system-akka.actor.default-dispatcher-7 INFO  - WorkflowActor [UUID(60d1afe2)]: persisting status of StripUnmappedBamSuffix to Done.
16-02-19 23:47:01,866 cromwell-system-akka.actor.default-dispatcher-25 INFO  - JES Run [UUID(60d1afe2):SamToFastqAndBwaMem:1]: JES Run ID is operations/ELjnt9-vKhjLucrz4e7x72Mg6a343KwYKg9wcm9kdWN0aW9uUXVldWU
16-02-19 23:47:01,928 cromwell-system-akka.actor.default-dispatcher-7 INFO  - JES Run [UUID(60d1afe2):SamToFastqAndBwaMem:1]: Status change from - to Initializing
16-02-19 23:48:01,480 cromwell-system-akka.actor.default-dispatcher-18 INFO  - JES Run [UUID(60d1afe2):StripBamExtension:0]: Status change from Running to Success
16-02-19 23:48:02,176 cromwell-system-akka.actor.default-dispatcher-18 INFO  - WorkflowActor [UUID(60d1afe2)]: persisting status of StripBamExtension:0 to Done.
16-02-19 23:48:02,278 cromwell-system-akka.actor.default-dispatcher-18 INFO  - WorkflowActor [UUID(60d1afe2)]: starting calls: PairedEndSingleSampleWorkflow.CollectQualityYieldMetrics
16-02-19 23:48:02,278 cromwell-system-akka.actor.default-dispatcher-18 INFO  - WorkflowActor [UUID(60d1afe2)]: persisting status of CollectQualityYieldMetrics:0 to Starting.
16-02-19 23:48:02,511 cromwell-system-akka.actor.default-dispatcher-5 INFO  - WorkflowActor [UUID(60d1afe2)]: inputs for call 'CollectQualityYieldMetrics:0':
16-02-19 23:48:02,511 cromwell-system-akka.actor.default-dispatcher-20 INFO  - WorkflowActor [UUID(60d1afe2)]: created call actor for CollectQualityYieldMetrics:0.
16-02-19 23:48:02,511 cromwell-system-akka.actor.default-dispatcher-24 INFO  - WorkflowActor [UUID(60d1afe2)]: persisting status of CollectQualityYieldMetrics:0 to Running.
16-02-19 23:48:02,511 cromwell-system-akka.actor.default-dispatcher-24 INFO  - JesBackend [UUID(60d1afe2):CollectQualityYieldMetrics:0]: Call GCS path: gs://broad-gp-gotc-pilot/cromwell_execution/PairedEndSingleSampleWorkflow/60d1afe2-dbd4-47e5-9cf5-e2a76d7947cd/call-CollectQualityYieldMetrics/shard-0
16-02-19 23:48:02,512 cromwell-system-akka.actor.default-dispatcher-24 INFO  - JesBackend [UUID(60d1afe2):CollectQualityYieldMetrics:0]: `java -Xmx128m -jar /usr/gitc/picard.jar \
16-02-19 23:48:02,722 cromwell-system-akka.actor.default-dispatcher-24 INFO  - JesBackend [UUID(60d1afe2):CollectQualityYieldMetrics:0]: Starting call with pre-emptible VM
16-02-19 23:48:02,722 cromwell-system-akka.actor.default-dispatcher-24 INFO  - JES Pipeline [UUID(60d1afe2):CollectQualityYieldMetrics:0]: Pipeline parameters are:
16-02-19 23:48:02,812 cromwell-system-akka.actor.default-dispatcher-24 INFO  - JES Pipeline [UUID(60d1afe2):CollectQualityYieldMetrics:0]: Pipeline ID is 18443552739799568830
16-02-19 23:48:02,812 cromwell-system-akka.actor.default-dispatcher-24 INFO  - JES Pipeline [UUID(60d1afe2):CollectQualityYieldMetrics:0]: Project ID: broad-gp-gotc-pilot
16-02-19 23:48:02,812 cromwell-system-akka.actor.default-dispatcher-24 INFO  - JES Run [UUID(60d1afe2):CollectQualityYieldMetrics:0]: Inputs:
xec -> gs://broad-gp-gotc-pilot/cromwell_execution/PairedEndSingleSampleWorkflow/60d1afe2-dbd4-47e5-9cf5-e2a76d7947cd/call-CollectQualityYieldMetrics/shard-0/exec.sh
16-02-19 23:48:02,812 cromwell-system-akka.actor.default-dispatcher-24 INFO  - JES Run [UUID(60d1afe2):CollectQualityYieldMetrics:0]: Outputs:
ollectQualityYieldMetrics-0-rc.txt -> gs://broad-gp-gotc-pilot/cromwell_execution/PairedEndSingleSampleWorkflow/60d1afe2-dbd4-47e5-9cf5-e2a76d7947cd/call-CollectQualityYieldMetrics/shard-0/CollectQualityYieldMetrics-0-rc.txt
H7LLCCXX.1.CCTACCAT-GCTTCCTA.unmapped.quality_yield_metrics -> gs://broad-gp-gotc-pilot/cromwell_execution/PairedEndSingleSampleWorkflow/60d1afe2-dbd4-47e5-9cf5-e2a76d7947cd/call-CollectQualityYieldMetrics/shard-0/HH7LLCCXX.1.CCTACCAT-GCTTCCTA.unmapped.quality_yield_metrics
onitoring -> gs://broad-gp-gotc-pilot/cromwell_execution/PairedEndSingleSampleWorkflow/60d1afe2-dbd4-47e5-9cf5-e2a76d7947cd/call-CollectQualityYieldMetrics/shard-0/monitoring.log
16-02-19 23:48:03,055 cromwell-system-akka.actor.default-dispatcher-24 INFO  - JES Run [UUID(60d1afe2):CollectQualityYieldMetrics:0]: JES Run ID is operations/ELzFu9-vKhi31przqafjg8YBIOmt-NysGCoPcHJvZHVjdGlvblF1ZXVl
16-02-19 23:48:03,126 cromwell-system-akka.actor.default-dispatcher-24 INFO  - JES Run [UUID(60d1afe2):CollectQualityYieldMetrics:0]: Status change from - to Initializing
16-02-20 00:13:06,716 cromwell-system-akka.actor.default-dispatcher-4 INFO  - JES Run [UUID(60d1afe2):SamToFastqAndBwaMem:4]: Status change from Initializing to Running
16-02-20 00:17:33,490 cromwell-system-akka.actor.default-dispatcher-4 INFO  - JES Run [UUID(60d1afe2):CollectQualityYieldMetrics:3]: Status change from Initializing to Running
16-02-20 00:22:04,064 cromwell-system-akka.actor.default-dispatcher-20 INFO  - WorkflowActor [UUID(60d1afe2)]: persisting status of CollectQualityYieldMetrics:1 to Done.
16-02-20 01:10:49,773 cromwell-system-akka.actor.default-dispatcher-2 INFO  - JES Run [UUID(60d1afe2):CollectQualityYieldMetrics:6]: Status change from Initializing to Running
16-02-20 01:24:55,758 cromwell-system-akka.actor.default-dispatcher-20 INFO  - JES Run [UUID(60d1afe2):CollectQualityYieldMetrics:6]: Status change from Running to Success
16-02-20 01:24:56,247 cromwell-system-akka.actor.default-dispatcher-24 INFO  - WorkflowActor [UUID(60d1afe2)]: persisting status of CollectQualityYieldMetrics:6 to Done.
16-02-20 01:24:56,351 cromwell-system-akka.actor.default-dispatcher-8 INFO  - WorkflowActor [UUID(60d1afe2)]: persisting status of CollectQualityYieldMetrics to Starting.
16-02-20 01:24:56,351 cromwell-system-akka.actor.default-dispatcher-8 INFO  - WorkflowActor [UUID(60d1afe2)]: Collection complete for Scattered Call CollectQualityYieldMetrics.
16-02-20 01:24:56,608 cromwell-system-akka.actor.default-dispatcher-8 INFO  - WorkflowActor [UUID(60d1afe2)]: persisting status of CollectQualityYieldMetrics to Done.
16-02-20 01:31:27,466 cromwell-system-akka.actor.default-dispatcher-3 INFO  - JES Run [UUID(60d1afe2):SamToFastqAndBwaMem:6]: Status change from Running to Failed
16-02-20 01:31:27,467 cromwell-system-akka.actor.default-dispatcher-23 ERROR - CallActor [UUID(60d1afe2):SamToFastqAndBwaMem:6]: Failing call with retryable Failure: Task 60d1afe2-dbd4-47e5-9cf5-e2a76d7947cd:SamToFastqAndBwaMem was preempted for the 1st time. The call will be re-started with another pre-emptible VM (max pre-emptible attempts number is 3).
omwell.engine.package$PreemptedException: Task 60d1afe2-dbd4-47e5-9cf5-e2a76d7947cd:SamToFastqAndBwaMem was preempted for the 1st time. The call will be re-started with another pre-emptible VM (max pre-emptible attempts number is 3).
16-02-20 01:31:27,851 cromwell-system-akka.actor.default-dispatcher-23 INFO  - WorkflowActor [UUID(60d1afe2)]: persisting status of SamToFastqAndBwaMem:6 to Preempted.
16-02-20 01:31:27,960 cromwell-system-akka.actor.default-dispatcher-21 INFO  - WorkflowActor [UUID(60d1afe2)]: starting calls: PairedEndSingleSampleWorkflow.SamToFastqAndBwaMem
16-02-20 01:31:27,960 cromwell-system-akka.actor.default-dispatcher-21 INFO  - WorkflowActor [UUID(60d1afe2)]: persisting status of SamToFastqAndBwaMem:6:2 to Starting.
16-02-20 01:31:28,082 cromwell-system-akka.actor.default-dispatcher-2 INFO  - WorkflowActor [UUID(60d1afe2)]: inputs for call 'SamToFastqAndBwaMem:6:2':
16-02-20 01:31:28,082 cromwell-system-akka.actor.default-dispatcher-3 INFO  - WorkflowActor [UUID(60d1afe2)]: created call actor for SamToFastqAndBwaMem:6:2.
16-02-20 01:31:28,082 cromwell-system-akka.actor.default-dispatcher-18 INFO  - WorkflowActor [UUID(60d1afe2)]: persisting status of SamToFastqAndBwaMem:6:2 to Running.
16-02-20 01:31:28,082 cromwell-system-akka.actor.default-dispatcher-2 INFO  - JesBackend [UUID(60d1afe2):SamToFastqAndBwaMem:6:2]: Call GCS path: gs://broad-gp-gotc-pilot/cromwell_execution/PairedEndSingleSampleWorkflow/60d1afe2-dbd4-47e5-9cf5-e2a76d7947cd/call-SamToFastqAndBwaMem/shard-6/attempt-2
16-02-20 01:31:28,082 cromwell-system-akka.actor.default-dispatcher-2 INFO  - JesBackend [UUID(60d1afe2):SamToFastqAndBwaMem:6:2]: `set -o pipefail
16-02-20 01:31:28,277 cromwell-system-akka.actor.default-dispatcher-2 INFO  - JesBackend [UUID(60d1afe2):SamToFastqAndBwaMem:6:2]: Starting call with pre-emptible VM
16-02-20 01:31:28,277 cromwell-system-akka.actor.default-dispatcher-2 INFO  - JES Pipeline [UUID(60d1afe2):SamToFastqAndBwaMem:6:2]: Pipeline parameters are:
16-02-20 01:31:28,314 cromwell-system-akka.actor.default-dispatcher-2 INFO  - JES Pipeline [UUID(60d1afe2):SamToFastqAndBwaMem:6:2]: Pipeline ID is 9295394283819134332
16-02-20 01:31:28,314 cromwell-system-akka.actor.default-dispatcher-2 INFO  - JES Pipeline [UUID(60d1afe2):SamToFastqAndBwaMem:6:2]: Project ID: broad-gp-gotc-pilot
16-02-20 01:31:28,314 cromwell-system-akka.actor.default-dispatcher-2 INFO  - JES Run [UUID(60d1afe2):SamToFastqAndBwaMem:6:2]: Inputs:
xec -> gs://broad-gp-gotc-pilot/cromwell_execution/PairedEndSingleSampleWorkflow/60d1afe2-dbd4-47e5-9cf5-e2a76d7947cd/call-SamToFastqAndBwaMem/shard-6/attempt-2/exec.sh
16-02-20 01:31:28,314 cromwell-system-akka.actor.default-dispatcher-2 INFO  - JES Run [UUID(60d1afe2):SamToFastqAndBwaMem:6:2]: Outputs:
amToFastqAndBwaMem-6-rc.txt -> gs://broad-gp-gotc-pilot/cromwell_execution/PairedEndSingleSampleWorkflow/60d1afe2-dbd4-47e5-9cf5-e2a76d7947cd/call-SamToFastqAndBwaMem/shard-6/attempt-2/SamToFastqAndBwaMem-6-rc.txt
H7LLCCXX.7.CCTACCAT-GCTTCCTA.unmerged.bam -> gs://broad-gp-gotc-pilot/cromwell_execution/PairedEndSingleSampleWorkflow/60d1afe2-dbd4-47e5-9cf5-e2a76d7947cd/call-SamToFastqAndBwaMem/shard-6/attempt-2/HH7LLCCXX.7.CCTACCAT-GCTTCCTA.unmerged.bam
onitoring -> gs://broad-gp-gotc-pilot/cromwell_execution/PairedEndSingleSampleWorkflow/60d1afe2-dbd4-47e5-9cf5-e2a76d7947cd/call-SamToFastqAndBwaMem/shard-6/attempt-2/monitoring.log
16-02-20 01:31:28,466 cromwell-system-akka.actor.default-dispatcher-2 INFO  - JES Run [UUID(60d1afe2):SamToFastqAndBwaMem:6:2]: JES Run ID is operations/ENGltuKvKhj0v66otujptZkBIOmt-NysGCoPcHJvZHVjdGlvblF1ZXVl
16-02-20 01:31:28,481 cromwell-system-akka.actor.default-dispatcher-18 INFO  - JES Run [UUID(60d1afe2):SamToFastqAndBwaMem:6:2]: Status change from - to Initializing
16-02-20 02:07:32,296 cromwell-system-akka.actor.default-dispatcher-23 INFO  - JES Run [UUID(60d1afe2):MergeBamAlignment:0]: Status change from Initializing to Running
16-02-20 02:40:13,647 cromwell-system-akka.actor.default-dispatcher-12 INFO  - JES Run [UUID(60d1afe2):SamToFastqAndBwaMem:4:2]: Status change from Initializing to Running
16-02-20 03:12:52,076 cromwell-system-akka.actor.default-dispatcher-8 INFO  - JES Run [UUID(60d1afe2):MergeBamAlignment:1]: Status change from Initializing to Running
16-02-20 04:24:56,142 cromwell-system-akka.actor.default-dispatcher-4 INFO  - JES Run [UUID(60d1afe2):ReadGroupMarkDuplicates:0]: Status change from Running to Success
16-02-20 04:24:56,666 cromwell-system-akka.actor.default-dispatcher-6 INFO  - WorkflowActor [UUID(60d1afe2)]: persisting status of ReadGroupMarkDuplicates:0 to Done.
16-02-20 04:24:56,760 cromwell-system-akka.actor.default-dispatcher-6 INFO  - WorkflowActor [UUID(60d1afe2)]: starting calls: PairedEndSingleSampleWorkflow.CollectReadgroupBamQualityMetrics, PairedEndSingleSampleWorkflow.ValidateReadGroupSamFile
16-02-20 04:24:56,760 cromwell-system-akka.actor.default-dispatcher-6 INFO  - WorkflowActor [UUID(60d1afe2)]: persisting status of CollectReadgroupBamQualityMetrics:0 to Starting.
16-02-20 04:24:56,761 cromwell-system-akka.actor.default-dispatcher-6 INFO  - WorkflowActor [UUID(60d1afe2)]: persisting status of ValidateReadGroupSamFile:0 to Starting.
16-02-20 04:24:56,881 cromwell-system-akka.actor.default-dispatcher-6 INFO  - WorkflowActor [UUID(60d1afe2)]: inputs for call 'CollectReadgroupBamQualityMetrics:0':
nput_bam -> WdlSingleFile(gs://broad-gp-gotc-pilot/cromwell_execution/PairedEndSingleSampleWorkflow/60d1afe2-dbd4-47e5-9cf5-e2a76d7947cd/call-ReadGroupMarkDuplicates/shard-0/HH7LLCCXX.1.CCTACCAT-GCTTCCTA.aligned.duplicates_marked.bam)
nput_bam_index -> WdlSingleFile(gs://broad-gp-gotc-pilot/cromwell_execution/PairedEndSingleSampleWorkflow/60d1afe2-dbd4-47e5-9cf5-e2a76d7947cd/call-ReadGroupMarkDuplicates/shard-0/HH7LLCCXX.1.CCTACCAT-GCTTCCTA.aligned.duplicates_marked.bai)
16-02-20 04:24:56,881 cromwell-system-akka.actor.default-dispatcher-19 INFO  - WorkflowActor [UUID(60d1afe2)]: created call actor for CollectReadgroupBamQualityMetrics:0.
16-02-20 04:24:56,881 cromwell-system-akka.actor.default-dispatcher-19 INFO  - JesBackend [UUID(60d1afe2):CollectReadgroupBamQualityMetrics:0]: Call GCS path: gs://broad-gp-gotc-pilot/cromwell_execution/PairedEndSingleSampleWorkflow/60d1afe2-dbd4-47e5-9cf5-e2a76d7947cd/call-CollectReadgroupBamQualityMetrics/shard-0
16-02-20 04:24:56,882 cromwell-system-akka.actor.default-dispatcher-19 INFO  - JesBackend [UUID(60d1afe2):CollectReadgroupBamQualityMetrics:0]: `java -Xmx5000m -jar /usr/gitc/picard.jar \
NPUT=/cromwell_root/broad-gp-gotc-pilot/cromwell_execution/PairedEndSingleSampleWorkflow/60d1afe2-dbd4-47e5-9cf5-e2a76d7947cd/call-ReadGroupMarkDuplicates/shard-0/HH7LLCCXX.1.CCTACCAT-GCTTCCTA.aligned.duplicates_marked.bam \
16-02-20 04:24:56,882 cromwell-system-akka.actor.default-dispatcher-6 INFO  - WorkflowActor [UUID(60d1afe2)]: inputs for call 'ValidateReadGroupSamFile:0':
nput_bam -> WdlSingleFile(gs://broad-gp-gotc-pilot/cromwell_execution/PairedEndSingleSampleWorkflow/60d1afe2-dbd4-47e5-9cf5-e2a76d7947cd/call-ReadGroupMarkDuplicates/shard-0/HH7LLCCXX.1.CCTACCAT-GCTTCCTA.aligned.duplicates_marked.bam)
nput_bam_index -> WdlSingleFile(gs://broad-gp-gotc-pilot/cromwell_execution/PairedEndSingleSampleWorkflow/60d1afe2-dbd4-47e5-9cf5-e2a76d7947cd/call-ReadGroupMarkDuplicates/shard-0/HH7LLCCXX.1.CCTACCAT-GCTTCCTA.aligned.duplicates_marked.bai)
16-02-20 04:24:56,882 cromwell-system-akka.actor.default-dispatcher-17 INFO  - WorkflowActor [UUID(60d1afe2)]: created call actor for ValidateReadGroupSamFile:0.
16-02-20 04:24:56,882 cromwell-system-akka.actor.default-dispatcher-17 INFO  - WorkflowActor [UUID(60d1afe2)]: persisting status of CollectReadgroupBamQualityMetrics:0 to Running.
16-02-20 04:24:56,882 cromwell-system-akka.actor.default-dispatcher-17 INFO  - WorkflowActor [UUID(60d1afe2)]: persisting status of ValidateReadGroupSamFile:0 to Running.
16-02-20 04:24:56,882 cromwell-system-akka.actor.default-dispatcher-6 INFO  - JesBackend [UUID(60d1afe2):ValidateReadGroupSamFile:0]: Call GCS path: gs://broad-gp-gotc-pilot/cromwell_execution/PairedEndSingleSampleWorkflow/60d1afe2-dbd4-47e5-9cf5-e2a76d7947cd/call-ValidateReadGroupSamFile/shard-0
16-02-20 04:24:56,882 cromwell-system-akka.actor.default-dispatcher-6 INFO  - JesBackend [UUID(60d1afe2):ValidateReadGroupSamFile:0]: `java -Xmx4000m -jar /usr/gitc/picard.jar \
NPUT=/cromwell_root/broad-gp-gotc-pilot/cromwell_execution/PairedEndSingleSampleWorkflow/60d1afe2-dbd4-47e5-9cf5-e2a76d7947cd/call-ReadGroupMarkDuplicates/shard-0/HH7LLCCXX.1.CCTACCAT-GCTTCCTA.aligned.duplicates_marked.bam \
16-02-20 04:24:57,025 cromwell-system-akka.actor.default-dispatcher-6 INFO  - JesBackend [UUID(60d1afe2):ValidateReadGroupSamFile:0]: Starting call with pre-emptible VM
16-02-20 04:24:57,025 cromwell-system-akka.actor.default-dispatcher-6 INFO  - JES Pipeline [UUID(60d1afe2):ValidateReadGroupSamFile:0]: Pipeline parameters are:
name=input_bam-0, type=REFERENCE, value=/cromwell_root/broad-gp-gotc-pilot/cromwell_execution/PairedEndSingleSampleWorkflow/60d1afe2-dbd4-47e5-9cf5-e2a76d7947cd/call-ReadGroupMarkDuplicates/shard-0/HH7LLCCXX.1.CCTACCAT-GCTTCCTA.aligned.duplicates_marked.bam}
name=input_bam_index-0, type=REFERENCE, value=/cromwell_root/broad-gp-gotc-pilot/cromwell_execution/PairedEndSingleSampleWorkflow/60d1afe2-dbd4-47e5-9cf5-e2a76d7947cd/call-ReadGroupMarkDuplicates/shard-0/HH7LLCCXX.1.CCTACCAT-GCTTCCTA.aligned.duplicates_marked.bai}
16-02-20 04:24:57,060 cromwell-system-akka.actor.default-dispatcher-6 INFO  - JES Pipeline [UUID(60d1afe2):ValidateReadGroupSamFile:0]: Pipeline ID is 15555063970540350497
16-02-20 04:24:57,060 cromwell-system-akka.actor.default-dispatcher-6 INFO  - JES Pipeline [UUID(60d1afe2):ValidateReadGroupSamFile:0]: Project ID: broad-gp-gotc-pilot
16-02-20 04:24:57,060 cromwell-system-akka.actor.default-dispatcher-6 INFO  - JES Run [UUID(60d1afe2):ValidateReadGroupSamFile:0]: Inputs:
nput_bam_index-0 -> gs://broad-gp-gotc-pilot/cromwell_execution/PairedEndSingleSampleWorkflow/60d1afe2-dbd4-47e5-9cf5-e2a76d7947cd/call-ReadGroupMarkDuplicates/shard-0/HH7LLCCXX.1.CCTACCAT-GCTTCCTA.aligned.duplicates_marked.bai
nput_bam-0 -> gs://broad-gp-gotc-pilot/cromwell_execution/PairedEndSingleSampleWorkflow/60d1afe2-dbd4-47e5-9cf5-e2a76d7947cd/call-ReadGroupMarkDuplicates/shard-0/HH7LLCCXX.1.CCTACCAT-GCTTCCTA.aligned.duplicates_marked.bam
xec -> gs://broad-gp-gotc-pilot/cromwell_execution/PairedEndSingleSampleWorkflow/60d1afe2-dbd4-47e5-9cf5-e2a76d7947cd/call-ValidateReadGroupSamFile/shard-0/exec.sh
16-02-20 04:24:57,060 cromwell-system-akka.actor.default-dispatcher-6 INFO  - JES Run [UUID(60d1afe2):ValidateReadGroupSamFile:0]: Outputs:
alidateReadGroupSamFile-0-rc.txt -> gs://broad-gp-gotc-pilot/cromwell_execution/PairedEndSingleSampleWorkflow/60d1afe2-dbd4-47e5-9cf5-e2a76d7947cd/call-ValidateReadGroupSamFile/shard-0/ValidateReadGroupSamFile-0-rc.txt
H7LLCCXX.1.CCTACCAT-GCTTCCTA.validation_report -> gs://broad-gp-gotc-pilot/cromwell_execution/PairedEndSingleSampleWorkflow/60d1afe2-dbd4-47e5-9cf5-e2a76d7947cd/call-ValidateReadGroupSamFile/shard-0/HH7LLCCXX.1.CCTACCAT-GCTTCCTA.validation_report
onitoring -> gs://broad-gp-gotc-pilot/cromwell_execution/PairedEndSingleSampleWorkflow/60d1afe2-dbd4-47e5-9cf5-e2a76d7947cd/call-ValidateReadGroupSamFile/shard-0/monitoring.log
16-02-20 04:24:57,061 cromwell-system-akka.actor.default-dispatcher-19 INFO  - JES Pipeline [UUID(60d1afe2):CollectReadgroupBamQualityMetrics:0]: Pipeline parameters are:
name=input_bam-0, type=REFERENCE, value=/cromwell_root/broad-gp-gotc-pilot/cromwell_execution/PairedEndSingleSampleWorkflow/60d1afe2-dbd4-47e5-9cf5-e2a76d7947cd/call-ReadGroupMarkDuplicates/shard-0/HH7LLCCXX.1.CCTACCAT-GCTTCCTA.aligned.duplicates_marked.bam}
name=input_bam_index-0, type=REFERENCE, value=/cromwell_root/broad-gp-gotc-pilot/cromwell_execution/PairedEndSingleSampleWorkflow/60d1afe2-dbd4-47e5-9cf5-e2a76d7947cd/call-ReadGroupMarkDuplicates/shard-0/HH7LLCCXX.1.CCTACCAT-GCTTCCTA.aligned.duplicates_marked.bai}
16-02-20 04:24:57,092 cromwell-system-akka.actor.default-dispatcher-19 INFO  - JES Pipeline [UUID(60d1afe2):CollectReadgroupBamQualityMetrics:0]: Pipeline ID is 6707291410576002331
16-02-20 04:24:57,092 cromwell-system-akka.actor.default-dispatcher-19 INFO  - JES Pipeline [UUID(60d1afe2):CollectReadgroupBamQualityMetrics:0]: Project ID: broad-gp-gotc-pilot
16-02-20 04:24:57,093 cromwell-system-akka.actor.default-dispatcher-19 INFO  - JES Run [UUID(60d1afe2):CollectReadgroupBamQualityMetrics:0]: Inputs:
nput_bam_index-0 -> gs://broad-gp-gotc-pilot/cromwell_execution/PairedEndSingleSampleWorkflow/60d1afe2-dbd4-47e5-9cf5-e2a76d7947cd/call-ReadGroupMarkDuplicates/shard-0/HH7LLCCXX.1.CCTACCAT-GCTTCCTA.aligned.duplicates_marked.bai
nput_bam-0 -> gs://broad-gp-gotc-pilot/cromwell_execution/PairedEndSingleSampleWorkflow/60d1afe2-dbd4-47e5-9cf5-e2a76d7947cd/call-ReadGroupMarkDuplicates/shard-0/HH7LLCCXX.1.CCTACCAT-GCTTCCTA.aligned.duplicates_marked.bam
xec -> gs://broad-gp-gotc-pilot/cromwell_execution/PairedEndSingleSampleWorkflow/60d1afe2-dbd4-47e5-9cf5-e2a76d7947cd/call-CollectReadgroupBamQualityMetrics/shard-0/exec.sh
16-02-20 04:24:57,093 cromwell-system-akka.actor.default-dispatcher-19 INFO  - JES Run [UUID(60d1afe2):CollectReadgroupBamQualityMetrics:0]: Outputs:
ollectReadgroupBamQualityMetrics-0-rc.txt -> gs://broad-gp-gotc-pilot/cromwell_execution/PairedEndSingleSampleWorkflow/60d1afe2-dbd4-47e5-9cf5-e2a76d7947cd/call-CollectReadgroupBamQualityMetrics/shard-0/CollectReadgroupBamQualityMetrics-0-rc.txt
H7LLCCXX.1.CCTACCAT-GCTTCCTA.* -> gs://broad-gp-gotc-pilot/cromwell_execution/PairedEndSingleSampleWorkflow/60d1afe2-dbd4-47e5-9cf5-e2a76d7947cd/call-CollectReadgroupBamQualityMetrics/shard-0/glob-565cbf80dc91604ad3c4ccab50c461c8/
onitoring -> gs://broad-gp-gotc-pilot/cromwell_execution/PairedEndSingleSampleWorkflow/60d1afe2-dbd4-47e5-9cf5-e2a76d7947cd/call-CollectReadgroupBamQualityMetrics/shard-0/monitoring.log
16-02-20 04:24:57,178 cromwell-system-akka.actor.default-dispatcher-6 INFO  - JES Run [UUID(60d1afe2):ValidateReadGroupSamFile:0]: JES Run ID is operations/EP_LseevKhj8-IrZtMrongEg6a343KwYKg9wcm9kdWN0aW9uUXVldWU
16-02-20 04:24:57,198 cromwell-system-akka.actor.default-dispatcher-10 INFO  - JES Run [UUID(60d1afe2):ValidateReadGroupSamFile:0]: Status change from - to Initializing
16-02-20 04:24:57,203 cromwell-system-akka.actor.default-dispatcher-19 INFO  - JES Run [UUID(60d1afe2):CollectReadgroupBamQualityMetrics:0]: JES Run ID is operations/EJzMseevKhjVuorMpojPkXcg6a343KwYKg9wcm9kdWN0aW9uUXVldWU
16-02-20 04:24:57,222 cromwell-system-akka.actor.default-dispatcher-19 INFO  - JES Run [UUID(60d1afe2):CollectReadgroupBamQualityMetrics:0]: Status change from - to Initializing
16-02-20 04:25:54,008 cromwell-system-akka.actor.default-dispatcher-18 INFO  - JES Run [UUID(60d1afe2):ValidateReadGroupSamFile:0]: Status change from Initializing to Running
16-02-20 04:25:57,959 cromwell-system-akka.actor.default-dispatcher-8 INFO  - JES Run [UUID(60d1afe2):CollectReadgroupBamQualityMetrics:0]: Status change from Initializing to Running
16-02-20 04:38:26,812 cromwell-system-akka.actor.default-dispatcher-4 INFO  - JES Run [UUID(60d1afe2):CollectReadgroupBamQualityMetrics:5]: Status change from Initializing to Running
16-02-20 04:39:28,762 cromwell-system-akka.actor.default-dispatcher-10 INFO  - JES Run [UUID(60d1afe2):ValidateReadGroupSamFile:5]: Status change from Initializing to Running
16-02-20 04:49:09,887 cromwell-system-akka.actor.default-dispatcher-11 INFO  - JES Run [UUID(60d1afe2):ValidateReadGroupSamFile:2]: Status change from Running to Success
16-02-20 04:49:10,356 cromwell-system-akka.actor.default-dispatcher-26 INFO  - WorkflowActor [UUID(60d1afe2)]: persisting status of ValidateReadGroupSamFile:2 to Done.
16-02-20 04:57:34,890 cromwell-system-akka.actor.default-dispatcher-3 INFO  - JES Run [UUID(60d1afe2):CollectReadgroupBamQualityMetrics:2]: Status change from Running to Success
16-02-20 04:57:35,442 cromwell-system-akka.actor.default-dispatcher-16 INFO  - WorkflowActor [UUID(60d1afe2)]: persisting status of CollectReadgroupBamQualityMetrics:2 to Done.
16-02-20 04:59:05,519 cromwell-system-akka.actor.default-dispatcher-16 INFO  - JES Run [UUID(60d1afe2):ValidateReadGroupSamFile:5]: Status change from Running to Success
16-02-20 04:59:06,038 cromwell-system-akka.actor.default-dispatcher-10 INFO  - WorkflowActor [UUID(60d1afe2)]: persisting status of ValidateReadGroupSamFile:5 to Done.
16-02-20 05:18:43,822 cromwell-system-akka.actor.default-dispatcher-4 INFO  - JES Run [UUID(60d1afe2):SamToFastqAndBwaMem:4:2]: Status change from Running to Success
16-02-20 05:19:40,951 cromwell-system-akka.actor.default-dispatcher-6 INFO  - JES Run [UUID(60d1afe2):MergeBamAlignment:4]: Status change from Initializing to Running
16-02-20 05:48:27,406 cromwell-system-akka.actor.default-dispatcher-5 INFO  - JES Run [UUID(60d1afe2):ValidateReadGroupSamFile:1]: Status change from Initializing to Running
16-02-20 05:58:04,887 cromwell-system-akka.actor.default-dispatcher-2 INFO  - JES Run [UUID(60d1afe2):MergeBamAlignment:7]: Status change from Running to Success
16-02-20 05:58:05,326 cromwell-system-akka.actor.default-dispatcher-11 INFO  - WorkflowActor [UUID(60d1afe2)]: persisting status of MergeBamAlignment:7 to Done.
16-02-20 05:58:05,423 cromwell-system-akka.actor.default-dispatcher-2 INFO  - WorkflowActor [UUID(60d1afe2)]: starting calls: PairedEndSingleSampleWorkflow.ReadGroupMarkDuplicates
16-02-20 05:58:05,423 cromwell-system-akka.actor.default-dispatcher-2 INFO  - WorkflowActor [UUID(60d1afe2)]: persisting status of ReadGroupMarkDuplicates:7 to Starting.
16-02-20 05:58:05,541 cromwell-system-akka.actor.default-dispatcher-25 INFO  - WorkflowActor [UUID(60d1afe2)]: inputs for call 'ReadGroupMarkDuplicates:7':
nput_bams -> ["gs://broad-gp-gotc-pilot/cromwell_execution/PairedEndSingleSampleWorkflow/60d1afe2-dbd4-47e5-9cf5-e2a76d7947cd/call-MergeBamAlignment/shard-7/HH7LLCCXX.8.CCTACCAT-GCTTCCTA.aligned.bam"]
nput_bam_indexes -> ["gs://broad-gp-gotc-pilot/cromwell_execution/PairedEndSingleSampleWorkflow/60d1afe2-dbd4-47e5-9cf5-e2a76d7947cd/call-MergeBamAlignment/shard-7/HH7LLCCXX.8.CCTACCAT-GCTTCCTA.aligned.bai"]
16-02-20 05:58:05,541 cromwell-system-akka.actor.default-dispatcher-2 INFO  - WorkflowActor [UUID(60d1afe2)]: created call actor for ReadGroupMarkDuplicates:7.
16-02-20 05:58:05,541 cromwell-system-akka.actor.default-dispatcher-25 INFO  - WorkflowActor [UUID(60d1afe2)]: persisting status of ReadGroupMarkDuplicates:7 to Running.
16-02-20 05:58:05,541 cromwell-system-akka.actor.default-dispatcher-17 INFO  - JesBackend [UUID(60d1afe2):ReadGroupMarkDuplicates:7]: Call GCS path: gs://broad-gp-gotc-pilot/cromwell_execution/PairedEndSingleSampleWorkflow/60d1afe2-dbd4-47e5-9cf5-e2a76d7947cd/call-ReadGroupMarkDuplicates/shard-7
16-02-20 05:58:05,541 cromwell-system-akka.actor.default-dispatcher-17 INFO  - JesBackend [UUID(60d1afe2):ReadGroupMarkDuplicates:7]: `java -Xmx4000m -jar /usr/gitc/picard.jar \
NPUT=/cromwell_root/broad-gp-gotc-pilot/cromwell_execution/PairedEndSingleSampleWorkflow/60d1afe2-dbd4-47e5-9cf5-e2a76d7947cd/call-MergeBamAlignment/shard-7/HH7LLCCXX.8.CCTACCAT-GCTTCCTA.aligned.bam \
16-02-20 05:58:05,672 cromwell-system-akka.actor.default-dispatcher-17 INFO  - JES Pipeline [UUID(60d1afe2):ReadGroupMarkDuplicates:7]: Pipeline parameters are:
name=input_bams-0, type=REFERENCE, value=/cromwell_root/broad-gp-gotc-pilot/cromwell_execution/PairedEndSingleSampleWorkflow/60d1afe2-dbd4-47e5-9cf5-e2a76d7947cd/call-MergeBamAlignment/shard-7/HH7LLCCXX.8.CCTACCAT-GCTTCCTA.aligned.bam}
name=input_bam_indexes-0, type=REFERENCE, value=/cromwell_root/broad-gp-gotc-pilot/cromwell_execution/PairedEndSingleSampleWorkflow/60d1afe2-dbd4-47e5-9cf5-e2a76d7947cd/call-MergeBamAlignment/shard-7/HH7LLCCXX.8.CCTACCAT-GCTTCCTA.aligned.bai}
16-02-20 05:58:05,763 cromwell-system-akka.actor.default-dispatcher-17 INFO  - JES Pipeline [UUID(60d1afe2):ReadGroupMarkDuplicates:7]: Pipeline ID is 17791570651574656474
16-02-20 05:58:05,763 cromwell-system-akka.actor.default-dispatcher-17 INFO  - JES Pipeline [UUID(60d1afe2):ReadGroupMarkDuplicates:7]: Project ID: broad-gp-gotc-pilot
16-02-20 05:58:05,763 cromwell-system-akka.actor.default-dispatcher-17 INFO  - JES Run [UUID(60d1afe2):ReadGroupMarkDuplicates:7]: Inputs:
nput_bams-0 -> gs://broad-gp-gotc-pilot/cromwell_execution/PairedEndSingleSampleWorkflow/60d1afe2-dbd4-47e5-9cf5-e2a76d7947cd/call-MergeBamAlignment/shard-7/HH7LLCCXX.8.CCTACCAT-GCTTCCTA.aligned.bam
nput_bam_indexes-0 -> gs://broad-gp-gotc-pilot/cromwell_execution/PairedEndSingleSampleWorkflow/60d1afe2-dbd4-47e5-9cf5-e2a76d7947cd/call-MergeBamAlignment/shard-7/HH7LLCCXX.8.CCTACCAT-GCTTCCTA.aligned.bai
xec -> gs://broad-gp-gotc-pilot/cromwell_execution/PairedEndSingleSampleWorkflow/60d1afe2-dbd4-47e5-9cf5-e2a76d7947cd/call-ReadGroupMarkDuplicates/shard-7/exec.sh
16-02-20 05:58:05,764 cromwell-system-akka.actor.default-dispatcher-17 INFO  - JES Run [UUID(60d1afe2):ReadGroupMarkDuplicates:7]: Outputs:
H7LLCCXX.8.CCTACCAT-GCTTCCTA.aligned.duplicates_marked.bam -> gs://broad-gp-gotc-pilot/cromwell_execution/PairedEndSingleSampleWorkflow/60d1afe2-dbd4-47e5-9cf5-e2a76d7947cd/call-ReadGroupMarkDuplicates/shard-7/HH7LLCCXX.8.CCTACCAT-GCTTCCTA.aligned.duplicates_marked.bam
H7LLCCXX.8.CCTACCAT-GCTTCCTA.duplicate_metrics -> gs://broad-gp-gotc-pilot/cromwell_execution/PairedEndSingleSampleWorkflow/60d1afe2-dbd4-47e5-9cf5-e2a76d7947cd/call-ReadGroupMarkDuplicates/shard-7/HH7LLCCXX.8.CCTACCAT-GCTTCCTA.duplicate_metrics
onitoring -> gs://broad-gp-gotc-pilot/cromwell_execution/PairedEndSingleSampleWorkflow/60d1afe2-dbd4-47e5-9cf5-e2a76d7947cd/call-ReadGroupMarkDuplicates/shard-7/monitoring.log
H7LLCCXX.8.CCTACCAT-GCTTCCTA.aligned.duplicates_marked.bam.md5 -> gs://broad-gp-gotc-pilot/cromwell_execution/PairedEndSingleSampleWorkflow/60d1afe2-dbd4-47e5-9cf5-e2a76d7947cd/call-ReadGroupMarkDuplicates/shard-7/HH7LLCCXX.8.CCTACCAT-GCTTCCTA.aligned.duplicates_marked.bam.md5
eadGroupMarkDuplicates-7-rc.txt -> gs://broad-gp-gotc-pilot/cromwell_execution/PairedEndSingleSampleWorkflow/60d1afe2-dbd4-47e5-9cf5-e2a76d7947cd/call-ReadGroupMarkDuplicates/shard-7/ReadGroupMarkDuplicates-7-rc.txt
H7LLCCXX.8.CCTACCAT-GCTTCCTA.aligned.duplicates_marked.bai -> gs://broad-gp-gotc-pilot/cromwell_execution/PairedEndSingleSampleWorkflow/60d1afe2-dbd4-47e5-9cf5-e2a76d7947cd/call-ReadGroupMarkDuplicates/shard-7/HH7LLCCXX.8.CCTACCAT-GCTTCCTA.aligned.duplicates_marked.bai
16-02-20 05:58:06,111 cromwell-system-akka.actor.default-dispatcher-17 INFO  - JES Run [UUID(60d1afe2):ReadGroupMarkDuplicates:7]: JES Run ID is operations/EN7ahuqvKhigkdyq7pnLmHEg6a343KwYKg9wcm9kdWN0aW9uUXVldWU
16-02-20 05:58:06,192 cromwell-system-akka.actor.default-dispatcher-2 INFO  - JES Run [UUID(60d1afe2):ReadGroupMarkDuplicates:7]: Status change from - to Initializing
16-02-20 06:09:02,819 cromwell-system-akka.actor.default-dispatcher-10 INFO  - JES Run [UUID(60d1afe2):ValidateReadGroupSamFile:1]: Status change from Running to Success
16-02-20 06:09:03,270 cromwell-system-akka.actor.default-dispatcher-22 INFO  - WorkflowActor [UUID(60d1afe2)]: persisting status of ValidateReadGroupSamFile:1 to Done.
16-02-20 06:16:37,542 cromwell-system-akka.actor.default-dispatcher-2 INFO  - JES Run [UUID(60d1afe2):CollectReadgroupBamQualityMetrics:1]: Status change from Running to Success
16-02-20 06:16:38,080 cromwell-system-akka.actor.default-dispatcher-16 INFO  - WorkflowActor [UUID(60d1afe2)]: persisting status of CollectReadgroupBamQualityMetrics:1 to Done.
16-02-20 06:34:16,502 cromwell-system-akka.actor.default-dispatcher-2 INFO  - JES Run [UUID(60d1afe2):ReadGroupMarkDuplicates:3]: Status change from Initializing to Running
16-02-20 07:18:07,534 cromwell-system-akka.actor.default-dispatcher-12 INFO  - JES Run [UUID(60d1afe2):ValidateReadGroupSamFile:7]: Status change from Running to Success
16-02-20 07:18:07,988 cromwell-system-akka.actor.default-dispatcher-12 INFO  - WorkflowActor [UUID(60d1afe2)]: persisting status of ValidateReadGroupSamFile:7 to Done.
16-02-20 07:27:40,049 cromwell-system-akka.actor.default-dispatcher-2 INFO  - JES Run [UUID(60d1afe2):CollectReadgroupBamQualityMetrics:7]: Status change from Running to Success
16-02-20 07:27:40,575 cromwell-system-akka.actor.default-dispatcher-26 INFO  - WorkflowActor [UUID(60d1afe2)]: persisting status of CollectReadgroupBamQualityMetrics:7 to Done.
16-02-20 07:29:14,632 cromwell-system-akka.actor.default-dispatcher-2 INFO  - JES Run [UUID(60d1afe2):AggregatedBamMarkDuplicates]: Status change from Initializing to Running
16-02-20 08:29:44,017 cromwell-system-akka.actor.default-dispatcher-13 INFO  - JES Run [UUID(60d1afe2):CrossCheckFingerprints]: Status change from Initializing to Running
16-02-20 08:29:44,313 cromwell-system-akka.actor.default-dispatcher-23 INFO  - JES Run [UUID(60d1afe2):CollectReadgroupBamQualityMetrics:4]: Status change from Initializing to Running
16-02-20 08:54:10,742 cromwell-system-akka.actor.default-dispatcher-24 INFO  - WorkflowActor [UUID(60d1afe2)]: persisting status of CrossCheckFingerprints to Done.
16-02-20 08:59:47,951 cromwell-system-akka.actor.default-dispatcher-24 INFO  - JES Run [UUID(60d1afe2):CollectReadgroupBamQualityMetrics:4]: Status change from Running to Success
16-02-20 08:59:48,429 cromwell-system-akka.actor.default-dispatcher-14 INFO  - WorkflowActor [UUID(60d1afe2)]: persisting status of CollectReadgroupBamQualityMetrics:4 to Done.
16-02-20 08:59:48,540 cromwell-system-akka.actor.default-dispatcher-17 INFO  - WorkflowActor [UUID(60d1afe2)]: persisting status of CollectReadgroupBamQualityMetrics to Starting.
16-02-20 08:59:48,540 cromwell-system-akka.actor.default-dispatcher-17 INFO  - WorkflowActor [UUID(60d1afe2)]: Collection complete for Scattered Call CollectReadgroupBamQualityMetrics.
16-02-20 08:59:48,798 cromwell-system-akka.actor.default-dispatcher-17 INFO  - WorkflowActor [UUID(60d1afe2)]: persisting status of CollectReadgroupBamQualityMetrics to Done.
16-02-20 14:24:31,845 cromwell-system-akka.actor.default-dispatcher-6 INFO  - JES Run [UUID(60d1afe2):BaseRecalibrator:12]: Status change from Initializing to Running
16-02-20 14:24:32,941 cromwell-system-akka.actor.default-dispatcher-22 INFO  - JES Run [UUID(60d1afe2):BaseRecalibrator:1]: Status change from Initializing to Running
16-02-20 14:25:04,130 cromwell-system-akka.actor.default-dispatcher-5 INFO  - JES Run [UUID(60d1afe2):BaseRecalibrator:2]: Status change from Initializing to Running
16-02-20 15:18:35,962 cromwell-system-akka.actor.default-dispatcher-21 INFO  - JES Run [UUID(60d1afe2):BaseRecalibrator:10]: Status change from Running to Failed
16-02-20 15:18:35,962 cromwell-system-akka.actor.default-dispatcher-20 ERROR - CallActor [UUID(60d1afe2):BaseRecalibrator:10]: Failing call with retryable Failure: Task 60d1afe2-dbd4-47e5-9cf5-e2a76d7947cd:BaseRecalibrator was preempted for the 1st time. The call will be re-started with another pre-emptible VM (max pre-emptible attempts number is 3).
omwell.engine.package$PreemptedException: Task 60d1afe2-dbd4-47e5-9cf5-e2a76d7947cd:BaseRecalibrator was preempted for the 1st time. The call will be re-started with another pre-emptible VM (max pre-emptible attempts number is 3).
16-02-20 15:37:39,201 cromwell-system-akka.actor.default-dispatcher-23 INFO  - JES Run [UUID(60d1afe2):BaseRecalibrator:8:2]: Status change from Initializing to Running
16-02-20 16:10:48,961 cromwell-system-akka.actor.default-dispatcher-2 INFO  - JES Run [UUID(60d1afe2):BaseRecalibrator:13]: Status change from Running to Failed
16-02-20 16:10:48,963 cromwell-system-akka.actor.default-dispatcher-15 ERROR - CallActor [UUID(60d1afe2):BaseRecalibrator:13]: Failing call with retryable Failure: Task 60d1afe2-dbd4-47e5-9cf5-e2a76d7947cd:BaseRecalibrator was preempted for the 1st time. The call will be re-started with another pre-emptible VM (max pre-emptible attempts number is 3).
omwell.engine.package$PreemptedException: Task 60d1afe2-dbd4-47e5-9cf5-e2a76d7947cd:BaseRecalibrator was preempted for the 1st time. The call will be re-started with another pre-emptible VM (max pre-emptible attempts number is 3).
16-02-20 16:10:49,333 cromwell-system-akka.actor.default-dispatcher-26 INFO  - WorkflowActor [UUID(60d1afe2)]: persisting status of BaseRecalibrator:13 to Preempted.
16-02-20 16:10:49,432 cromwell-system-akka.actor.default-dispatcher-26 INFO  - WorkflowActor [UUID(60d1afe2)]: starting calls: PairedEndSingleSampleWorkflow.BaseRecalibrator
16-02-20 16:10:49,432 cromwell-system-akka.actor.default-dispatcher-26 INFO  - WorkflowActor [UUID(60d1afe2)]: persisting status of BaseRecalibrator:13:2 to Starting.
16-02-20 16:10:49,552 cromwell-system-akka.actor.default-dispatcher-25 INFO  - WorkflowActor [UUID(60d1afe2)]: inputs for call 'BaseRecalibrator:13:2':
nput_bam -> WdlSingleFile(gs://broad-gp-gotc-pilot/cromwell_execution/PairedEndSingleSampleWorkflow/60d1afe2-dbd4-47e5-9cf5-e2a76d7947cd/call-AggregatedBamMarkDuplicates/VIR_3885.aligned.duplicates_marked.bam)
nput_bam_index -> WdlSingleFile(gs://broad-gp-gotc-pilot/cromwell_execution/PairedEndSingleSampleWorkflow/60d1afe2-dbd4-47e5-9cf5-e2a76d7947cd/call-AggregatedBamMarkDuplicates/VIR_3885.aligned.duplicates_marked.bai)
16-02-20 16:10:49,552 cromwell-system-akka.actor.default-dispatcher-26 INFO  - WorkflowActor [UUID(60d1afe2)]: created call actor for BaseRecalibrator:13:2.
16-02-20 16:10:49,552 cromwell-system-akka.actor.default-dispatcher-14 INFO  - WorkflowActor [UUID(60d1afe2)]: persisting status of BaseRecalibrator:13:2 to Running.
16-02-20 16:10:49,552 cromwell-system-akka.actor.default-dispatcher-14 INFO  - JesBackend [UUID(60d1afe2):BaseRecalibrator:13:2]: Call GCS path: gs://broad-gp-gotc-pilot/cromwell_execution/PairedEndSingleSampleWorkflow/60d1afe2-dbd4-47e5-9cf5-e2a76d7947cd/call-BaseRecalibrator/shard-13/attempt-2
16-02-20 16:10:49,553 cromwell-system-akka.actor.default-dispatcher-14 INFO  - JesBackend [UUID(60d1afe2):BaseRecalibrator:13:2]: `java -XX:GCTimeLimit=50 -XX:GCHeapFreeLimit=10 -Xmx4000m \
I /cromwell_root/broad-gp-gotc-pilot/cromwell_execution/PairedEndSingleSampleWorkflow/60d1afe2-dbd4-47e5-9cf5-e2a76d7947cd/call-AggregatedBamMarkDuplicates/VIR_3885.aligned.duplicates_marked.bam \
16-02-20 16:10:49,685 cromwell-system-akka.actor.default-dispatcher-14 INFO  - JesBackend [UUID(60d1afe2):BaseRecalibrator:13:2]: Starting call with pre-emptible VM
16-02-20 16:10:49,686 cromwell-system-akka.actor.default-dispatcher-14 INFO  - JES Pipeline [UUID(60d1afe2):BaseRecalibrator:13:2]: Pipeline parameters are:
name=input_bam-0, type=REFERENCE, value=/cromwell_root/broad-gp-gotc-pilot/cromwell_execution/PairedEndSingleSampleWorkflow/60d1afe2-dbd4-47e5-9cf5-e2a76d7947cd/call-AggregatedBamMarkDuplicates/VIR_3885.aligned.duplicates_marked.bam}
name=input_bam_index-0, type=REFERENCE, value=/cromwell_root/broad-gp-gotc-pilot/cromwell_execution/PairedEndSingleSampleWorkflow/60d1afe2-dbd4-47e5-9cf5-e2a76d7947cd/call-AggregatedBamMarkDuplicates/VIR_3885.aligned.duplicates_marked.bai}
16-02-20 16:10:49,723 cromwell-system-akka.actor.default-dispatcher-14 INFO  - JES Pipeline [UUID(60d1afe2):BaseRecalibrator:13:2]: Pipeline ID is 12361099216458061200
16-02-20 16:10:49,723 cromwell-system-akka.actor.default-dispatcher-14 INFO  - JES Pipeline [UUID(60d1afe2):BaseRecalibrator:13:2]: Project ID: broad-gp-gotc-pilot
16-02-20 16:10:49,723 cromwell-system-akka.actor.default-dispatcher-14 INFO  - JES Run [UUID(60d1afe2):BaseRecalibrator:13:2]: Inputs:
nput_bam_index-0 -> gs://broad-gp-gotc-pilot/cromwell_execution/PairedEndSingleSampleWorkflow/60d1afe2-dbd4-47e5-9cf5-e2a76d7947cd/call-AggregatedBamMarkDuplicates/VIR_3885.aligned.duplicates_marked.bai
nput_bam-0 -> gs://broad-gp-gotc-pilot/cromwell_execution/PairedEndSingleSampleWorkflow/60d1afe2-dbd4-47e5-9cf5-e2a76d7947cd/call-AggregatedBamMarkDuplicates/VIR_3885.aligned.duplicates_marked.bam
xec -> gs://broad-gp-gotc-pilot/cromwell_execution/PairedEndSingleSampleWorkflow/60d1afe2-dbd4-47e5-9cf5-e2a76d7947cd/call-BaseRecalibrator/shard-13/attempt-2/exec.sh
16-02-20 16:10:49,723 cromwell-system-akka.actor.default-dispatcher-14 INFO  - JES Run [UUID(60d1afe2):BaseRecalibrator:13:2]: Outputs:
aseRecalibrator-13-rc.txt -> gs://broad-gp-gotc-pilot/cromwell_execution/PairedEndSingleSampleWorkflow/60d1afe2-dbd4-47e5-9cf5-e2a76d7947cd/call-BaseRecalibrator/shard-13/attempt-2/BaseRecalibrator-13-rc.txt
IR_3885.recal_data.csv -> gs://broad-gp-gotc-pilot/cromwell_execution/PairedEndSingleSampleWorkflow/60d1afe2-dbd4-47e5-9cf5-e2a76d7947cd/call-BaseRecalibrator/shard-13/attempt-2/VIR_3885.recal_data.csv
onitoring -> gs://broad-gp-gotc-pilot/cromwell_execution/PairedEndSingleSampleWorkflow/60d1afe2-dbd4-47e5-9cf5-e2a76d7947cd/call-BaseRecalibrator/shard-13/attempt-2/monitoring.log
16-02-20 16:10:49,869 cromwell-system-akka.actor.default-dispatcher-14 INFO  - JES Run [UUID(60d1afe2):BaseRecalibrator:13:2]: JES Run ID is operations/ELDMyvuvKhjv2seihLHOgigg6a343KwYKg9wcm9kdWN0aW9uUXVldWU
16-02-20 16:10:49,889 cromwell-system-akka.actor.default-dispatcher-15 INFO  - JES Run [UUID(60d1afe2):BaseRecalibrator:13:2]: Status change from - to Initializing
16-02-20 16:20:59,292 cromwell-system-akka.actor.default-dispatcher-12 INFO  - JES Run [UUID(60d1afe2):BaseRecalibrator:12:2]: Status change from Initializing to Running
16-02-20 16:24:31,817 cromwell-system-akka.actor.default-dispatcher-15 INFO  - JES Run [UUID(60d1afe2):BaseRecalibrator:6]: Status change from Running to Success
16-02-20 16:30:30,991 cromwell-system-akka.actor.default-dispatcher-2 INFO  - JES Run [UUID(60d1afe2):BaseRecalibrator:1]: Status change from Running to Failed
16-02-20 16:30:30,991 cromwell-system-akka.actor.default-dispatcher-2 ERROR - CallActor [UUID(60d1afe2):BaseRecalibrator:1]: Failing call with retryable Failure: Task 60d1afe2-dbd4-47e5-9cf5-e2a76d7947cd:BaseRecalibrator was preempted for the 1st time. The call will be re-started with another pre-emptible VM (max pre-emptible attempts number is 3).
omwell.engine.package$PreemptedException: Task 60d1afe2-dbd4-47e5-9cf5-e2a76d7947cd:BaseRecalibrator was preempted for the 1st time. The call will be re-started with another pre-emptible VM (max pre-emptible attempts number is 3).
16-02-20 16:30:31,366 cromwell-system-akka.actor.default-dispatcher-21 INFO  - WorkflowActor [UUID(60d1afe2)]: persisting status of BaseRecalibrator:1 to Preempted.
16-02-20 16:30:31,472 cromwell-system-akka.actor.default-dispatcher-21 INFO  - WorkflowActor [UUID(60d1afe2)]: starting calls: PairedEndSingleSampleWorkflow.BaseRecalibrator
16-02-20 16:30:31,472 cromwell-system-akka.actor.default-dispatcher-21 INFO  - WorkflowActor [UUID(60d1afe2)]: persisting status of BaseRecalibrator:1:2 to Starting.
16-02-20 16:30:31,602 cromwell-system-akka.actor.default-dispatcher-3 INFO  - WorkflowActor [UUID(60d1afe2)]: inputs for call 'BaseRecalibrator:1:2':
nput_bam -> WdlSingleFile(gs://broad-gp-gotc-pilot/cromwell_execution/PairedEndSingleSampleWorkflow/60d1afe2-dbd4-47e5-9cf5-e2a76d7947cd/call-AggregatedBamMarkDuplicates/VIR_3885.aligned.duplicates_marked.bam)
nput_bam_index -> WdlSingleFile(gs://broad-gp-gotc-pilot/cromwell_execution/PairedEndSingleSampleWorkflow/60d1afe2-dbd4-47e5-9cf5-e2a76d7947cd/call-AggregatedBamMarkDuplicates/VIR_3885.aligned.duplicates_marked.bai)
16-02-20 16:30:31,602 cromwell-system-akka.actor.default-dispatcher-3 INFO  - WorkflowActor [UUID(60d1afe2)]: created call actor for BaseRecalibrator:1:2.
16-02-20 16:30:31,602 cromwell-system-akka.actor.default-dispatcher-3 INFO  - WorkflowActor [UUID(60d1afe2)]: persisting status of BaseRecalibrator:1:2 to Running.
16-02-20 16:30:31,602 cromwell-system-akka.actor.default-dispatcher-18 INFO  - JesBackend [UUID(60d1afe2):BaseRecalibrator:1:2]: Call GCS path: gs://broad-gp-gotc-pilot/cromwell_execution/PairedEndSingleSampleWorkflow/60d1afe2-dbd4-47e5-9cf5-e2a76d7947cd/call-BaseRecalibrator/shard-1/attempt-2
16-02-20 16:30:31,602 cromwell-system-akka.actor.default-dispatcher-18 INFO  - JesBackend [UUID(60d1afe2):BaseRecalibrator:1:2]: `java -XX:GCTimeLimit=50 -XX:GCHeapFreeLimit=10 -Xmx4000m \
I /cromwell_root/broad-gp-gotc-pilot/cromwell_execution/PairedEndSingleSampleWorkflow/60d1afe2-dbd4-47e5-9cf5-e2a76d7947cd/call-AggregatedBamMarkDuplicates/VIR_3885.aligned.duplicates_marked.bam \
16-02-20 16:30:31,723 cromwell-system-akka.actor.default-dispatcher-18 INFO  - JesBackend [UUID(60d1afe2):BaseRecalibrator:1:2]: Starting call with pre-emptible VM
16-02-20 16:30:31,724 cromwell-system-akka.actor.default-dispatcher-18 INFO  - JES Pipeline [UUID(60d1afe2):BaseRecalibrator:1:2]: Pipeline parameters are:
name=input_bam-0, type=REFERENCE, value=/cromwell_root/broad-gp-gotc-pilot/cromwell_execution/PairedEndSingleSampleWorkflow/60d1afe2-dbd4-47e5-9cf5-e2a76d7947cd/call-AggregatedBamMarkDuplicates/VIR_3885.aligned.duplicates_marked.bam}
name=input_bam_index-0, type=REFERENCE, value=/cromwell_root/broad-gp-gotc-pilot/cromwell_execution/PairedEndSingleSampleWorkflow/60d1afe2-dbd4-47e5-9cf5-e2a76d7947cd/call-AggregatedBamMarkDuplicates/VIR_3885.aligned.duplicates_marked.bai}
16-02-20 16:30:31,771 cromwell-system-akka.actor.default-dispatcher-18 INFO  - JES Pipeline [UUID(60d1afe2):BaseRecalibrator:1:2]: Pipeline ID is 9483013427147310160
16-02-20 16:30:31,771 cromwell-system-akka.actor.default-dispatcher-18 INFO  - JES Pipeline [UUID(60d1afe2):BaseRecalibrator:1:2]: Project ID: broad-gp-gotc-pilot
16-02-20 16:30:31,771 cromwell-system-akka.actor.default-dispatcher-18 INFO  - JES Run [UUID(60d1afe2):BaseRecalibrator:1:2]: Inputs:
nput_bam_index-0 -> gs://broad-gp-gotc-pilot/cromwell_execution/PairedEndSingleSampleWorkflow/60d1afe2-dbd4-47e5-9cf5-e2a76d7947cd/call-AggregatedBamMarkDuplicates/VIR_3885.aligned.duplicates_marked.bai
nput_bam-0 -> gs://broad-gp-gotc-pilot/cromwell_execution/PairedEndSingleSampleWorkflow/60d1afe2-dbd4-47e5-9cf5-e2a76d7947cd/call-AggregatedBamMarkDuplicates/VIR_3885.aligned.duplicates_marked.bam
xec -> gs://broad-gp-gotc-pilot/cromwell_execution/PairedEndSingleSampleWorkflow/60d1afe2-dbd4-47e5-9cf5-e2a76d7947cd/call-BaseRecalibrator/shard-1/attempt-2/exec.sh
16-02-20 16:30:31,771 cromwell-system-akka.actor.default-dispatcher-18 INFO  - JES Run [UUID(60d1afe2):BaseRecalibrator:1:2]: Outputs:
aseRecalibrator-1-rc.txt -> gs://broad-gp-gotc-pilot/cromwell_execution/PairedEndSingleSampleWorkflow/60d1afe2-dbd4-47e5-9cf5-e2a76d7947cd/call-BaseRecalibrator/shard-1/attempt-2/BaseRecalibrator-1-rc.txt
IR_3885.recal_data.csv -> gs://broad-gp-gotc-pilot/cromwell_execution/PairedEndSingleSampleWorkflow/60d1afe2-dbd4-47e5-9cf5-e2a76d7947cd/call-BaseRecalibrator/shard-1/attempt-2/VIR_3885.recal_data.csv
onitoring -> gs://broad-gp-gotc-pilot/cromwell_execution/PairedEndSingleSampleWorkflow/60d1afe2-dbd4-47e5-9cf5-e2a76d7947cd/call-BaseRecalibrator/shard-1/attempt-2/monitoring.log
16-02-20 16:30:31,897 cromwell-system-akka.actor.default-dispatcher-18 INFO  - JES Run [UUID(60d1afe2):BaseRecalibrator:1:2]: JES Run ID is operations/EPjekvyvKhjZ69PH6-C2owwg6a343KwYKg9wcm9kdWN0aW9uUXVldWU
16-02-20 16:30:31,918 cromwell-system-akka.actor.default-dispatcher-25 INFO  - JES Run [UUID(60d1afe2):BaseRecalibrator:1:2]: Status change from - to Initializing
16-02-20 16:44:01,904 cromwell-system-akka.actor.default-dispatcher-25 INFO  - JES Run [UUID(60d1afe2):BaseRecalibrator:13:2]: Status change from Running to Failed
16-02-20 16:44:01,905 cromwell-system-akka.actor.default-dispatcher-25 ERROR - CallActor [UUID(60d1afe2):BaseRecalibrator:13:2]: Failing call with retryable Failure: Task 60d1afe2-dbd4-47e5-9cf5-e2a76d7947cd:BaseRecalibrator was preempted for the 2nd time. The call will be re-started with another pre-emptible VM (max pre-emptible attempts number is 3).
omwell.engine.package$PreemptedException: Task 60d1afe2-dbd4-47e5-9cf5-e2a76d7947cd:BaseRecalibrator was preempted for the 2nd time. The call will be re-started with another pre-emptible VM (max pre-emptible attempts number is 3).
16-02-20 16:44:02,260 cromwell-system-akka.actor.default-dispatcher-4 INFO  - WorkflowActor [UUID(60d1afe2)]: persisting status of BaseRecalibrator:13:2 to Preempted.
16-02-20 16:44:02,355 cromwell-system-akka.actor.default-dispatcher-4 INFO  - WorkflowActor [UUID(60d1afe2)]: starting calls: PairedEndSingleSampleWorkflow.BaseRecalibrator
16-02-20 16:44:02,355 cromwell-system-akka.actor.default-dispatcher-4 INFO  - WorkflowActor [UUID(60d1afe2)]: persisting status of BaseRecalibrator:13:3 to Starting.
16-02-20 16:44:02,473 cromwell-system-akka.actor.default-dispatcher-25 INFO  - WorkflowActor [UUID(60d1afe2)]: inputs for call 'BaseRecalibrator:13:3':
nput_bam -> WdlSingleFile(gs://broad-gp-gotc-pilot/cromwell_execution/PairedEndSingleSampleWorkflow/60d1afe2-dbd4-47e5-9cf5-e2a76d7947cd/call-AggregatedBamMarkDuplicates/VIR_3885.aligned.duplicates_marked.bam)
nput_bam_index -> WdlSingleFile(gs://broad-gp-gotc-pilot/cromwell_execution/PairedEndSingleSampleWorkflow/60d1afe2-dbd4-47e5-9cf5-e2a76d7947cd/call-AggregatedBamMarkDuplicates/VIR_3885.aligned.duplicates_marked.bai)
16-02-20 16:44:02,473 cromwell-system-akka.actor.default-dispatcher-25 INFO  - WorkflowActor [UUID(60d1afe2)]: created call actor for BaseRecalibrator:13:3.
16-02-20 16:44:02,473 cromwell-system-akka.actor.default-dispatcher-15 INFO  - WorkflowActor [UUID(60d1afe2)]: persisting status of BaseRecalibrator:13:3 to Running.
16-02-20 16:44:02,473 cromwell-system-akka.actor.default-dispatcher-25 INFO  - JesBackend [UUID(60d1afe2):BaseRecalibrator:13:3]: Call GCS path: gs://broad-gp-gotc-pilot/cromwell_execution/PairedEndSingleSampleWorkflow/60d1afe2-dbd4-47e5-9cf5-e2a76d7947cd/call-BaseRecalibrator/shard-13/attempt-3
16-02-20 16:44:02,473 cromwell-system-akka.actor.default-dispatcher-25 INFO  - JesBackend [UUID(60d1afe2):BaseRecalibrator:13:3]: `java -XX:GCTimeLimit=50 -XX:GCHeapFreeLimit=10 -Xmx4000m \
I /cromwell_root/broad-gp-gotc-pilot/cromwell_execution/PairedEndSingleSampleWorkflow/60d1afe2-dbd4-47e5-9cf5-e2a76d7947cd/call-AggregatedBamMarkDuplicates/VIR_3885.aligned.duplicates_marked.bam \
16-02-20 16:44:02,654 cromwell-system-akka.actor.default-dispatcher-25 INFO  - JesBackend [UUID(60d1afe2):BaseRecalibrator:13:3]: Starting call with pre-emptible VM
16-02-20 16:44:02,654 cromwell-system-akka.actor.default-dispatcher-25 INFO  - JES Pipeline [UUID(60d1afe2):BaseRecalibrator:13:3]: Pipeline parameters are:
name=input_bam-0, type=REFERENCE, value=/cromwell_root/broad-gp-gotc-pilot/cromwell_execution/PairedEndSingleSampleWorkflow/60d1afe2-dbd4-47e5-9cf5-e2a76d7947cd/call-AggregatedBamMarkDuplicates/VIR_3885.aligned.duplicates_marked.bam}
name=input_bam_index-0, type=REFERENCE, value=/cromwell_root/broad-gp-gotc-pilot/cromwell_execution/PairedEndSingleSampleWorkflow/60d1afe2-dbd4-47e5-9cf5-e2a76d7947cd/call-AggregatedBamMarkDuplicates/VIR_3885.aligned.duplicates_marked.bai}
16-02-20 16:44:02,690 cromwell-system-akka.actor.default-dispatcher-25 INFO  - JES Pipeline [UUID(60d1afe2):BaseRecalibrator:13:3]: Pipeline ID is 6258793207288677832
16-02-20 16:44:02,690 cromwell-system-akka.actor.default-dispatcher-25 INFO  - JES Pipeline [UUID(60d1afe2):BaseRecalibrator:13:3]: Project ID: broad-gp-gotc-pilot
16-02-20 16:44:02,690 cromwell-system-akka.actor.default-dispatcher-25 INFO  - JES Run [UUID(60d1afe2):BaseRecalibrator:13:3]: Inputs:
nput_bam_index-0 -> gs://broad-gp-gotc-pilot/cromwell_execution/PairedEndSingleSampleWorkflow/60d1afe2-dbd4-47e5-9cf5-e2a76d7947cd/call-AggregatedBamMarkDuplicates/VIR_3885.aligned.duplicates_marked.bai
nput_bam-0 -> gs://broad-gp-gotc-pilot/cromwell_execution/PairedEndSingleSampleWorkflow/60d1afe2-dbd4-47e5-9cf5-e2a76d7947cd/call-AggregatedBamMarkDuplicates/VIR_3885.aligned.duplicates_marked.bam
xec -> gs://broad-gp-gotc-pilot/cromwell_execution/PairedEndSingleSampleWorkflow/60d1afe2-dbd4-47e5-9cf5-e2a76d7947cd/call-BaseRecalibrator/shard-13/attempt-3/exec.sh
16-02-20 16:44:02,690 cromwell-system-akka.actor.default-dispatcher-25 INFO  - JES Run [UUID(60d1afe2):BaseRecalibrator:13:3]: Outputs:
aseRecalibrator-13-rc.txt -> gs://broad-gp-gotc-pilot/cromwell_execution/PairedEndSingleSampleWorkflow/60d1afe2-dbd4-47e5-9cf5-e2a76d7947cd/call-BaseRecalibrator/shard-13/attempt-3/BaseRecalibrator-13-rc.txt
IR_3885.recal_data.csv -> gs://broad-gp-gotc-pilot/cromwell_execution/PairedEndSingleSampleWorkflow/60d1afe2-dbd4-47e5-9cf5-e2a76d7947cd/call-BaseRecalibrator/shard-13/attempt-3/VIR_3885.recal_data.csv
onitoring -> gs://broad-gp-gotc-pilot/cromwell_execution/PairedEndSingleSampleWorkflow/60d1afe2-dbd4-47e5-9cf5-e2a76d7947cd/call-BaseRecalibrator/shard-13/attempt-3/monitoring.log
16-02-20 16:44:02,777 cromwell-system-akka.actor.default-dispatcher-25 INFO  - JES Run [UUID(60d1afe2):BaseRecalibrator:13:3]: JES Run ID is operations/EJaexPyvKhiqlpb40-vwv8gBIOmt-NysGCoPcHJvZHVjdGlvblF1ZXVl
16-02-20 16:44:02,799 cromwell-system-akka.actor.default-dispatcher-4 INFO  - JES Run [UUID(60d1afe2):BaseRecalibrator:13:3]: Status change from - to Initializing
16-02-20 16:56:36,205 cromwell-system-akka.actor.default-dispatcher-2 INFO  - JES Run [UUID(60d1afe2):BaseRecalibrator:10:2]: Status change from Running to Failed
16-02-20 16:56:36,206 cromwell-system-akka.actor.default-dispatcher-2 ERROR - CallActor [UUID(60d1afe2):BaseRecalibrator:10:2]: Failing call with retryable Failure: Task 60d1afe2-dbd4-47e5-9cf5-e2a76d7947cd:BaseRecalibrator was preempted for the 2nd time. The call will be re-started with another pre-emptible VM (max pre-emptible attempts number is 3).
omwell.engine.package$PreemptedException: Task 60d1afe2-dbd4-47e5-9cf5-e2a76d7947cd:BaseRecalibrator was preempted for the 2nd time. The call will be re-started with another pre-emptible VM (max pre-emptible attempts number is 3).
16-02-20 16:56:36,592 cromwell-system-akka.actor.default-dispatcher-2 INFO  - WorkflowActor [UUID(60d1afe2)]: persisting status of BaseRecalibrator:10:2 to Preempted.
16-02-20 16:56:36,698 cromwell-system-akka.actor.default-dispatcher-12 INFO  - WorkflowActor [UUID(60d1afe2)]: starting calls: PairedEndSingleSampleWorkflow.BaseRecalibrator
16-02-20 16:56:36,698 cromwell-system-akka.actor.default-dispatcher-12 INFO  - WorkflowActor [UUID(60d1afe2)]: persisting status of BaseRecalibrator:10:3 to Starting.
16-02-20 16:56:36,828 cromwell-system-akka.actor.default-dispatcher-12 INFO  - WorkflowActor [UUID(60d1afe2)]: inputs for call 'BaseRecalibrator:10:3':
nput_bam -> WdlSingleFile(gs://broad-gp-gotc-pilot/cromwell_execution/PairedEndSingleSampleWorkflow/60d1afe2-dbd4-47e5-9cf5-e2a76d7947cd/call-AggregatedBamMarkDuplicates/VIR_3885.aligned.duplicates_marked.bam)
nput_bam_index -> WdlSingleFile(gs://broad-gp-gotc-pilot/cromwell_execution/PairedEndSingleSampleWorkflow/60d1afe2-dbd4-47e5-9cf5-e2a76d7947cd/call-AggregatedBamMarkDuplicates/VIR_3885.aligned.duplicates_marked.bai)
16-02-20 16:56:36,828 cromwell-system-akka.actor.default-dispatcher-12 INFO  - WorkflowActor [UUID(60d1afe2)]: created call actor for BaseRecalibrator:10:3.
16-02-20 16:56:36,828 cromwell-system-akka.actor.default-dispatcher-12 INFO  - WorkflowActor [UUID(60d1afe2)]: persisting status of BaseRecalibrator:10:3 to Running.
16-02-20 16:56:36,828 cromwell-system-akka.actor.default-dispatcher-2 INFO  - JesBackend [UUID(60d1afe2):BaseRecalibrator:10:3]: Call GCS path: gs://broad-gp-gotc-pilot/cromwell_execution/PairedEndSingleSampleWorkflow/60d1afe2-dbd4-47e5-9cf5-e2a76d7947cd/call-BaseRecalibrator/shard-10/attempt-3
16-02-20 16:56:36,829 cromwell-system-akka.actor.default-dispatcher-2 INFO  - JesBackend [UUID(60d1afe2):BaseRecalibrator:10:3]: `java -XX:GCTimeLimit=50 -XX:GCHeapFreeLimit=10 -Xmx4000m \
I /cromwell_root/broad-gp-gotc-pilot/cromwell_execution/PairedEndSingleSampleWorkflow/60d1afe2-dbd4-47e5-9cf5-e2a76d7947cd/call-AggregatedBamMarkDuplicates/VIR_3885.aligned.duplicates_marked.bam \
16-02-20 16:56:36,995 cromwell-system-akka.actor.default-dispatcher-2 INFO  - JesBackend [UUID(60d1afe2):BaseRecalibrator:10:3]: Starting call with pre-emptible VM
16-02-20 16:56:36,995 cromwell-system-akka.actor.default-dispatcher-2 INFO  - JES Pipeline [UUID(60d1afe2):BaseRecalibrator:10:3]: Pipeline parameters are:
name=input_bam-0, type=REFERENCE, value=/cromwell_root/broad-gp-gotc-pilot/cromwell_execution/PairedEndSingleSampleWorkflow/60d1afe2-dbd4-47e5-9cf5-e2a76d7947cd/call-AggregatedBamMarkDuplicates/VIR_3885.aligned.duplicates_marked.bam}
name=input_bam_index-0, type=REFERENCE, value=/cromwell_root/broad-gp-gotc-pilot/cromwell_execution/PairedEndSingleSampleWorkflow/60d1afe2-dbd4-47e5-9cf5-e2a76d7947cd/call-AggregatedBamMarkDuplicates/VIR_3885.aligned.duplicates_marked.bai}
16-02-20 16:56:37,031 cromwell-system-akka.actor.default-dispatcher-2 INFO  - JES Pipeline [UUID(60d1afe2):BaseRecalibrator:10:3]: Pipeline ID is 3161923846961832242
16-02-20 16:56:37,031 cromwell-system-akka.actor.default-dispatcher-2 INFO  - JES Pipeline [UUID(60d1afe2):BaseRecalibrator:10:3]: Project ID: broad-gp-gotc-pilot
16-02-20 16:56:37,031 cromwell-system-akka.actor.default-dispatcher-2 INFO  - JES Run [UUID(60d1afe2):BaseRecalibrator:10:3]: Inputs:
nput_bam_index-0 -> gs://broad-gp-gotc-pilot/cromwell_execution/PairedEndSingleSampleWorkflow/60d1afe2-dbd4-47e5-9cf5-e2a76d7947cd/call-AggregatedBamMarkDuplicates/VIR_3885.aligned.duplicates_marked.bai
nput_bam-0 -> gs://broad-gp-gotc-pilot/cromwell_execution/PairedEndSingleSampleWorkflow/60d1afe2-dbd4-47e5-9cf5-e2a76d7947cd/call-AggregatedBamMarkDuplicates/VIR_3885.aligned.duplicates_marked.bam
xec -> gs://broad-gp-gotc-pilot/cromwell_execution/PairedEndSingleSampleWorkflow/60d1afe2-dbd4-47e5-9cf5-e2a76d7947cd/call-BaseRecalibrator/shard-10/attempt-3/exec.sh
16-02-20 16:56:37,031 cromwell-system-akka.actor.default-dispatcher-2 INFO  - JES Run [UUID(60d1afe2):BaseRecalibrator:10:3]: Outputs:
aseRecalibrator-10-rc.txt -> gs://broad-gp-gotc-pilot/cromwell_execution/PairedEndSingleSampleWorkflow/60d1afe2-dbd4-47e5-9cf5-e2a76d7947cd/call-BaseRecalibrator/shard-10/attempt-3/BaseRecalibrator-10-rc.txt
IR_3885.recal_data.csv -> gs://broad-gp-gotc-pilot/cromwell_execution/PairedEndSingleSampleWorkflow/60d1afe2-dbd4-47e5-9cf5-e2a76d7947cd/call-BaseRecalibrator/shard-10/attempt-3/VIR_3885.recal_data.csv
onitoring -> gs://broad-gp-gotc-pilot/cromwell_execution/PairedEndSingleSampleWorkflow/60d1afe2-dbd4-47e5-9cf5-e2a76d7947cd/call-BaseRecalibrator/shard-10/attempt-3/monitoring.log
16-02-20 16:56:37,150 cromwell-system-akka.actor.default-dispatcher-2 INFO  - JES Run [UUID(60d1afe2):BaseRecalibrator:10:3]: JES Run ID is operations/EMSj8vyvKhjY65C84q_Z4zUg6a343KwYKg9wcm9kdWN0aW9uUXVldWU
16-02-20 16:56:37,171 cromwell-system-akka.actor.default-dispatcher-2 INFO  - JES Run [UUID(60d1afe2):BaseRecalibrator:10:3]: Status change from - to Initializing
16-02-20 17:04:39,448 cromwell-system-akka.actor.default-dispatcher-11 INFO  - JES Run [UUID(60d1afe2):BaseRecalibrator:0]: Status change from Running to Success
16-02-20 17:04:39,942 cromwell-system-akka.actor.default-dispatcher-15 INFO  - WorkflowActor [UUID(60d1afe2)]: persisting status of BaseRecalibrator:0 to Done.
16-02-20 17:26:47,811 cromwell-system-akka.actor.default-dispatcher-22 INFO  - JES Run [UUID(60d1afe2):BaseRecalibrator:1:2]: Status change from Running to Failed
16-02-20 17:26:47,812 cromwell-system-akka.actor.default-dispatcher-22 ERROR - CallActor [UUID(60d1afe2):BaseRecalibrator:1:2]: Failing call with retryable Failure: Task 60d1afe2-dbd4-47e5-9cf5-e2a76d7947cd:BaseRecalibrator was preempted for the 2nd time. The call will be re-started with another pre-emptible VM (max pre-emptible attempts number is 3).
omwell.engine.package$PreemptedException: Task 60d1afe2-dbd4-47e5-9cf5-e2a76d7947cd:BaseRecalibrator was preempted for the 2nd time. The call will be re-started with another pre-emptible VM (max pre-emptible attempts number is 3).
16-02-20 17:26:48,191 cromwell-system-akka.actor.default-dispatcher-6 INFO  - WorkflowActor [UUID(60d1afe2)]: persisting status of BaseRecalibrator:1:2 to Preempted.
16-02-20 17:26:48,299 cromwell-system-akka.actor.default-dispatcher-26 INFO  - WorkflowActor [UUID(60d1afe2)]: starting calls: PairedEndSingleSampleWorkflow.BaseRecalibrator
16-02-20 17:26:48,299 cromwell-system-akka.actor.default-dispatcher-26 INFO  - WorkflowActor [UUID(60d1afe2)]: persisting status of BaseRecalibrator:1:3 to Starting.
16-02-20 17:26:48,422 cromwell-system-akka.actor.default-dispatcher-16 INFO  - WorkflowActor [UUID(60d1afe2)]: inputs for call 'BaseRecalibrator:1:3':
nput_bam -> WdlSingleFile(gs://broad-gp-gotc-pilot/cromwell_execution/PairedEndSingleSampleWorkflow/60d1afe2-dbd4-47e5-9cf5-e2a76d7947cd/call-AggregatedBamMarkDuplicates/VIR_3885.aligned.duplicates_marked.bam)
nput_bam_index -> WdlSingleFile(gs://broad-gp-gotc-pilot/cromwell_execution/PairedEndSingleSampleWorkflow/60d1afe2-dbd4-47e5-9cf5-e2a76d7947cd/call-AggregatedBamMarkDuplicates/VIR_3885.aligned.duplicates_marked.bai)
16-02-20 17:26:48,422 cromwell-system-akka.actor.default-dispatcher-8 INFO  - WorkflowActor [UUID(60d1afe2)]: created call actor for BaseRecalibrator:1:3.
16-02-20 17:26:48,422 cromwell-system-akka.actor.default-dispatcher-26 INFO  - WorkflowActor [UUID(60d1afe2)]: persisting status of BaseRecalibrator:1:3 to Running.
16-02-20 17:26:48,422 cromwell-system-akka.actor.default-dispatcher-16 INFO  - JesBackend [UUID(60d1afe2):BaseRecalibrator:1:3]: Call GCS path: gs://broad-gp-gotc-pilot/cromwell_execution/PairedEndSingleSampleWorkflow/60d1afe2-dbd4-47e5-9cf5-e2a76d7947cd/call-BaseRecalibrator/shard-1/attempt-3
16-02-20 17:26:48,423 cromwell-system-akka.actor.default-dispatcher-16 INFO  - JesBackend [UUID(60d1afe2):BaseRecalibrator:1:3]: `java -XX:GCTimeLimit=50 -XX:GCHeapFreeLimit=10 -Xmx4000m \
I /cromwell_root/broad-gp-gotc-pilot/cromwell_execution/PairedEndSingleSampleWorkflow/60d1afe2-dbd4-47e5-9cf5-e2a76d7947cd/call-AggregatedBamMarkDuplicates/VIR_3885.aligned.duplicates_marked.bam \
16-02-20 17:26:48,561 cromwell-system-akka.actor.default-dispatcher-16 INFO  - JesBackend [UUID(60d1afe2):BaseRecalibrator:1:3]: Starting call with pre-emptible VM
16-02-20 17:26:48,561 cromwell-system-akka.actor.default-dispatcher-16 INFO  - JES Pipeline [UUID(60d1afe2):BaseRecalibrator:1:3]: Pipeline parameters are:
name=input_bam-0, type=REFERENCE, value=/cromwell_root/broad-gp-gotc-pilot/cromwell_execution/PairedEndSingleSampleWorkflow/60d1afe2-dbd4-47e5-9cf5-e2a76d7947cd/call-AggregatedBamMarkDuplicates/VIR_3885.aligned.duplicates_marked.bam}
name=input_bam_index-0, type=REFERENCE, value=/cromwell_root/broad-gp-gotc-pilot/cromwell_execution/PairedEndSingleSampleWorkflow/60d1afe2-dbd4-47e5-9cf5-e2a76d7947cd/call-AggregatedBamMarkDuplicates/VIR_3885.aligned.duplicates_marked.bai}
16-02-20 17:26:48,598 cromwell-system-akka.actor.default-dispatcher-16 INFO  - JES Pipeline [UUID(60d1afe2):BaseRecalibrator:1:3]: Pipeline ID is 77601924682311581
16-02-20 17:26:48,598 cromwell-system-akka.actor.default-dispatcher-16 INFO  - JES Pipeline [UUID(60d1afe2):BaseRecalibrator:1:3]: Project ID: broad-gp-gotc-pilot
16-02-20 17:26:48,598 cromwell-system-akka.actor.default-dispatcher-16 INFO  - JES Run [UUID(60d1afe2):BaseRecalibrator:1:3]: Inputs:
nput_bam_index-0 -> gs://broad-gp-gotc-pilot/cromwell_execution/PairedEndSingleSampleWorkflow/60d1afe2-dbd4-47e5-9cf5-e2a76d7947cd/call-AggregatedBamMarkDuplicates/VIR_3885.aligned.duplicates_marked.bai
nput_bam-0 -> gs://broad-gp-gotc-pilot/cromwell_execution/PairedEndSingleSampleWorkflow/60d1afe2-dbd4-47e5-9cf5-e2a76d7947cd/call-AggregatedBamMarkDuplicates/VIR_3885.aligned.duplicates_marked.bam
xec -> gs://broad-gp-gotc-pilot/cromwell_execution/PairedEndSingleSampleWorkflow/60d1afe2-dbd4-47e5-9cf5-e2a76d7947cd/call-BaseRecalibrator/shard-1/attempt-3/exec.sh
16-02-20 17:26:48,598 cromwell-system-akka.actor.default-dispatcher-16 INFO  - JES Run [UUID(60d1afe2):BaseRecalibrator:1:3]: Outputs:
aseRecalibrator-1-rc.txt -> gs://broad-gp-gotc-pilot/cromwell_execution/PairedEndSingleSampleWorkflow/60d1afe2-dbd4-47e5-9cf5-e2a76d7947cd/call-BaseRecalibrator/shard-1/attempt-3/BaseRecalibrator-1-rc.txt
IR_3885.recal_data.csv -> gs://broad-gp-gotc-pilot/cromwell_execution/PairedEndSingleSampleWorkflow/60d1afe2-dbd4-47e5-9cf5-e2a76d7947cd/call-BaseRecalibrator/shard-1/attempt-3/VIR_3885.recal_data.csv
onitoring -> gs://broad-gp-gotc-pilot/cromwell_execution/PairedEndSingleSampleWorkflow/60d1afe2-dbd4-47e5-9cf5-e2a76d7947cd/call-BaseRecalibrator/shard-1/attempt-3/monitoring.log
16-02-20 17:26:48,727 cromwell-system-akka.actor.default-dispatcher-16 INFO  - JES Run [UUID(60d1afe2):BaseRecalibrator:1:3]: JES Run ID is operations/ELrs4P2vKhi6hMytpaK-_Gog6a343KwYKg9wcm9kdWN0aW9uUXVldWU
16-02-20 17:26:48,750 cromwell-system-akka.actor.default-dispatcher-19 INFO  - JES Run [UUID(60d1afe2):BaseRecalibrator:1:3]: Status change from - to Initializing
16-02-20 18:29:16,008 cromwell-system-akka.actor.default-dispatcher-8 INFO  - JES Run [UUID(60d1afe2):PreBqsrCheckContamination:2]: Status change from Running to Success
16-02-20 18:29:16,640 cromwell-system-akka.actor.default-dispatcher-15 INFO  - WorkflowActor [UUID(60d1afe2)]: persisting status of PreBqsrCheckContamination:2 to Done.
16-02-20 20:52:48,052 cromwell-system-akka.actor.default-dispatcher-20 INFO  - JES Run [UUID(60d1afe2):GatherBqsrReports]: Status change from Running to Success
16-02-20 20:52:48,491 cromwell-system-akka.actor.default-dispatcher-8 INFO  - WorkflowActor [UUID(60d1afe2)]: persisting status of GatherBqsrReports to Done.
16-02-20 20:52:48,588 cromwell-system-akka.actor.default-dispatcher-8 INFO  - WorkflowActor [UUID(60d1afe2)]: starting calls: PairedEndSingleSampleWorkflow.PrintUnmappedReads, PairedEndSingleSampleWorkflow.ScatteredPrintReads, PairedEndSingleSampleWorkflow.ScatteredPrintReads, PairedEndSingleSampleWorkflow.ScatteredPrintReads, PairedEndSingleSampleWorkflow.ScatteredPrintReads, PairedEndSingleSampleWorkflow.ScatteredPrintReads, PairedEndSingleSampleWorkflow.ScatteredPrintReads, PairedEndSingleSampleWorkflow.ScatteredPrintReads, PairedEndSingleSampleWorkflow.ScatteredPrintReads, PairedEndSingleSampleWorkflow.ScatteredPrintReads, PairedEndSingleSampleWorkflow.ScatteredPrintReads, PairedEndSingleSampleWorkflow.ScatteredPrintReads, PairedEndSingleSampleWorkflow.ScatteredPrintReads, PairedEndSingleSampleWorkflow.ScatteredPrintReads, PairedEndSingleSampleWorkflow.ScatteredPrintReads, PairedEndSingleSampleWorkflow.ScatteredPrintReads, PairedEndSingleSampleWorkflow.ScatteredPrintReads, PairedEndSingleSampleWorkflow.ScatteredPrintReads, PairedEndSingleSampleWorkflow.ScatteredPrintReads
16-02-20 20:52:48,589 cromwell-system-akka.actor.default-dispatcher-8 INFO  - WorkflowActor [UUID(60d1afe2)]: persisting status of ScatteredPrintReads:2 to Starting.
16-02-20 20:52:48,590 cromwell-system-akka.actor.default-dispatcher-8 INFO  - WorkflowActor [UUID(60d1afe2)]: persisting status of ScatteredPrintReads:15 to Starting.
16-02-20 20:52:48,591 cromwell-system-akka.actor.default-dispatcher-8 INFO  - WorkflowActor [UUID(60d1afe2)]: persisting status of ScatteredPrintReads:4 to Starting.
16-02-20 20:52:48,592 cromwell-system-akka.actor.default-dispatcher-8 INFO  - WorkflowActor [UUID(60d1afe2)]: persisting status of ScatteredPrintReads:7 to Starting.
16-02-20 20:52:48,593 cromwell-system-akka.actor.default-dispatcher-8 INFO  - WorkflowActor [UUID(60d1afe2)]: persisting status of PrintUnmappedReads to Starting.
16-02-20 20:52:48,594 cromwell-system-akka.actor.default-dispatcher-8 INFO  - WorkflowActor [UUID(60d1afe2)]: persisting status of ScatteredPrintReads:10 to Starting.
16-02-20 20:52:48,595 cromwell-system-akka.actor.default-dispatcher-8 INFO  - WorkflowActor [UUID(60d1afe2)]: persisting status of ScatteredPrintReads:13 to Starting.
16-02-20 20:52:48,596 cromwell-system-akka.actor.default-dispatcher-8 INFO  - WorkflowActor [UUID(60d1afe2)]: persisting status of ScatteredPrintReads:3 to Starting.
16-02-20 20:52:48,597 cromwell-system-akka.actor.default-dispatcher-8 INFO  - WorkflowActor [UUID(60d1afe2)]: persisting status of ScatteredPrintReads:8 to Starting.
16-02-20 20:52:48,598 cromwell-system-akka.actor.default-dispatcher-8 INFO  - WorkflowActor [UUID(60d1afe2)]: persisting status of ScatteredPrintReads:11 to Starting.
16-02-20 20:52:48,599 cromwell-system-akka.actor.default-dispatcher-8 INFO  - WorkflowActor [UUID(60d1afe2)]: persisting status of ScatteredPrintReads:6 to Starting.
16-02-20 20:52:48,600 cromwell-system-akka.actor.default-dispatcher-12 INFO  - WorkflowActor [UUID(60d1afe2)]: persisting status of ScatteredPrintReads:12 to Starting.
16-02-20 20:52:48,602 cromwell-system-akka.actor.default-dispatcher-12 INFO  - WorkflowActor [UUID(60d1afe2)]: persisting status of ScatteredPrintReads:5 to Starting.
16-02-20 20:52:48,603 cromwell-system-akka.actor.default-dispatcher-12 INFO  - WorkflowActor [UUID(60d1afe2)]: persisting status of ScatteredPrintReads:17 to Starting.
16-02-20 20:52:48,604 cromwell-system-akka.actor.default-dispatcher-12 INFO  - WorkflowActor [UUID(60d1afe2)]: persisting status of ScatteredPrintReads:16 to Starting.
16-02-20 20:52:48,605 cromwell-system-akka.actor.default-dispatcher-12 INFO  - WorkflowActor [UUID(60d1afe2)]: persisting status of ScatteredPrintReads:1 to Starting.
16-02-20 20:52:48,606 cromwell-system-akka.actor.default-dispatcher-12 INFO  - WorkflowActor [UUID(60d1afe2)]: persisting status of ScatteredPrintReads:0 to Starting.
16-02-20 20:52:48,607 cromwell-system-akka.actor.default-dispatcher-12 INFO  - WorkflowActor [UUID(60d1afe2)]: persisting status of ScatteredPrintReads:14 to Starting.
16-02-20 20:52:48,608 cromwell-system-akka.actor.default-dispatcher-12 INFO  - WorkflowActor [UUID(60d1afe2)]: persisting status of ScatteredPrintReads:9 to Starting.
16-02-20 20:52:48,731 cromwell-system-akka.actor.default-dispatcher-21 INFO  - WorkflowActor [UUID(60d1afe2)]: inputs for call 'ScatteredPrintReads:2':
nput_bam -> WdlSingleFile(gs://broad-gp-gotc-pilot/cromwell_execution/PairedEndSingleSampleWorkflow/60d1afe2-dbd4-47e5-9cf5-e2a76d7947cd/call-AggregatedBamMarkDuplicates/VIR_3885.aligned.duplicates_marked.bam)
ecalibration_report -> WdlSingleFile(gs://broad-gp-gotc-pilot/cromwell_execution/PairedEndSingleSampleWorkflow/60d1afe2-dbd4-47e5-9cf5-e2a76d7947cd/call-GatherBqsrReports/VIR_3885.recal_data.csv)
nput_bam_index -> WdlSingleFile(gs://broad-gp-gotc-pilot/cromwell_execution/PairedEndSingleSampleWorkflow/60d1afe2-dbd4-47e5-9cf5-e2a76d7947cd/call-AggregatedBamMarkDuplicates/VIR_3885.aligned.duplicates_marked.bai)
16-02-20 20:52:48,731 cromwell-system-akka.actor.default-dispatcher-21 INFO  - WorkflowActor [UUID(60d1afe2)]: created call actor for ScatteredPrintReads:2.
16-02-20 20:52:48,732 cromwell-system-akka.actor.default-dispatcher-21 INFO  - JesBackend [UUID(60d1afe2):ScatteredPrintReads:2]: Call GCS path: gs://broad-gp-gotc-pilot/cromwell_execution/PairedEndSingleSampleWorkflow/60d1afe2-dbd4-47e5-9cf5-e2a76d7947cd/call-ScatteredPrintReads/shard-2
16-02-20 20:52:48,732 cromwell-system-akka.actor.default-dispatcher-21 INFO  - JesBackend [UUID(60d1afe2):ScatteredPrintReads:2]: `java -Dsamjdk.use_async_io=true -XX:GCTimeLimit=50 -XX:GCHeapFreeLimit=10 -Xmx3000m \
I /cromwell_root/broad-gp-gotc-pilot/cromwell_execution/PairedEndSingleSampleWorkflow/60d1afe2-dbd4-47e5-9cf5-e2a76d7947cd/call-AggregatedBamMarkDuplicates/VIR_3885.aligned.duplicates_marked.bam \
BQSR /cromwell_root/broad-gp-gotc-pilot/cromwell_execution/PairedEndSingleSampleWorkflow/60d1afe2-dbd4-47e5-9cf5-e2a76d7947cd/call-GatherBqsrReports/VIR_3885.recal_data.csv \
16-02-20 20:52:48,733 cromwell-system-akka.actor.default-dispatcher-18 INFO  - WorkflowActor [UUID(60d1afe2)]: persisting status of ScatteredPrintReads:2 to Running.
16-02-20 20:53:44,721 cromwell-system-akka.actor.default-dispatcher-13 INFO  - JES Run [UUID(60d1afe2):ScatteredPrintReads:3]: Status change from Initializing to Running
16-02-20 20:54:15,156 cromwell-system-akka.actor.default-dispatcher-7 INFO  - JES Run [UUID(60d1afe2):ScatteredPrintReads:14]: Status change from Initializing to Running
16-02-20 20:54:19,200 cromwell-system-akka.actor.default-dispatcher-16 INFO  - JES Run [UUID(60d1afe2):PrintUnmappedReads]: Status change from Initializing to Running
16-02-20 20:54:19,334 cromwell-system-akka.actor.default-dispatcher-4 INFO  - JES Run [UUID(60d1afe2):ScatteredPrintReads:0]: Status change from Initializing to Running
16-02-20 20:54:48,616 cromwell-system-akka.actor.default-dispatcher-21 INFO  - JES Run [UUID(60d1afe2):ScatteredPrintReads:11]: Status change from Initializing to Running
16-02-20 21:16:53,625 cromwell-system-akka.actor.default-dispatcher-7 INFO  - JES Run [UUID(60d1afe2):PrintUnmappedReads]: Status change from Running to Success
16-02-20 21:16:54,106 cromwell-system-akka.actor.default-dispatcher-7 INFO  - WorkflowActor [UUID(60d1afe2)]: persisting status of PrintUnmappedReads to Done.
16-02-20 21:55:46,244 cromwell-system-akka.actor.default-dispatcher-18 INFO  - JES Run [UUID(60d1afe2):ScatteredPrintReads:8]: Status change from Running to Success
16-02-20 21:55:46,719 cromwell-system-akka.actor.default-dispatcher-16 INFO  - WorkflowActor [UUID(60d1afe2)]: persisting status of ScatteredPrintReads:8 to Done.
16-02-20 22:07:12,359 cromwell-system-akka.actor.default-dispatcher-3 INFO  - JES Run [UUID(60d1afe2):ScatteredPrintReads:9]: Status change from Running to Success
16-02-20 22:07:12,883 cromwell-system-akka.actor.default-dispatcher-7 INFO  - WorkflowActor [UUID(60d1afe2)]: persisting status of ScatteredPrintReads:9 to Done.
16-02-20 22:09:43,192 cromwell-system-akka.actor.default-dispatcher-23 INFO  - JES Run [UUID(60d1afe2):ScatteredPrintReads:6]: Status change from Running to Success
16-02-20 22:09:43,674 cromwell-system-akka.actor.default-dispatcher-26 INFO  - WorkflowActor [UUID(60d1afe2)]: persisting status of ScatteredPrintReads:6 to Done.
16-02-20 22:16:15,842 cromwell-system-akka.actor.default-dispatcher-24 INFO  - JES Run [UUID(60d1afe2):ScatteredPrintReads:4]: Status change from Running to Success
16-02-20 22:16:16,308 cromwell-system-akka.actor.default-dispatcher-19 INFO  - WorkflowActor [UUID(60d1afe2)]: persisting status of ScatteredPrintReads:4 to Done.
16-02-20 22:17:47,790 cromwell-system-akka.actor.default-dispatcher-16 INFO  - JES Run [UUID(60d1afe2):ScatteredPrintReads:13]: Status change from Running to Success
16-02-20 22:17:48,258 cromwell-system-akka.actor.default-dispatcher-23 INFO  - WorkflowActor [UUID(60d1afe2)]: persisting status of ScatteredPrintReads:13 to Done.
16-02-20 22:23:20,397 cromwell-system-akka.actor.default-dispatcher-17 INFO  - JES Run [UUID(60d1afe2):ScatteredPrintReads:3]: Status change from Running to Success
16-02-20 22:23:20,854 cromwell-system-akka.actor.default-dispatcher-13 INFO  - WorkflowActor [UUID(60d1afe2)]: persisting status of ScatteredPrintReads:3 to Done.
16-02-20 22:29:56,508 cromwell-system-akka.actor.default-dispatcher-21 INFO  - JES Run [UUID(60d1afe2):ScatteredPrintReads:16]: Status change from Running to Success
16-02-20 22:29:57,019 cromwell-system-akka.actor.default-dispatcher-8 INFO  - WorkflowActor [UUID(60d1afe2)]: persisting status of ScatteredPrintReads:16 to Done.
16-02-21 00:33:38,374 cromwell-system-akka.actor.default-dispatcher-23 INFO  - JES Run [UUID(60d1afe2):HaplotypeCaller:40]: Status change from Initializing to Running
16-02-21 00:34:07,401 cromwell-system-akka.actor.default-dispatcher-5 INFO  - JES Run [UUID(60d1afe2):HaplotypeCaller:22]: Status change from Initializing to Running
16-02-21 00:34:37,861 cromwell-system-akka.actor.default-dispatcher-4 INFO  - JES Run [UUID(60d1afe2):HaplotypeCaller:14]: Status change from Initializing to Running
16-02-21 00:34:39,303 cromwell-system-akka.actor.default-dispatcher-4 INFO  - JES Run [UUID(60d1afe2):HaplotypeCaller:45]: Status change from Initializing to Running
16-02-21 00:35:08,033 cromwell-system-akka.actor.default-dispatcher-16 INFO  - JES Run [UUID(60d1afe2):HaplotypeCaller:28]: Status change from Initializing to Running
16-02-21 00:35:09,721 cromwell-system-akka.actor.default-dispatcher-18 INFO  - JES Run [UUID(60d1afe2):HaplotypeCaller:29]: Status change from Initializing to Running
16-02-21 00:35:10,094 cromwell-system-akka.actor.default-dispatcher-19 INFO  - JES Run [UUID(60d1afe2):HaplotypeCaller:5]: Status change from Initializing to Running
16-02-21 00:35:38,491 cromwell-system-akka.actor.default-dispatcher-8 INFO  - JES Run [UUID(60d1afe2):HaplotypeCaller:48]: Status change from Initializing to Running
16-02-21 00:35:41,260 cromwell-system-akka.actor.default-dispatcher-5 INFO  - JES Run [UUID(60d1afe2):HaplotypeCaller:23]: Status change from Initializing to Running
16-02-21 00:35:42,521 cromwell-system-akka.actor.default-dispatcher-11 INFO  - JES Run [UUID(60d1afe2):HaplotypeCaller:2]: Status change from Initializing to Running
16-02-21 00:35:42,692 cromwell-system-akka.actor.default-dispatcher-21 INFO  - JES Run [UUID(60d1afe2):HaplotypeCaller:7]: Status change from Initializing to Running
16-02-21 00:37:09,390 cromwell-system-akka.actor.default-dispatcher-19 INFO  - JES Run [UUID(60d1afe2):CollectWgsMetrics]: Status change from Initializing to Running
16-02-21 00:38:09,863 cromwell-system-akka.actor.default-dispatcher-3 INFO  - JES Run [UUID(60d1afe2):HaplotypeCaller:25]: Status change from Initializing to Running
16-02-21 00:38:39,693 cromwell-system-akka.actor.default-dispatcher-2 INFO  - JES Run [UUID(60d1afe2):HaplotypeCaller:31]: Status change from Initializing to Running
16-02-21 00:56:50,408 cromwell-system-akka.actor.default-dispatcher-20 INFO  - JES Run [UUID(60d1afe2):HaplotypeCaller:22]: Status change from Running to Failed
16-02-21 00:56:50,409 cromwell-system-akka.actor.default-dispatcher-20 ERROR - CallActor [UUID(60d1afe2):HaplotypeCaller:22]: Failing call with retryable Failure: Task 60d1afe2-dbd4-47e5-9cf5-e2a76d7947cd:HaplotypeCaller was preempted for the 1st time. The call will be re-started with another pre-emptible VM (max pre-emptible attempts number is 3).
omwell.engine.package$PreemptedException: Task 60d1afe2-dbd4-47e5-9cf5-e2a76d7947cd:HaplotypeCaller was preempted for the 1st time. The call will be re-started with another pre-emptible VM (max pre-emptible attempts number is 3).
16-02-21 00:56:50,759 cromwell-system-akka.actor.default-dispatcher-17 INFO  - WorkflowActor [UUID(60d1afe2)]: persisting status of HaplotypeCaller:22 to Preempted.
16-02-21 00:56:50,852 cromwell-system-akka.actor.default-dispatcher-18 INFO  - WorkflowActor [UUID(60d1afe2)]: starting calls: PairedEndSingleSampleWorkflow.HaplotypeCaller
16-02-21 00:56:50,852 cromwell-system-akka.actor.default-dispatcher-18 INFO  - WorkflowActor [UUID(60d1afe2)]: persisting status of HaplotypeCaller:22:2 to Starting.
16-02-21 00:56:50,971 cromwell-system-akka.actor.default-dispatcher-25 INFO  - WorkflowActor [UUID(60d1afe2)]: inputs for call 'HaplotypeCaller:22:2':
nput_bam -> WdlSingleFile(gs://broad-gp-gotc-pilot/cromwell_execution/PairedEndSingleSampleWorkflow/60d1afe2-dbd4-47e5-9cf5-e2a76d7947cd/call-GatherBamFiles/VIR_3885.bam)
nterval_list -> WdlSingleFile(gs://broad-gp-gotc-pilot/cromwell_execution/PairedEndSingleSampleWorkflow/60d1afe2-dbd4-47e5-9cf5-e2a76d7947cd/call-ScatterIntervalList/glob-cb4648beeaff920acb03de7603c06f98/2scattered.interval_list)
nput_bam_index -> WdlSingleFile(gs://broad-gp-gotc-pilot/cromwell_execution/PairedEndSingleSampleWorkflow/60d1afe2-dbd4-47e5-9cf5-e2a76d7947cd/call-GatherBamFiles/VIR_3885.bai)
16-02-21 00:56:50,971 cromwell-system-akka.actor.default-dispatcher-4 INFO  - WorkflowActor [UUID(60d1afe2)]: created call actor for HaplotypeCaller:22:2.
16-02-21 00:56:50,971 cromwell-system-akka.actor.default-dispatcher-4 INFO  - WorkflowActor [UUID(60d1afe2)]: persisting status of HaplotypeCaller:22:2 to Running.
16-02-21 00:56:50,971 cromwell-system-akka.actor.default-dispatcher-10 INFO  - JesBackend [UUID(60d1afe2):HaplotypeCaller:22:2]: Call GCS path: gs://broad-gp-gotc-pilot/cromwell_execution/PairedEndSingleSampleWorkflow/60d1afe2-dbd4-47e5-9cf5-e2a76d7947cd/call-HaplotypeCaller/shard-22/attempt-2
16-02-21 00:56:50,972 cromwell-system-akka.actor.default-dispatcher-10 INFO  - JesBackend [UUID(60d1afe2):HaplotypeCaller:22:2]: `java -XX:GCTimeLimit=50 -XX:GCHeapFreeLimit=10 -Xmx6000m \
I /cromwell_root/broad-gp-gotc-pilot/cromwell_execution/PairedEndSingleSampleWorkflow/60d1afe2-dbd4-47e5-9cf5-e2a76d7947cd/call-GatherBamFiles/VIR_3885.bam \
L /cromwell_root/broad-gp-gotc-pilot/cromwell_execution/PairedEndSingleSampleWorkflow/60d1afe2-dbd4-47e5-9cf5-e2a76d7947cd/call-ScatterIntervalList/glob-cb4648beeaff920acb03de7603c06f98/2scattered.interval_list \
16-02-21 00:56:51,131 cromwell-system-akka.actor.default-dispatcher-10 INFO  - JesBackend [UUID(60d1afe2):HaplotypeCaller:22:2]: Starting call with pre-emptible VM
16-02-21 00:56:51,131 cromwell-system-akka.actor.default-dispatcher-10 INFO  - JES Pipeline [UUID(60d1afe2):HaplotypeCaller:22:2]: Pipeline parameters are:
name=input_bam-0, type=REFERENCE, value=/cromwell_root/broad-gp-gotc-pilot/cromwell_execution/PairedEndSingleSampleWorkflow/60d1afe2-dbd4-47e5-9cf5-e2a76d7947cd/call-GatherBamFiles/VIR_3885.bam}
name=interval_list-0, type=REFERENCE, value=/cromwell_root/broad-gp-gotc-pilot/cromwell_execution/PairedEndSingleSampleWorkflow/60d1afe2-dbd4-47e5-9cf5-e2a76d7947cd/call-ScatterIntervalList/glob-cb4648beeaff920acb03de7603c06f98/2scattered.interval_list}
name=input_bam_index-0, type=REFERENCE, value=/cromwell_root/broad-gp-gotc-pilot/cromwell_execution/PairedEndSingleSampleWorkflow/60d1afe2-dbd4-47e5-9cf5-e2a76d7947cd/call-GatherBamFiles/VIR_3885.bai}
16-02-21 00:56:51,164 cromwell-system-akka.actor.default-dispatcher-10 INFO  - JES Pipeline [UUID(60d1afe2):HaplotypeCaller:22:2]: Pipeline ID is 8781052396282022285
16-02-21 00:56:51,164 cromwell-system-akka.actor.default-dispatcher-10 INFO  - JES Pipeline [UUID(60d1afe2):HaplotypeCaller:22:2]: Project ID: broad-gp-gotc-pilot
16-02-21 00:56:51,164 cromwell-system-akka.actor.default-dispatcher-10 INFO  - JES Run [UUID(60d1afe2):HaplotypeCaller:22:2]: Inputs:
nterval_list-0 -> gs://broad-gp-gotc-pilot/cromwell_execution/PairedEndSingleSampleWorkflow/60d1afe2-dbd4-47e5-9cf5-e2a76d7947cd/call-ScatterIntervalList/glob-cb4648beeaff920acb03de7603c06f98/2scattered.interval_list
nput_bam_index-0 -> gs://broad-gp-gotc-pilot/cromwell_execution/PairedEndSingleSampleWorkflow/60d1afe2-dbd4-47e5-9cf5-e2a76d7947cd/call-GatherBamFiles/VIR_3885.bai
nput_bam-0 -> gs://broad-gp-gotc-pilot/cromwell_execution/PairedEndSingleSampleWorkflow/60d1afe2-dbd4-47e5-9cf5-e2a76d7947cd/call-GatherBamFiles/VIR_3885.bam
xec -> gs://broad-gp-gotc-pilot/cromwell_execution/PairedEndSingleSampleWorkflow/60d1afe2-dbd4-47e5-9cf5-e2a76d7947cd/call-HaplotypeCaller/shard-22/attempt-2/exec.sh
16-02-21 00:56:51,164 cromwell-system-akka.actor.default-dispatcher-10 INFO  - JES Run [UUID(60d1afe2):HaplotypeCaller:22:2]: Outputs:
aplotypeCaller-22-rc.txt -> gs://broad-gp-gotc-pilot/cromwell_execution/PairedEndSingleSampleWorkflow/60d1afe2-dbd4-47e5-9cf5-e2a76d7947cd/call-HaplotypeCaller/shard-22/attempt-2/HaplotypeCaller-22-rc.txt
IR_3885.vcf.gz -> gs://broad-gp-gotc-pilot/cromwell_execution/PairedEndSingleSampleWorkflow/60d1afe2-dbd4-47e5-9cf5-e2a76d7947cd/call-HaplotypeCaller/shard-22/attempt-2/VIR_3885.vcf.gz
IR_3885.vcf.gz.tbi -> gs://broad-gp-gotc-pilot/cromwell_execution/PairedEndSingleSampleWorkflow/60d1afe2-dbd4-47e5-9cf5-e2a76d7947cd/call-HaplotypeCaller/shard-22/attempt-2/VIR_3885.vcf.gz.tbi
onitoring -> gs://broad-gp-gotc-pilot/cromwell_execution/PairedEndSingleSampleWorkflow/60d1afe2-dbd4-47e5-9cf5-e2a76d7947cd/call-HaplotypeCaller/shard-22/attempt-2/monitoring.log
16-02-21 00:56:51,275 cromwell-system-akka.actor.default-dispatcher-10 INFO  - JES Run [UUID(60d1afe2):HaplotypeCaller:22:2]: JES Run ID is operations/EPT50IqwKhiZw7O0qL_wuWEg6a343KwYKg9wcm9kdWN0aW9uUXVldWU
16-02-21 00:56:51,301 cromwell-system-akka.actor.default-dispatcher-26 INFO  - JES Run [UUID(60d1afe2):HaplotypeCaller:22:2]: Status change from - to Initializing
16-02-21 01:01:18,996 cromwell-system-akka.actor.default-dispatcher-10 INFO  - JES Run [UUID(60d1afe2):CalculateReadGroupChecksum]: Status change from Running to Success
16-02-21 01:01:19,448 cromwell-system-akka.actor.default-dispatcher-10 INFO  - WorkflowActor [UUID(60d1afe2)]: persisting status of CalculateReadGroupChecksum to Done.
16-02-21 01:02:20,169 cromwell-system-akka.actor.default-dispatcher-15 INFO  - JES Run [UUID(60d1afe2):HaplotypeCaller:28]: Status change from Running to Failed
16-02-21 01:02:20,171 cromwell-system-akka.actor.default-dispatcher-13 ERROR - CallActor [UUID(60d1afe2):HaplotypeCaller:28]: Failing call with retryable Failure: Task 60d1afe2-dbd4-47e5-9cf5-e2a76d7947cd:HaplotypeCaller was preempted for the 1st time. The call will be re-started with another pre-emptible VM (max pre-emptible attempts number is 3).
omwell.engine.package$PreemptedException: Task 60d1afe2-dbd4-47e5-9cf5-e2a76d7947cd:HaplotypeCaller was preempted for the 1st time. The call will be re-started with another pre-emptible VM (max pre-emptible attempts number is 3).
16-02-21 01:02:20,534 cromwell-system-akka.actor.default-dispatcher-13 INFO  - WorkflowActor [UUID(60d1afe2)]: persisting status of HaplotypeCaller:28 to Preempted.
16-02-21 01:02:20,653 cromwell-system-akka.actor.default-dispatcher-25 INFO  - WorkflowActor [UUID(60d1afe2)]: starting calls: PairedEndSingleSampleWorkflow.HaplotypeCaller
16-02-21 01:02:20,653 cromwell-system-akka.actor.default-dispatcher-25 INFO  - WorkflowActor [UUID(60d1afe2)]: persisting status of HaplotypeCaller:28:2 to Starting.
16-02-21 01:02:20,772 cromwell-system-akka.actor.default-dispatcher-13 INFO  - WorkflowActor [UUID(60d1afe2)]: inputs for call 'HaplotypeCaller:28:2':
nput_bam -> WdlSingleFile(gs://broad-gp-gotc-pilot/cromwell_execution/PairedEndSingleSampleWorkflow/60d1afe2-dbd4-47e5-9cf5-e2a76d7947cd/call-GatherBamFiles/VIR_3885.bam)
nterval_list -> WdlSingleFile(gs://broad-gp-gotc-pilot/cromwell_execution/PairedEndSingleSampleWorkflow/60d1afe2-dbd4-47e5-9cf5-e2a76d7947cd/call-ScatterIntervalList/glob-cb4648beeaff920acb03de7603c06f98/35scattered.interval_list)
nput_bam_index -> WdlSingleFile(gs://broad-gp-gotc-pilot/cromwell_execution/PairedEndSingleSampleWorkflow/60d1afe2-dbd4-47e5-9cf5-e2a76d7947cd/call-GatherBamFiles/VIR_3885.bai)
16-02-21 01:02:20,772 cromwell-system-akka.actor.default-dispatcher-25 INFO  - WorkflowActor [UUID(60d1afe2)]: created call actor for HaplotypeCaller:28:2.
16-02-21 01:02:20,772 cromwell-system-akka.actor.default-dispatcher-25 INFO  - WorkflowActor [UUID(60d1afe2)]: persisting status of HaplotypeCaller:28:2 to Running.
16-02-21 01:02:20,772 cromwell-system-akka.actor.default-dispatcher-8 INFO  - JesBackend [UUID(60d1afe2):HaplotypeCaller:28:2]: Call GCS path: gs://broad-gp-gotc-pilot/cromwell_execution/PairedEndSingleSampleWorkflow/60d1afe2-dbd4-47e5-9cf5-e2a76d7947cd/call-HaplotypeCaller/shard-28/attempt-2
16-02-21 01:02:20,772 cromwell-system-akka.actor.default-dispatcher-8 INFO  - JesBackend [UUID(60d1afe2):HaplotypeCaller:28:2]: `java -XX:GCTimeLimit=50 -XX:GCHeapFreeLimit=10 -Xmx6000m \
I /cromwell_root/broad-gp-gotc-pilot/cromwell_execution/PairedEndSingleSampleWorkflow/60d1afe2-dbd4-47e5-9cf5-e2a76d7947cd/call-GatherBamFiles/VIR_3885.bam \
L /cromwell_root/broad-gp-gotc-pilot/cromwell_execution/PairedEndSingleSampleWorkflow/60d1afe2-dbd4-47e5-9cf5-e2a76d7947cd/call-ScatterIntervalList/glob-cb4648beeaff920acb03de7603c06f98/35scattered.interval_list \
16-02-21 01:02:20,910 cromwell-system-akka.actor.default-dispatcher-8 INFO  - JesBackend [UUID(60d1afe2):HaplotypeCaller:28:2]: Starting call with pre-emptible VM
16-02-21 01:02:20,910 cromwell-system-akka.actor.default-dispatcher-8 INFO  - JES Pipeline [UUID(60d1afe2):HaplotypeCaller:28:2]: Pipeline parameters are:
name=input_bam-0, type=REFERENCE, value=/cromwell_root/broad-gp-gotc-pilot/cromwell_execution/PairedEndSingleSampleWorkflow/60d1afe2-dbd4-47e5-9cf5-e2a76d7947cd/call-GatherBamFiles/VIR_3885.bam}
name=interval_list-0, type=REFERENCE, value=/cromwell_root/broad-gp-gotc-pilot/cromwell_execution/PairedEndSingleSampleWorkflow/60d1afe2-dbd4-47e5-9cf5-e2a76d7947cd/call-ScatterIntervalList/glob-cb4648beeaff920acb03de7603c06f98/35scattered.interval_list}
name=input_bam_index-0, type=REFERENCE, value=/cromwell_root/broad-gp-gotc-pilot/cromwell_execution/PairedEndSingleSampleWorkflow/60d1afe2-dbd4-47e5-9cf5-e2a76d7947cd/call-GatherBamFiles/VIR_3885.bai}
16-02-21 01:02:21,003 cromwell-system-akka.actor.default-dispatcher-8 INFO  - JES Pipeline [UUID(60d1afe2):HaplotypeCaller:28:2]: Pipeline ID is 15775065906124882579
16-02-21 01:05:22,447 cromwell-system-akka.actor.default-dispatcher-3 INFO  - JES Run [UUID(60d1afe2):HaplotypeCaller:34]: Status change from Running to Failed
16-02-21 01:05:22,449 cromwell-system-akka.actor.default-dispatcher-22 ERROR - CallActor [UUID(60d1afe2):HaplotypeCaller:34]: Failing call with retryable Failure: Task 60d1afe2-dbd4-47e5-9cf5-e2a76d7947cd:HaplotypeCaller was preempted for the 1st time. The call will be re-started with another pre-emptible VM (max pre-emptible attempts number is 3).
omwell.engine.package$PreemptedException: Task 60d1afe2-dbd4-47e5-9cf5-e2a76d7947cd:HaplotypeCaller was preempted for the 1st time. The call will be re-started with another pre-emptible VM (max pre-emptible attempts number is 3).
16-02-21 01:19:00,001 cromwell-system-akka.actor.default-dispatcher-20 INFO  - JES Run [UUID(60d1afe2):HaplotypeCaller:39:2]: Status change from Initializing to Running
16-02-21 01:22:27,487 cromwell-system-akka.actor.default-dispatcher-11 INFO  - JES Run [UUID(60d1afe2):HaplotypeCaller:10]: Status change from Running to Failed
16-02-21 01:22:27,488 cromwell-system-akka.actor.default-dispatcher-11 ERROR - CallActor [UUID(60d1afe2):HaplotypeCaller:10]: Failing call with retryable Failure: Task 60d1afe2-dbd4-47e5-9cf5-e2a76d7947cd:HaplotypeCaller was preempted for the 1st time. The call will be re-started with another pre-emptible VM (max pre-emptible attempts number is 3).
omwell.engine.package$PreemptedException: Task 60d1afe2-dbd4-47e5-9cf5-e2a76d7947cd:HaplotypeCaller was preempted for the 1st time. The call will be re-started with another pre-emptible VM (max pre-emptible attempts number is 3).
16-02-21 01:22:27,828 cromwell-system-akka.actor.default-dispatcher-26 INFO  - WorkflowActor [UUID(60d1afe2)]: persisting status of HaplotypeCaller:10 to Preempted.
16-02-21 01:22:27,922 cromwell-system-akka.actor.default-dispatcher-21 INFO  - WorkflowActor [UUID(60d1afe2)]: starting calls: PairedEndSingleSampleWorkflow.HaplotypeCaller
16-02-21 01:22:27,922 cromwell-system-akka.actor.default-dispatcher-21 INFO  - WorkflowActor [UUID(60d1afe2)]: persisting status of HaplotypeCaller:10:2 to Starting.
16-02-21 01:22:28,041 cromwell-system-akka.actor.default-dispatcher-16 INFO  - WorkflowActor [UUID(60d1afe2)]: inputs for call 'HaplotypeCaller:10:2':
nput_bam -> WdlSingleFile(gs://broad-gp-gotc-pilot/cromwell_execution/PairedEndSingleSampleWorkflow/60d1afe2-dbd4-47e5-9cf5-e2a76d7947cd/call-GatherBamFiles/VIR_3885.bam)
nterval_list -> WdlSingleFile(gs://broad-gp-gotc-pilot/cromwell_execution/PairedEndSingleSampleWorkflow/60d1afe2-dbd4-47e5-9cf5-e2a76d7947cd/call-ScatterIntervalList/glob-cb4648beeaff920acb03de7603c06f98/19scattered.interval_list)
nput_bam_index -> WdlSingleFile(gs://broad-gp-gotc-pilot/cromwell_execution/PairedEndSingleSampleWorkflow/60d1afe2-dbd4-47e5-9cf5-e2a76d7947cd/call-GatherBamFiles/VIR_3885.bai)
16-02-21 01:22:28,041 cromwell-system-akka.actor.default-dispatcher-21 INFO  - WorkflowActor [UUID(60d1afe2)]: created call actor for HaplotypeCaller:10:2.
16-02-21 01:22:28,041 cromwell-system-akka.actor.default-dispatcher-12 INFO  - WorkflowActor [UUID(60d1afe2)]: persisting status of HaplotypeCaller:10:2 to Running.
16-02-21 01:22:28,041 cromwell-system-akka.actor.default-dispatcher-21 INFO  - JesBackend [UUID(60d1afe2):HaplotypeCaller:10:2]: Call GCS path: gs://broad-gp-gotc-pilot/cromwell_execution/PairedEndSingleSampleWorkflow/60d1afe2-dbd4-47e5-9cf5-e2a76d7947cd/call-HaplotypeCaller/shard-10/attempt-2
16-02-21 01:22:28,042 cromwell-system-akka.actor.default-dispatcher-21 INFO  - JesBackend [UUID(60d1afe2):HaplotypeCaller:10:2]: `java -XX:GCTimeLimit=50 -XX:GCHeapFreeLimit=10 -Xmx6000m \
I /cromwell_root/broad-gp-gotc-pilot/cromwell_execution/PairedEndSingleSampleWorkflow/60d1afe2-dbd4-47e5-9cf5-e2a76d7947cd/call-GatherBamFiles/VIR_3885.bam \
L /cromwell_root/broad-gp-gotc-pilot/cromwell_execution/PairedEndSingleSampleWorkflow/60d1afe2-dbd4-47e5-9cf5-e2a76d7947cd/call-ScatterIntervalList/glob-cb4648beeaff920acb03de7603c06f98/19scattered.interval_list \
16-02-21 01:22:28,201 cromwell-system-akka.actor.default-dispatcher-21 INFO  - JesBackend [UUID(60d1afe2):HaplotypeCaller:10:2]: Starting call with pre-emptible VM
16-02-21 01:22:28,201 cromwell-system-akka.actor.default-dispatcher-21 INFO  - JES Pipeline [UUID(60d1afe2):HaplotypeCaller:10:2]: Pipeline parameters are:
name=input_bam-0, type=REFERENCE, value=/cromwell_root/broad-gp-gotc-pilot/cromwell_execution/PairedEndSingleSampleWorkflow/60d1afe2-dbd4-47e5-9cf5-e2a76d7947cd/call-GatherBamFiles/VIR_3885.bam}
name=interval_list-0, type=REFERENCE, value=/cromwell_root/broad-gp-gotc-pilot/cromwell_execution/PairedEndSingleSampleWorkflow/60d1afe2-dbd4-47e5-9cf5-e2a76d7947cd/call-ScatterIntervalList/glob-cb4648beeaff920acb03de7603c06f98/19scattered.interval_list}
name=input_bam_index-0, type=REFERENCE, value=/cromwell_root/broad-gp-gotc-pilot/cromwell_execution/PairedEndSingleSampleWorkflow/60d1afe2-dbd4-47e5-9cf5-e2a76d7947cd/call-GatherBamFiles/VIR_3885.bai}
16-02-21 01:22:28,236 cromwell-system-akka.actor.default-dispatcher-21 INFO  - JES Pipeline [UUID(60d1afe2):HaplotypeCaller:10:2]: Pipeline ID is 11946663422419317778
16-02-21 01:22:28,236 cromwell-system-akka.actor.default-dispatcher-21 INFO  - JES Pipeline [UUID(60d1afe2):HaplotypeCaller:10:2]: Project ID: broad-gp-gotc-pilot
16-02-21 01:22:28,236 cromwell-system-akka.actor.default-dispatcher-21 INFO  - JES Run [UUID(60d1afe2):HaplotypeCaller:10:2]: Inputs:
nterval_list-0 -> gs://broad-gp-gotc-pilot/cromwell_execution/PairedEndSingleSampleWorkflow/60d1afe2-dbd4-47e5-9cf5-e2a76d7947cd/call-ScatterIntervalList/glob-cb4648beeaff920acb03de7603c06f98/19scattered.interval_list
nput_bam_index-0 -> gs://broad-gp-gotc-pilot/cromwell_execution/PairedEndSingleSampleWorkflow/60d1afe2-dbd4-47e5-9cf5-e2a76d7947cd/call-GatherBamFiles/VIR_3885.bai
nput_bam-0 -> gs://broad-gp-gotc-pilot/cromwell_execution/PairedEndSingleSampleWorkflow/60d1afe2-dbd4-47e5-9cf5-e2a76d7947cd/call-GatherBamFiles/VIR_3885.bam
xec -> gs://broad-gp-gotc-pilot/cromwell_execution/PairedEndSingleSampleWorkflow/60d1afe2-dbd4-47e5-9cf5-e2a76d7947cd/call-HaplotypeCaller/shard-10/attempt-2/exec.sh
16-02-21 01:22:28,236 cromwell-system-akka.actor.default-dispatcher-21 INFO  - JES Run [UUID(60d1afe2):HaplotypeCaller:10:2]: Outputs:
aplotypeCaller-10-rc.txt -> gs://broad-gp-gotc-pilot/cromwell_execution/PairedEndSingleSampleWorkflow/60d1afe2-dbd4-47e5-9cf5-e2a76d7947cd/call-HaplotypeCaller/shard-10/attempt-2/HaplotypeCaller-10-rc.txt
IR_3885.vcf.gz -> gs://broad-gp-gotc-pilot/cromwell_execution/PairedEndSingleSampleWorkflow/60d1afe2-dbd4-47e5-9cf5-e2a76d7947cd/call-HaplotypeCaller/shard-10/attempt-2/VIR_3885.vcf.gz
IR_3885.vcf.gz.tbi -> gs://broad-gp-gotc-pilot/cromwell_execution/PairedEndSingleSampleWorkflow/60d1afe2-dbd4-47e5-9cf5-e2a76d7947cd/call-HaplotypeCaller/shard-10/attempt-2/VIR_3885.vcf.gz.tbi
onitoring -> gs://broad-gp-gotc-pilot/cromwell_execution/PairedEndSingleSampleWorkflow/60d1afe2-dbd4-47e5-9cf5-e2a76d7947cd/call-HaplotypeCaller/shard-10/attempt-2/monitoring.log
16-02-21 01:22:28,350 cromwell-system-akka.actor.default-dispatcher-21 INFO  - JES Run [UUID(60d1afe2):HaplotypeCaller:10:2]: JES Run ID is operations/EKnirouwKhj79YLq95O8jhAg6a343KwYKg9wcm9kdWN0aW9uUXVldWU
16-02-21 01:22:28,371 cromwell-system-akka.actor.default-dispatcher-21 INFO  - JES Run [UUID(60d1afe2):HaplotypeCaller:10:2]: Status change from - to Initializing
16-02-21 01:23:03,194 cromwell-system-akka.actor.default-dispatcher-16 INFO  - JES Run [UUID(60d1afe2):HaplotypeCaller:40]: Status change from Running to Failed
16-02-21 01:23:03,195 cromwell-system-akka.actor.default-dispatcher-16 ERROR - CallActor [UUID(60d1afe2):HaplotypeCaller:40]: Failing call with retryable Failure: Task 60d1afe2-dbd4-47e5-9cf5-e2a76d7947cd:HaplotypeCaller was preempted for the 1st time. The call will be re-started with another pre-emptible VM (max pre-emptible attempts number is 3).
omwell.engine.package$PreemptedException: Task 60d1afe2-dbd4-47e5-9cf5-e2a76d7947cd:HaplotypeCaller was preempted for the 1st time. The call will be re-started with another pre-emptible VM (max pre-emptible attempts number is 3).
16-02-21 01:23:03,558 cromwell-system-akka.actor.default-dispatcher-17 INFO  - WorkflowActor [UUID(60d1afe2)]: persisting status of HaplotypeCaller:40 to Preempted.
16-02-21 01:23:03,659 cromwell-system-akka.actor.default-dispatcher-17 INFO  - WorkflowActor [UUID(60d1afe2)]: starting calls: PairedEndSingleSampleWorkflow.HaplotypeCaller
16-02-21 01:23:03,659 cromwell-system-akka.actor.default-dispatcher-17 INFO  - WorkflowActor [UUID(60d1afe2)]: persisting status of HaplotypeCaller:40:2 to Starting.
16-02-21 01:23:03,772 cromwell-system-akka.actor.default-dispatcher-11 INFO  - WorkflowActor [UUID(60d1afe2)]: inputs for call 'HaplotypeCaller:40:2':
nput_bam -> WdlSingleFile(gs://broad-gp-gotc-pilot/cromwell_execution/PairedEndSingleSampleWorkflow/60d1afe2-dbd4-47e5-9cf5-e2a76d7947cd/call-GatherBamFiles/VIR_3885.bam)
nterval_list -> WdlSingleFile(gs://broad-gp-gotc-pilot/cromwell_execution/PairedEndSingleSampleWorkflow/60d1afe2-dbd4-47e5-9cf5-e2a76d7947cd/call-ScatterIntervalList/glob-cb4648beeaff920acb03de7603c06f98/46scattered.interval_list)
nput_bam_index -> WdlSingleFile(gs://broad-gp-gotc-pilot/cromwell_execution/PairedEndSingleSampleWorkflow/60d1afe2-dbd4-47e5-9cf5-e2a76d7947cd/call-GatherBamFiles/VIR_3885.bai)
16-02-21 01:23:03,772 cromwell-system-akka.actor.default-dispatcher-11 INFO  - WorkflowActor [UUID(60d1afe2)]: created call actor for HaplotypeCaller:40:2.
16-02-21 01:23:03,772 cromwell-system-akka.actor.default-dispatcher-21 INFO  - WorkflowActor [UUID(60d1afe2)]: persisting status of HaplotypeCaller:40:2 to Running.
16-02-21 01:23:03,772 cromwell-system-akka.actor.default-dispatcher-11 INFO  - JesBackend [UUID(60d1afe2):HaplotypeCaller:40:2]: Call GCS path: gs://broad-gp-gotc-pilot/cromwell_execution/PairedEndSingleSampleWorkflow/60d1afe2-dbd4-47e5-9cf5-e2a76d7947cd/call-HaplotypeCaller/shard-40/attempt-2
16-02-21 01:23:03,772 cromwell-system-akka.actor.default-dispatcher-11 INFO  - JesBackend [UUID(60d1afe2):HaplotypeCaller:40:2]: `java -XX:GCTimeLimit=50 -XX:GCHeapFreeLimit=10 -Xmx6000m \
I /cromwell_root/broad-gp-gotc-pilot/cromwell_execution/PairedEndSingleSampleWorkflow/60d1afe2-dbd4-47e5-9cf5-e2a76d7947cd/call-GatherBamFiles/VIR_3885.bam \
L /cromwell_root/broad-gp-gotc-pilot/cromwell_execution/PairedEndSingleSampleWorkflow/60d1afe2-dbd4-47e5-9cf5-e2a76d7947cd/call-ScatterIntervalList/glob-cb4648beeaff920acb03de7603c06f98/46scattered.interval_list \
16-02-21 01:23:03,924 cromwell-system-akka.actor.default-dispatcher-11 INFO  - JesBackend [UUID(60d1afe2):HaplotypeCaller:40:2]: Starting call with pre-emptible VM
16-02-21 01:23:03,924 cromwell-system-akka.actor.default-dispatcher-11 INFO  - JES Pipeline [UUID(60d1afe2):HaplotypeCaller:40:2]: Pipeline parameters are:
name=input_bam-0, type=REFERENCE, value=/cromwell_root/broad-gp-gotc-pilot/cromwell_execution/PairedEndSingleSampleWorkflow/60d1afe2-dbd4-47e5-9cf5-e2a76d7947cd/call-GatherBamFiles/VIR_3885.bam}
name=interval_list-0, type=REFERENCE, value=/cromwell_root/broad-gp-gotc-pilot/cromwell_execution/PairedEndSingleSampleWorkflow/60d1afe2-dbd4-47e5-9cf5-e2a76d7947cd/call-ScatterIntervalList/glob-cb4648beeaff920acb03de7603c06f98/46scattered.interval_list}
name=input_bam_index-0, type=REFERENCE, value=/cromwell_root/broad-gp-gotc-pilot/cromwell_execution/PairedEndSingleSampleWorkflow/60d1afe2-dbd4-47e5-9cf5-e2a76d7947cd/call-GatherBamFiles/VIR_3885.bai}
16-02-21 01:23:03,957 cromwell-system-akka.actor.default-dispatcher-11 INFO  - JES Pipeline [UUID(60d1afe2):HaplotypeCaller:40:2]: Pipeline ID is 4342853356834697525
16-02-21 01:23:03,957 cromwell-system-akka.actor.default-dispatcher-11 INFO  - JES Pipeline [UUID(60d1afe2):HaplotypeCaller:40:2]: Project ID: broad-gp-gotc-pilot
16-02-21 01:23:03,957 cromwell-system-akka.actor.default-dispatcher-11 INFO  - JES Run [UUID(60d1afe2):HaplotypeCaller:40:2]: Inputs:
nterval_list-0 -> gs://broad-gp-gotc-pilot/cromwell_execution/PairedEndSingleSampleWorkflow/60d1afe2-dbd4-47e5-9cf5-e2a76d7947cd/call-ScatterIntervalList/glob-cb4648beeaff920acb03de7603c06f98/46scattered.interval_list
nput_bam_index-0 -> gs://broad-gp-gotc-pilot/cromwell_execution/PairedEndSingleSampleWorkflow/60d1afe2-dbd4-47e5-9cf5-e2a76d7947cd/call-GatherBamFiles/VIR_3885.bai
nput_bam-0 -> gs://broad-gp-gotc-pilot/cromwell_execution/PairedEndSingleSampleWorkflow/60d1afe2-dbd4-47e5-9cf5-e2a76d7947cd/call-GatherBamFiles/VIR_3885.bam
xec -> gs://broad-gp-gotc-pilot/cromwell_execution/PairedEndSingleSampleWorkflow/60d1afe2-dbd4-47e5-9cf5-e2a76d7947cd/call-HaplotypeCaller/shard-40/attempt-2/exec.sh
16-02-21 01:23:03,957 cromwell-system-akka.actor.default-dispatcher-11 INFO  - JES Run [UUID(60d1afe2):HaplotypeCaller:40:2]: Outputs:
aplotypeCaller-40-rc.txt -> gs://broad-gp-gotc-pilot/cromwell_execution/PairedEndSingleSampleWorkflow/60d1afe2-dbd4-47e5-9cf5-e2a76d7947cd/call-HaplotypeCaller/shard-40/attempt-2/HaplotypeCaller-40-rc.txt
IR_3885.vcf.gz -> gs://broad-gp-gotc-pilot/cromwell_execution/PairedEndSingleSampleWorkflow/60d1afe2-dbd4-47e5-9cf5-e2a76d7947cd/call-HaplotypeCaller/shard-40/attempt-2/VIR_3885.vcf.gz
IR_3885.vcf.gz.tbi -> gs://broad-gp-gotc-pilot/cromwell_execution/PairedEndSingleSampleWorkflow/60d1afe2-dbd4-47e5-9cf5-e2a76d7947cd/call-HaplotypeCaller/shard-40/attempt-2/VIR_3885.vcf.gz.tbi
onitoring -> gs://broad-gp-gotc-pilot/cromwell_execution/PairedEndSingleSampleWorkflow/60d1afe2-dbd4-47e5-9cf5-e2a76d7947cd/call-HaplotypeCaller/shard-40/attempt-2/monitoring.log
16-02-21 01:23:04,075 cromwell-system-akka.actor.default-dispatcher-11 INFO  - JES Run [UUID(60d1afe2):HaplotypeCaller:40:2]: JES Run ID is operations/EK75sIuwKhjV25fV2qWS1N8BIOmt-NysGCoPcHJvZHVjdGlvblF1ZXVl
16-02-21 01:23:04,101 cromwell-system-akka.actor.default-dispatcher-21 INFO  - JES Run [UUID(60d1afe2):HaplotypeCaller:40:2]: Status change from - to Initializing
16-02-21 01:24:25,668 cromwell-system-akka.actor.default-dispatcher-26 INFO  - JES Run [UUID(60d1afe2):HaplotypeCaller:0:2]: Status change from - to Initializing
16-02-21 01:26:00,786 cromwell-system-akka.actor.default-dispatcher-13 INFO  - JES Run [UUID(60d1afe2):HaplotypeCaller:12]: Status change from Running to Failed
16-02-21 01:26:00,787 cromwell-system-akka.actor.default-dispatcher-13 ERROR - CallActor [UUID(60d1afe2):HaplotypeCaller:12]: Failing call with retryable Failure: Task 60d1afe2-dbd4-47e5-9cf5-e2a76d7947cd:HaplotypeCaller was preempted for the 1st time. The call will be re-started with another pre-emptible VM (max pre-emptible attempts number is 3).
omwell.engine.package$PreemptedException: Task 60d1afe2-dbd4-47e5-9cf5-e2a76d7947cd:HaplotypeCaller was preempted for the 1st time. The call will be re-started with another pre-emptible VM (max pre-emptible attempts number is 3).
16-02-21 01:26:01,545 cromwell-system-akka.actor.default-dispatcher-14 INFO  - WorkflowActor [UUID(60d1afe2)]: persisting status of HaplotypeCaller:12 to Preempted.
16-02-21 01:26:01,642 cromwell-system-akka.actor.default-dispatcher-14 INFO  - WorkflowActor [UUID(60d1afe2)]: starting calls: PairedEndSingleSampleWorkflow.HaplotypeCaller
16-02-21 01:26:01,642 cromwell-system-akka.actor.default-dispatcher-14 INFO  - WorkflowActor [UUID(60d1afe2)]: persisting status of HaplotypeCaller:12:2 to Starting.
16-02-21 01:26:01,761 cromwell-system-akka.actor.default-dispatcher-14 INFO  - WorkflowActor [UUID(60d1afe2)]: inputs for call 'HaplotypeCaller:12:2':
nput_bam -> WdlSingleFile(gs://broad-gp-gotc-pilot/cromwell_execution/PairedEndSingleSampleWorkflow/60d1afe2-dbd4-47e5-9cf5-e2a76d7947cd/call-GatherBamFiles/VIR_3885.bam)
nterval_list -> WdlSingleFile(gs://broad-gp-gotc-pilot/cromwell_execution/PairedEndSingleSampleWorkflow/60d1afe2-dbd4-47e5-9cf5-e2a76d7947cd/call-ScatterIntervalList/glob-cb4648beeaff920acb03de7603c06f98/20scattered.interval_list)
nput_bam_index -> WdlSingleFile(gs://broad-gp-gotc-pilot/cromwell_execution/PairedEndSingleSampleWorkflow/60d1afe2-dbd4-47e5-9cf5-e2a76d7947cd/call-GatherBamFiles/VIR_3885.bai)
16-02-21 01:26:01,761 cromwell-system-akka.actor.default-dispatcher-15 INFO  - WorkflowActor [UUID(60d1afe2)]: created call actor for HaplotypeCaller:12:2.
16-02-21 01:26:01,761 cromwell-system-akka.actor.default-dispatcher-21 INFO  - WorkflowActor [UUID(60d1afe2)]: persisting status of HaplotypeCaller:12:2 to Running.
16-02-21 01:26:01,761 cromwell-system-akka.actor.default-dispatcher-21 INFO  - JesBackend [UUID(60d1afe2):HaplotypeCaller:12:2]: Call GCS path: gs://broad-gp-gotc-pilot/cromwell_execution/PairedEndSingleSampleWorkflow/60d1afe2-dbd4-47e5-9cf5-e2a76d7947cd/call-HaplotypeCaller/shard-12/attempt-2
16-02-21 01:26:01,762 cromwell-system-akka.actor.default-dispatcher-21 INFO  - JesBackend [UUID(60d1afe2):HaplotypeCaller:12:2]: `java -XX:GCTimeLimit=50 -XX:GCHeapFreeLimit=10 -Xmx6000m \
I /cromwell_root/broad-gp-gotc-pilot/cromwell_execution/PairedEndSingleSampleWorkflow/60d1afe2-dbd4-47e5-9cf5-e2a76d7947cd/call-GatherBamFiles/VIR_3885.bam \
L /cromwell_root/broad-gp-gotc-pilot/cromwell_execution/PairedEndSingleSampleWorkflow/60d1afe2-dbd4-47e5-9cf5-e2a76d7947cd/call-ScatterIntervalList/glob-cb4648beeaff920acb03de7603c06f98/20scattered.interval_list \
16-02-21 01:26:01,899 cromwell-system-akka.actor.default-dispatcher-21 INFO  - JesBackend [UUID(60d1afe2):HaplotypeCaller:12:2]: Starting call with pre-emptible VM
16-02-21 01:26:01,899 cromwell-system-akka.actor.default-dispatcher-21 INFO  - JES Pipeline [UUID(60d1afe2):HaplotypeCaller:12:2]: Pipeline parameters are:
name=input_bam-0, type=REFERENCE, value=/cromwell_root/broad-gp-gotc-pilot/cromwell_execution/PairedEndSingleSampleWorkflow/60d1afe2-dbd4-47e5-9cf5-e2a76d7947cd/call-GatherBamFiles/VIR_3885.bam}
name=interval_list-0, type=REFERENCE, value=/cromwell_root/broad-gp-gotc-pilot/cromwell_execution/PairedEndSingleSampleWorkflow/60d1afe2-dbd4-47e5-9cf5-e2a76d7947cd/call-ScatterIntervalList/glob-cb4648beeaff920acb03de7603c06f98/20scattered.interval_list}
name=input_bam_index-0, type=REFERENCE, value=/cromwell_root/broad-gp-gotc-pilot/cromwell_execution/PairedEndSingleSampleWorkflow/60d1afe2-dbd4-47e5-9cf5-e2a76d7947cd/call-GatherBamFiles/VIR_3885.bai}
16-02-21 01:26:01,932 cromwell-system-akka.actor.default-dispatcher-21 INFO  - JES Pipeline [UUID(60d1afe2):HaplotypeCaller:12:2]: Pipeline ID is 3916314795636448345
16-02-21 01:26:01,932 cromwell-system-akka.actor.default-dispatcher-21 INFO  - JES Pipeline [UUID(60d1afe2):HaplotypeCaller:12:2]: Project ID: broad-gp-gotc-pilot
16-02-21 01:26:01,932 cromwell-system-akka.actor.default-dispatcher-21 INFO  - JES Run [UUID(60d1afe2):HaplotypeCaller:12:2]: Inputs:
nterval_list-0 -> gs://broad-gp-gotc-pilot/cromwell_execution/PairedEndSingleSampleWorkflow/60d1afe2-dbd4-47e5-9cf5-e2a76d7947cd/call-ScatterIntervalList/glob-cb4648beeaff920acb03de7603c06f98/20scattered.interval_list
nput_bam_index-0 -> gs://broad-gp-gotc-pilot/cromwell_execution/PairedEndSingleSampleWorkflow/60d1afe2-dbd4-47e5-9cf5-e2a76d7947cd/call-GatherBamFiles/VIR_3885.bai
nput_bam-0 -> gs://broad-gp-gotc-pilot/cromwell_execution/PairedEndSingleSampleWorkflow/60d1afe2-dbd4-47e5-9cf5-e2a76d7947cd/call-GatherBamFiles/VIR_3885.bam
xec -> gs://broad-gp-gotc-pilot/cromwell_execution/PairedEndSingleSampleWorkflow/60d1afe2-dbd4-47e5-9cf5-e2a76d7947cd/call-HaplotypeCaller/shard-12/attempt-2/exec.sh
16-02-21 01:26:01,933 cromwell-system-akka.actor.default-dispatcher-21 INFO  - JES Run [UUID(60d1afe2):HaplotypeCaller:12:2]: Outputs:
aplotypeCaller-12-rc.txt -> gs://broad-gp-gotc-pilot/cromwell_execution/PairedEndSingleSampleWorkflow/60d1afe2-dbd4-47e5-9cf5-e2a76d7947cd/call-HaplotypeCaller/shard-12/attempt-2/HaplotypeCaller-12-rc.txt
IR_3885.vcf.gz -> gs://broad-gp-gotc-pilot/cromwell_execution/PairedEndSingleSampleWorkflow/60d1afe2-dbd4-47e5-9cf5-e2a76d7947cd/call-HaplotypeCaller/shard-12/attempt-2/VIR_3885.vcf.gz
IR_3885.vcf.gz.tbi -> gs://broad-gp-gotc-pilot/cromwell_execution/PairedEndSingleSampleWorkflow/60d1afe2-dbd4-47e5-9cf5-e2a76d7947cd/call-HaplotypeCaller/shard-12/attempt-2/VIR_3885.vcf.gz.tbi
onitoring -> gs://broad-gp-gotc-pilot/cromwell_execution/PairedEndSingleSampleWorkflow/60d1afe2-dbd4-47e5-9cf5-e2a76d7947cd/call-HaplotypeCaller/shard-12/attempt-2/monitoring.log
16-02-21 01:26:02,060 cromwell-system-akka.actor.default-dispatcher-21 INFO  - JES Run [UUID(60d1afe2):HaplotypeCaller:12:2]: JES Run ID is operations/EOznu4uwKhjRh7_c9tHiykUg6a343KwYKg9wcm9kdWN0aW9uUXVldWU
16-02-21 01:26:02,089 cromwell-system-akka.actor.default-dispatcher-20 INFO  - JES Run [UUID(60d1afe2):HaplotypeCaller:12:2]: Status change from - to Initializing
16-02-21 01:26:33,130 cromwell-system-akka.actor.default-dispatcher-11 INFO  - JES Run [UUID(60d1afe2):HaplotypeCaller:10:2]: Status change from Initializing to Running
16-02-21 01:27:02,033 cromwell-system-akka.actor.default-dispatcher-22 INFO  - JES Run [UUID(60d1afe2):HaplotypeCaller:40:2]: Status change from Initializing to Running
16-02-21 01:29:01,452 cromwell-system-akka.actor.default-dispatcher-22 INFO  - JES Run [UUID(60d1afe2):HaplotypeCaller:1]: Status change from Running to Success
16-02-21 01:29:01,944 cromwell-system-akka.actor.default-dispatcher-15 INFO  - WorkflowActor [UUID(60d1afe2)]: persisting status of HaplotypeCaller:1 to Done.
16-02-21 01:34:05,339 cromwell-system-akka.actor.default-dispatcher-3 INFO  - JES Run [UUID(60d1afe2):HaplotypeCaller:46:2]: Status change from Initializing to Running
16-02-21 01:42:03,493 cromwell-system-akka.actor.default-dispatcher-12 INFO  - JES Run [UUID(60d1afe2):HaplotypeCaller:21]: Status change from Running to Success
16-02-21 01:42:03,961 cromwell-system-akka.actor.default-dispatcher-12 INFO  - WorkflowActor [UUID(60d1afe2)]: persisting status of HaplotypeCaller:21 to Done.
16-02-21 01:44:35,482 cromwell-system-akka.actor.default-dispatcher-20 INFO  - JES Run [UUID(60d1afe2):HaplotypeCaller:37]: Status change from Running to Failed
16-02-21 01:44:35,483 cromwell-system-akka.actor.default-dispatcher-20 ERROR - CallActor [UUID(60d1afe2):HaplotypeCaller:37]: Failing call with retryable Failure: Task 60d1afe2-dbd4-47e5-9cf5-e2a76d7947cd:HaplotypeCaller was preempted for the 1st time. The call will be re-started with another pre-emptible VM (max pre-emptible attempts number is 3).
omwell.engine.package$PreemptedException: Task 60d1afe2-dbd4-47e5-9cf5-e2a76d7947cd:HaplotypeCaller was preempted for the 1st time. The call will be re-started with another pre-emptible VM (max pre-emptible attempts number is 3).
16-02-21 01:44:35,842 cromwell-system-akka.actor.default-dispatcher-26 INFO  - WorkflowActor [UUID(60d1afe2)]: persisting status of HaplotypeCaller:37 to Preempted.
16-02-21 01:44:35,935 cromwell-system-akka.actor.default-dispatcher-23 INFO  - WorkflowActor [UUID(60d1afe2)]: starting calls: PairedEndSingleSampleWorkflow.HaplotypeCaller
16-02-21 01:44:35,935 cromwell-system-akka.actor.default-dispatcher-23 INFO  - WorkflowActor [UUID(60d1afe2)]: persisting status of HaplotypeCaller:37:2 to Starting.
16-02-21 01:44:36,051 cromwell-system-akka.actor.default-dispatcher-26 INFO  - WorkflowActor [UUID(60d1afe2)]: inputs for call 'HaplotypeCaller:37:2':
nput_bam -> WdlSingleFile(gs://broad-gp-gotc-pilot/cromwell_execution/PairedEndSingleSampleWorkflow/60d1afe2-dbd4-47e5-9cf5-e2a76d7947cd/call-GatherBamFiles/VIR_3885.bam)
nterval_list -> WdlSingleFile(gs://broad-gp-gotc-pilot/cromwell_execution/PairedEndSingleSampleWorkflow/60d1afe2-dbd4-47e5-9cf5-e2a76d7947cd/call-ScatterIntervalList/glob-cb4648beeaff920acb03de7603c06f98/43scattered.interval_list)
nput_bam_index -> WdlSingleFile(gs://broad-gp-gotc-pilot/cromwell_execution/PairedEndSingleSampleWorkflow/60d1afe2-dbd4-47e5-9cf5-e2a76d7947cd/call-GatherBamFiles/VIR_3885.bai)
16-02-21 01:44:36,051 cromwell-system-akka.actor.default-dispatcher-23 INFO  - WorkflowActor [UUID(60d1afe2)]: created call actor for HaplotypeCaller:37:2.
16-02-21 01:44:36,051 cromwell-system-akka.actor.default-dispatcher-21 INFO  - WorkflowActor [UUID(60d1afe2)]: persisting status of HaplotypeCaller:37:2 to Running.
16-02-21 01:44:36,051 cromwell-system-akka.actor.default-dispatcher-20 INFO  - JesBackend [UUID(60d1afe2):HaplotypeCaller:37:2]: Call GCS path: gs://broad-gp-gotc-pilot/cromwell_execution/PairedEndSingleSampleWorkflow/60d1afe2-dbd4-47e5-9cf5-e2a76d7947cd/call-HaplotypeCaller/shard-37/attempt-2
16-02-21 01:44:36,052 cromwell-system-akka.actor.default-dispatcher-20 INFO  - JesBackend [UUID(60d1afe2):HaplotypeCaller:37:2]: `java -XX:GCTimeLimit=50 -XX:GCHeapFreeLimit=10 -Xmx6000m \
I /cromwell_root/broad-gp-gotc-pilot/cromwell_execution/PairedEndSingleSampleWorkflow/60d1afe2-dbd4-47e5-9cf5-e2a76d7947cd/call-GatherBamFiles/VIR_3885.bam \
L /cromwell_root/broad-gp-gotc-pilot/cromwell_execution/PairedEndSingleSampleWorkflow/60d1afe2-dbd4-47e5-9cf5-e2a76d7947cd/call-ScatterIntervalList/glob-cb4648beeaff920acb03de7603c06f98/43scattered.interval_list \
16-02-21 01:44:36,223 cromwell-system-akka.actor.default-dispatcher-20 INFO  - JesBackend [UUID(60d1afe2):HaplotypeCaller:37:2]: Starting call with pre-emptible VM
16-02-21 01:44:36,223 cromwell-system-akka.actor.default-dispatcher-20 INFO  - JES Pipeline [UUID(60d1afe2):HaplotypeCaller:37:2]: Pipeline parameters are:
name=input_bam-0, type=REFERENCE, value=/cromwell_root/broad-gp-gotc-pilot/cromwell_execution/PairedEndSingleSampleWorkflow/60d1afe2-dbd4-47e5-9cf5-e2a76d7947cd/call-GatherBamFiles/VIR_3885.bam}
name=interval_list-0, type=REFERENCE, value=/cromwell_root/broad-gp-gotc-pilot/cromwell_execution/PairedEndSingleSampleWorkflow/60d1afe2-dbd4-47e5-9cf5-e2a76d7947cd/call-ScatterIntervalList/glob-cb4648beeaff920acb03de7603c06f98/43scattered.interval_list}
name=input_bam_index-0, type=REFERENCE, value=/cromwell_root/broad-gp-gotc-pilot/cromwell_execution/PairedEndSingleSampleWorkflow/60d1afe2-dbd4-47e5-9cf5-e2a76d7947cd/call-GatherBamFiles/VIR_3885.bai}
16-02-21 01:44:36,255 cromwell-system-akka.actor.default-dispatcher-20 INFO  - JES Pipeline [UUID(60d1afe2):HaplotypeCaller:37:2]: Pipeline ID is 14765208371574660227
16-02-21 01:44:36,255 cromwell-system-akka.actor.default-dispatcher-20 INFO  - JES Pipeline [UUID(60d1afe2):HaplotypeCaller:37:2]: Project ID: broad-gp-gotc-pilot
16-02-21 01:44:36,255 cromwell-system-akka.actor.default-dispatcher-20 INFO  - JES Run [UUID(60d1afe2):HaplotypeCaller:37:2]: Inputs:
nterval_list-0 -> gs://broad-gp-gotc-pilot/cromwell_execution/PairedEndSingleSampleWorkflow/60d1afe2-dbd4-47e5-9cf5-e2a76d7947cd/call-ScatterIntervalList/glob-cb4648beeaff920acb03de7603c06f98/43scattered.interval_list
nput_bam_index-0 -> gs://broad-gp-gotc-pilot/cromwell_execution/PairedEndSingleSampleWorkflow/60d1afe2-dbd4-47e5-9cf5-e2a76d7947cd/call-GatherBamFiles/VIR_3885.bai
nput_bam-0 -> gs://broad-gp-gotc-pilot/cromwell_execution/PairedEndSingleSampleWorkflow/60d1afe2-dbd4-47e5-9cf5-e2a76d7947cd/call-GatherBamFiles/VIR_3885.bam
xec -> gs://broad-gp-gotc-pilot/cromwell_execution/PairedEndSingleSampleWorkflow/60d1afe2-dbd4-47e5-9cf5-e2a76d7947cd/call-HaplotypeCaller/shard-37/attempt-2/exec.sh
16-02-21 01:44:36,255 cromwell-system-akka.actor.default-dispatcher-20 INFO  - JES Run [UUID(60d1afe2):HaplotypeCaller:37:2]: Outputs:
aplotypeCaller-37-rc.txt -> gs://broad-gp-gotc-pilot/cromwell_execution/PairedEndSingleSampleWorkflow/60d1afe2-dbd4-47e5-9cf5-e2a76d7947cd/call-HaplotypeCaller/shard-37/attempt-2/HaplotypeCaller-37-rc.txt
IR_3885.vcf.gz -> gs://broad-gp-gotc-pilot/cromwell_execution/PairedEndSingleSampleWorkflow/60d1afe2-dbd4-47e5-9cf5-e2a76d7947cd/call-HaplotypeCaller/shard-37/attempt-2/VIR_3885.vcf.gz
IR_3885.vcf.gz.tbi -> gs://broad-gp-gotc-pilot/cromwell_execution/PairedEndSingleSampleWorkflow/60d1afe2-dbd4-47e5-9cf5-e2a76d7947cd/call-HaplotypeCaller/shard-37/attempt-2/VIR_3885.vcf.gz.tbi
onitoring -> gs://broad-gp-gotc-pilot/cromwell_execution/PairedEndSingleSampleWorkflow/60d1afe2-dbd4-47e5-9cf5-e2a76d7947cd/call-HaplotypeCaller/shard-37/attempt-2/monitoring.log
16-02-21 01:44:36,376 cromwell-system-akka.actor.default-dispatcher-20 INFO  - JES Run [UUID(60d1afe2):HaplotypeCaller:37:2]: JES Run ID is operations/EL7p_4uwKhip4tz1gYaA5iAg6a343KwYKg9wcm9kdWN0aW9uUXVldWU
16-02-21 01:44:36,396 cromwell-system-akka.actor.default-dispatcher-21 INFO  - JES Run [UUID(60d1afe2):HaplotypeCaller:37:2]: Status change from - to Initializing
16-02-21 01:44:36,443 cromwell-system-akka.actor.default-dispatcher-23 INFO  - JES Run [UUID(60d1afe2):HaplotypeCaller:26]: Status change from Running to Success
16-02-21 01:44:36,927 cromwell-system-akka.actor.default-dispatcher-15 INFO  - WorkflowActor [UUID(60d1afe2)]: persisting status of HaplotypeCaller:26 to Done.
16-02-21 01:45:06,105 cromwell-system-akka.actor.default-dispatcher-23 INFO  - JES Run [UUID(60d1afe2):HaplotypeCaller:9]: Status change from Running to Success
16-02-21 01:45:06,582 cromwell-system-akka.actor.default-dispatcher-6 INFO  - WorkflowActor [UUID(60d1afe2)]: persisting status of HaplotypeCaller:9 to Done.
16-02-21 01:50:37,293 cromwell-system-akka.actor.default-dispatcher-22 INFO  - JES Run [UUID(60d1afe2):HaplotypeCaller:22:2]: Status change from Running to Failed
16-02-21 01:50:37,295 cromwell-system-akka.actor.default-dispatcher-19 ERROR - CallActor [UUID(60d1afe2):HaplotypeCaller:22:2]: Failing call with retryable Failure: Task 60d1afe2-dbd4-47e5-9cf5-e2a76d7947cd:HaplotypeCaller was preempted for the 2nd time. The call will be re-started with another pre-emptible VM (max pre-emptible attempts number is 3).
omwell.engine.package$PreemptedException: Task 60d1afe2-dbd4-47e5-9cf5-e2a76d7947cd:HaplotypeCaller was preempted for the 2nd time. The call will be re-started with another pre-emptible VM (max pre-emptible attempts number is 3).
16-02-21 01:50:37,649 cromwell-system-akka.actor.default-dispatcher-20 INFO  - WorkflowActor [UUID(60d1afe2)]: persisting status of HaplotypeCaller:22:2 to Preempted.
16-02-21 01:50:37,745 cromwell-system-akka.actor.default-dispatcher-20 INFO  - WorkflowActor [UUID(60d1afe2)]: starting calls: PairedEndSingleSampleWorkflow.HaplotypeCaller
16-02-21 01:50:37,746 cromwell-system-akka.actor.default-dispatcher-20 INFO  - WorkflowActor [UUID(60d1afe2)]: persisting status of HaplotypeCaller:22:3 to Starting.
16-02-21 01:50:37,862 cromwell-system-akka.actor.default-dispatcher-25 INFO  - WorkflowActor [UUID(60d1afe2)]: inputs for call 'HaplotypeCaller:22:3':
nput_bam -> WdlSingleFile(gs://broad-gp-gotc-pilot/cromwell_execution/PairedEndSingleSampleWorkflow/60d1afe2-dbd4-47e5-9cf5-e2a76d7947cd/call-GatherBamFiles/VIR_3885.bam)
nterval_list -> WdlSingleFile(gs://broad-gp-gotc-pilot/cromwell_execution/PairedEndSingleSampleWorkflow/60d1afe2-dbd4-47e5-9cf5-e2a76d7947cd/call-ScatterIntervalList/glob-cb4648beeaff920acb03de7603c06f98/2scattered.interval_list)
nput_bam_index -> WdlSingleFile(gs://broad-gp-gotc-pilot/cromwell_execution/PairedEndSingleSampleWorkflow/60d1afe2-dbd4-47e5-9cf5-e2a76d7947cd/call-GatherBamFiles/VIR_3885.bai)
16-02-21 01:50:37,862 cromwell-system-akka.actor.default-dispatcher-25 INFO  - WorkflowActor [UUID(60d1afe2)]: created call actor for HaplotypeCaller:22:3.
16-02-21 01:50:37,862 cromwell-system-akka.actor.default-dispatcher-5 INFO  - WorkflowActor [UUID(60d1afe2)]: persisting status of HaplotypeCaller:22:3 to Running.
16-02-21 01:50:37,862 cromwell-system-akka.actor.default-dispatcher-20 INFO  - JesBackend [UUID(60d1afe2):HaplotypeCaller:22:3]: Call GCS path: gs://broad-gp-gotc-pilot/cromwell_execution/PairedEndSingleSampleWorkflow/60d1afe2-dbd4-47e5-9cf5-e2a76d7947cd/call-HaplotypeCaller/shard-22/attempt-3
16-02-21 01:50:37,863 cromwell-system-akka.actor.default-dispatcher-20 INFO  - JesBackend [UUID(60d1afe2):HaplotypeCaller:22:3]: `java -XX:GCTimeLimit=50 -XX:GCHeapFreeLimit=10 -Xmx6000m \
I /cromwell_root/broad-gp-gotc-pilot/cromwell_execution/PairedEndSingleSampleWorkflow/60d1afe2-dbd4-47e5-9cf5-e2a76d7947cd/call-GatherBamFiles/VIR_3885.bam \
L /cromwell_root/broad-gp-gotc-pilot/cromwell_execution/PairedEndSingleSampleWorkflow/60d1afe2-dbd4-47e5-9cf5-e2a76d7947cd/call-ScatterIntervalList/glob-cb4648beeaff920acb03de7603c06f98/2scattered.interval_list \
16-02-21 01:50:38,011 cromwell-system-akka.actor.default-dispatcher-20 INFO  - JesBackend [UUID(60d1afe2):HaplotypeCaller:22:3]: Starting call with pre-emptible VM
16-02-21 01:50:38,011 cromwell-system-akka.actor.default-dispatcher-20 INFO  - JES Pipeline [UUID(60d1afe2):HaplotypeCaller:22:3]: Pipeline parameters are:
name=input_bam-0, type=REFERENCE, value=/cromwell_root/broad-gp-gotc-pilot/cromwell_execution/PairedEndSingleSampleWorkflow/60d1afe2-dbd4-47e5-9cf5-e2a76d7947cd/call-GatherBamFiles/VIR_3885.bam}
name=interval_list-0, type=REFERENCE, value=/cromwell_root/broad-gp-gotc-pilot/cromwell_execution/PairedEndSingleSampleWorkflow/60d1afe2-dbd4-47e5-9cf5-e2a76d7947cd/call-ScatterIntervalList/glob-cb4648beeaff920acb03de7603c06f98/2scattered.interval_list}
name=input_bam_index-0, type=REFERENCE, value=/cromwell_root/broad-gp-gotc-pilot/cromwell_execution/PairedEndSingleSampleWorkflow/60d1afe2-dbd4-47e5-9cf5-e2a76d7947cd/call-GatherBamFiles/VIR_3885.bai}
16-02-21 01:50:38,046 cromwell-system-akka.actor.default-dispatcher-20 INFO  - JES Pipeline [UUID(60d1afe2):HaplotypeCaller:22:3]: Pipeline ID is 15465499358718266457
16-02-21 01:50:38,046 cromwell-system-akka.actor.default-dispatcher-20 INFO  - JES Pipeline [UUID(60d1afe2):HaplotypeCaller:22:3]: Project ID: broad-gp-gotc-pilot
16-02-21 01:50:38,046 cromwell-system-akka.actor.default-dispatcher-20 INFO  - JES Run [UUID(60d1afe2):HaplotypeCaller:22:3]: Inputs:
nterval_list-0 -> gs://broad-gp-gotc-pilot/cromwell_execution/PairedEndSingleSampleWorkflow/60d1afe2-dbd4-47e5-9cf5-e2a76d7947cd/call-ScatterIntervalList/glob-cb4648beeaff920acb03de7603c06f98/2scattered.interval_list
nput_bam_index-0 -> gs://broad-gp-gotc-pilot/cromwell_execution/PairedEndSingleSampleWorkflow/60d1afe2-dbd4-47e5-9cf5-e2a76d7947cd/call-GatherBamFiles/VIR_3885.bai
nput_bam-0 -> gs://broad-gp-gotc-pilot/cromwell_execution/PairedEndSingleSampleWorkflow/60d1afe2-dbd4-47e5-9cf5-e2a76d7947cd/call-GatherBamFiles/VIR_3885.bam
xec -> gs://broad-gp-gotc-pilot/cromwell_execution/PairedEndSingleSampleWorkflow/60d1afe2-dbd4-47e5-9cf5-e2a76d7947cd/call-HaplotypeCaller/shard-22/attempt-3/exec.sh
16-02-21 01:50:38,046 cromwell-system-akka.actor.default-dispatcher-20 INFO  - JES Run [UUID(60d1afe2):HaplotypeCaller:22:3]: Outputs:
aplotypeCaller-22-rc.txt -> gs://broad-gp-gotc-pilot/cromwell_execution/PairedEndSingleSampleWorkflow/60d1afe2-dbd4-47e5-9cf5-e2a76d7947cd/call-HaplotypeCaller/shard-22/attempt-3/HaplotypeCaller-22-rc.txt
IR_3885.vcf.gz -> gs://broad-gp-gotc-pilot/cromwell_execution/PairedEndSingleSampleWorkflow/60d1afe2-dbd4-47e5-9cf5-e2a76d7947cd/call-HaplotypeCaller/shard-22/attempt-3/VIR_3885.vcf.gz
IR_3885.vcf.gz.tbi -> gs://broad-gp-gotc-pilot/cromwell_execution/PairedEndSingleSampleWorkflow/60d1afe2-dbd4-47e5-9cf5-e2a76d7947cd/call-HaplotypeCaller/shard-22/attempt-3/VIR_3885.vcf.gz.tbi
onitoring -> gs://broad-gp-gotc-pilot/cromwell_execution/PairedEndSingleSampleWorkflow/60d1afe2-dbd4-47e5-9cf5-e2a76d7947cd/call-HaplotypeCaller/shard-22/attempt-3/monitoring.log
16-02-21 01:50:38,119 cromwell-system-akka.actor.default-dispatcher-20 INFO  - JES Run [UUID(60d1afe2):HaplotypeCaller:22:3]: JES Run ID is operations/EPDzlYywKhiTqsKoovyd8dwBIOmt-NysGCoPcHJvZHVjdGlvblF1ZXVl
16-02-21 01:50:38,140 cromwell-system-akka.actor.default-dispatcher-2 INFO  - JES Run [UUID(60d1afe2):HaplotypeCaller:22:3]: Status change from - to Initializing
16-02-21 01:53:38,252 cromwell-system-akka.actor.default-dispatcher-22 INFO  - JES Run [UUID(60d1afe2):HaplotypeCaller:14]: Status change from Running to Failed
16-02-21 01:53:38,253 cromwell-system-akka.actor.default-dispatcher-6 ERROR - CallActor [UUID(60d1afe2):HaplotypeCaller:14]: Failing call with retryable Failure: Task 60d1afe2-dbd4-47e5-9cf5-e2a76d7947cd:HaplotypeCaller was preempted for the 1st time. The call will be re-started with another pre-emptible VM (max pre-emptible attempts number is 3).
omwell.engine.package$PreemptedException: Task 60d1afe2-dbd4-47e5-9cf5-e2a76d7947cd:HaplotypeCaller was preempted for the 1st time. The call will be re-started with another pre-emptible VM (max pre-emptible attempts number is 3).
16-02-21 01:53:38,629 cromwell-system-akka.actor.default-dispatcher-24 INFO  - WorkflowActor [UUID(60d1afe2)]: persisting status of HaplotypeCaller:14 to Preempted.
16-02-21 01:53:38,721 cromwell-system-akka.actor.default-dispatcher-6 INFO  - WorkflowActor [UUID(60d1afe2)]: starting calls: PairedEndSingleSampleWorkflow.HaplotypeCaller
16-02-21 01:53:38,721 cromwell-system-akka.actor.default-dispatcher-6 INFO  - WorkflowActor [UUID(60d1afe2)]: persisting status of HaplotypeCaller:14:2 to Starting.
16-02-21 01:53:38,842 cromwell-system-akka.actor.default-dispatcher-24 INFO  - WorkflowActor [UUID(60d1afe2)]: inputs for call 'HaplotypeCaller:14:2':
nput_bam -> WdlSingleFile(gs://broad-gp-gotc-pilot/cromwell_execution/PairedEndSingleSampleWorkflow/60d1afe2-dbd4-47e5-9cf5-e2a76d7947cd/call-GatherBamFiles/VIR_3885.bam)
nterval_list -> WdlSingleFile(gs://broad-gp-gotc-pilot/cromwell_execution/PairedEndSingleSampleWorkflow/60d1afe2-dbd4-47e5-9cf5-e2a76d7947cd/call-ScatterIntervalList/glob-cb4648beeaff920acb03de7603c06f98/22scattered.interval_list)
nput_bam_index -> WdlSingleFile(gs://broad-gp-gotc-pilot/cromwell_execution/PairedEndSingleSampleWorkflow/60d1afe2-dbd4-47e5-9cf5-e2a76d7947cd/call-GatherBamFiles/VIR_3885.bai)
16-02-21 01:53:38,842 cromwell-system-akka.actor.default-dispatcher-8 INFO  - WorkflowActor [UUID(60d1afe2)]: created call actor for HaplotypeCaller:14:2.
16-02-21 01:53:38,842 cromwell-system-akka.actor.default-dispatcher-8 INFO  - WorkflowActor [UUID(60d1afe2)]: persisting status of HaplotypeCaller:14:2 to Running.
16-02-21 01:53:38,842 cromwell-system-akka.actor.default-dispatcher-26 INFO  - JesBackend [UUID(60d1afe2):HaplotypeCaller:14:2]: Call GCS path: gs://broad-gp-gotc-pilot/cromwell_execution/PairedEndSingleSampleWorkflow/60d1afe2-dbd4-47e5-9cf5-e2a76d7947cd/call-HaplotypeCaller/shard-14/attempt-2
16-02-21 01:53:38,842 cromwell-system-akka.actor.default-dispatcher-26 INFO  - JesBackend [UUID(60d1afe2):HaplotypeCaller:14:2]: `java -XX:GCTimeLimit=50 -XX:GCHeapFreeLimit=10 -Xmx6000m \
I /cromwell_root/broad-gp-gotc-pilot/cromwell_execution/PairedEndSingleSampleWorkflow/60d1afe2-dbd4-47e5-9cf5-e2a76d7947cd/call-GatherBamFiles/VIR_3885.bam \
L /cromwell_root/broad-gp-gotc-pilot/cromwell_execution/PairedEndSingleSampleWorkflow/60d1afe2-dbd4-47e5-9cf5-e2a76d7947cd/call-ScatterIntervalList/glob-cb4648beeaff920acb03de7603c06f98/22scattered.interval_list \
16-02-21 01:53:38,993 cromwell-system-akka.actor.default-dispatcher-26 INFO  - JesBackend [UUID(60d1afe2):HaplotypeCaller:14:2]: Starting call with pre-emptible VM
16-02-21 01:53:38,993 cromwell-system-akka.actor.default-dispatcher-26 INFO  - JES Pipeline [UUID(60d1afe2):HaplotypeCaller:14:2]: Pipeline parameters are:
name=input_bam-0, type=REFERENCE, value=/cromwell_root/broad-gp-gotc-pilot/cromwell_execution/PairedEndSingleSampleWorkflow/60d1afe2-dbd4-47e5-9cf5-e2a76d7947cd/call-GatherBamFiles/VIR_3885.bam}
name=interval_list-0, type=REFERENCE, value=/cromwell_root/broad-gp-gotc-pilot/cromwell_execution/PairedEndSingleSampleWorkflow/60d1afe2-dbd4-47e5-9cf5-e2a76d7947cd/call-ScatterIntervalList/glob-cb4648beeaff920acb03de7603c06f98/22scattered.interval_list}
name=input_bam_index-0, type=REFERENCE, value=/cromwell_root/broad-gp-gotc-pilot/cromwell_execution/PairedEndSingleSampleWorkflow/60d1afe2-dbd4-47e5-9cf5-e2a76d7947cd/call-GatherBamFiles/VIR_3885.bai}
16-02-21 01:53:39,025 cromwell-system-akka.actor.default-dispatcher-26 INFO  - JES Pipeline [UUID(60d1afe2):HaplotypeCaller:14:2]: Pipeline ID is 7873825871980332541
16-02-21 01:53:39,026 cromwell-system-akka.actor.default-dispatcher-26 INFO  - JES Pipeline [UUID(60d1afe2):HaplotypeCaller:14:2]: Project ID: broad-gp-gotc-pilot
16-02-21 01:53:39,026 cromwell-system-akka.actor.default-dispatcher-26 INFO  - JES Run [UUID(60d1afe2):HaplotypeCaller:14:2]: Inputs:
nterval_list-0 -> gs://broad-gp-gotc-pilot/cromwell_execution/PairedEndSingleSampleWorkflow/60d1afe2-dbd4-47e5-9cf5-e2a76d7947cd/call-ScatterIntervalList/glob-cb4648beeaff920acb03de7603c06f98/22scattered.interval_list
nput_bam_index-0 -> gs://broad-gp-gotc-pilot/cromwell_execution/PairedEndSingleSampleWorkflow/60d1afe2-dbd4-47e5-9cf5-e2a76d7947cd/call-GatherBamFiles/VIR_3885.bai
nput_bam-0 -> gs://broad-gp-gotc-pilot/cromwell_execution/PairedEndSingleSampleWorkflow/60d1afe2-dbd4-47e5-9cf5-e2a76d7947cd/call-GatherBamFiles/VIR_3885.bam
xec -> gs://broad-gp-gotc-pilot/cromwell_execution/PairedEndSingleSampleWorkflow/60d1afe2-dbd4-47e5-9cf5-e2a76d7947cd/call-HaplotypeCaller/shard-14/attempt-2/exec.sh
16-02-21 01:53:39,026 cromwell-system-akka.actor.default-dispatcher-26 INFO  - JES Run [UUID(60d1afe2):HaplotypeCaller:14:2]: Outputs:
aplotypeCaller-14-rc.txt -> gs://broad-gp-gotc-pilot/cromwell_execution/PairedEndSingleSampleWorkflow/60d1afe2-dbd4-47e5-9cf5-e2a76d7947cd/call-HaplotypeCaller/shard-14/attempt-2/HaplotypeCaller-14-rc.txt
IR_3885.vcf.gz -> gs://broad-gp-gotc-pilot/cromwell_execution/PairedEndSingleSampleWorkflow/60d1afe2-dbd4-47e5-9cf5-e2a76d7947cd/call-HaplotypeCaller/shard-14/attempt-2/VIR_3885.vcf.gz
IR_3885.vcf.gz.tbi -> gs://broad-gp-gotc-pilot/cromwell_execution/PairedEndSingleSampleWorkflow/60d1afe2-dbd4-47e5-9cf5-e2a76d7947cd/call-HaplotypeCaller/shard-14/attempt-2/VIR_3885.vcf.gz.tbi
onitoring -> gs://broad-gp-gotc-pilot/cromwell_execution/PairedEndSingleSampleWorkflow/60d1afe2-dbd4-47e5-9cf5-e2a76d7947cd/call-HaplotypeCaller/shard-14/attempt-2/monitoring.log
16-02-21 01:53:39,102 cromwell-system-akka.actor.default-dispatcher-26 INFO  - JES Run [UUID(60d1afe2):HaplotypeCaller:14:2]: JES Run ID is operations/EOb5oIywKhi0gMzy3sz616ABIOmt-NysGCoPcHJvZHVjdGlvblF1ZXVl
16-02-21 01:53:39,121 cromwell-system-akka.actor.default-dispatcher-26 INFO  - JES Run [UUID(60d1afe2):HaplotypeCaller:14:2]: Status change from - to Initializing
16-02-21 02:08:48,181 cromwell-system-akka.actor.default-dispatcher-24 INFO  - JES Run [UUID(60d1afe2):HaplotypeCaller:23]: Status change from Running to Success
16-02-21 02:08:48,653 cromwell-system-akka.actor.default-dispatcher-4 INFO  - WorkflowActor [UUID(60d1afe2)]: persisting status of HaplotypeCaller:23 to Done.
16-02-21 02:21:22,663 cromwell-system-akka.actor.default-dispatcher-6 INFO  - JES Run [UUID(60d1afe2):HaplotypeCaller:39:2]: Status change from Running to Success
16-02-21 02:21:23,121 cromwell-system-akka.actor.default-dispatcher-14 INFO  - WorkflowActor [UUID(60d1afe2)]: persisting status of HaplotypeCaller:39:2 to Done.
16-02-21 02:28:55,605 cromwell-system-akka.actor.default-dispatcher-6 INFO  - JES Run [UUID(60d1afe2):HaplotypeCaller:6]: Status change from Running to Success
16-02-21 02:28:56,165 cromwell-system-akka.actor.default-dispatcher-19 INFO  - WorkflowActor [UUID(60d1afe2)]: persisting status of HaplotypeCaller:6 to Done.
16-02-21 02:29:52,714 cromwell-system-akka.actor.default-dispatcher-17 INFO  - WorkflowActor [UUID(60d1afe2)]: starting calls: PairedEndSingleSampleWorkflow.HaplotypeCaller
16-02-21 02:29:52,714 cromwell-system-akka.actor.default-dispatcher-17 INFO  - WorkflowActor [UUID(60d1afe2)]: persisting status of HaplotypeCaller:31:3 to Starting.
16-02-21 02:29:52,831 cromwell-system-akka.actor.default-dispatcher-22 INFO  - WorkflowActor [UUID(60d1afe2)]: inputs for call 'HaplotypeCaller:31:3':
nput_bam -> WdlSingleFile(gs://broad-gp-gotc-pilot/cromwell_execution/PairedEndSingleSampleWorkflow/60d1afe2-dbd4-47e5-9cf5-e2a76d7947cd/call-GatherBamFiles/VIR_3885.bam)
nterval_list -> WdlSingleFile(gs://broad-gp-gotc-pilot/cromwell_execution/PairedEndSingleSampleWorkflow/60d1afe2-dbd4-47e5-9cf5-e2a76d7947cd/call-ScatterIntervalList/glob-cb4648beeaff920acb03de7603c06f98/38scattered.interval_list)
nput_bam_index -> WdlSingleFile(gs://broad-gp-gotc-pilot/cromwell_execution/PairedEndSingleSampleWorkflow/60d1afe2-dbd4-47e5-9cf5-e2a76d7947cd/call-GatherBamFiles/VIR_3885.bai)
16-02-21 02:29:52,832 cromwell-system-akka.actor.default-dispatcher-17 INFO  - WorkflowActor [UUID(60d1afe2)]: created call actor for HaplotypeCaller:31:3.
16-02-21 02:29:52,832 cromwell-system-akka.actor.default-dispatcher-17 INFO  - WorkflowActor [UUID(60d1afe2)]: persisting status of HaplotypeCaller:31:3 to Running.
16-02-21 02:29:52,832 cromwell-system-akka.actor.default-dispatcher-14 INFO  - JesBackend [UUID(60d1afe2):HaplotypeCaller:31:3]: Call GCS path: gs://broad-gp-gotc-pilot/cromwell_execution/PairedEndSingleSampleWorkflow/60d1afe2-dbd4-47e5-9cf5-e2a76d7947cd/call-HaplotypeCaller/shard-31/attempt-3
16-02-21 02:29:52,832 cromwell-system-akka.actor.default-dispatcher-14 INFO  - JesBackend [UUID(60d1afe2):HaplotypeCaller:31:3]: `java -XX:GCTimeLimit=50 -XX:GCHeapFreeLimit=10 -Xmx6000m \
I /cromwell_root/broad-gp-gotc-pilot/cromwell_execution/PairedEndSingleSampleWorkflow/60d1afe2-dbd4-47e5-9cf5-e2a76d7947cd/call-GatherBamFiles/VIR_3885.bam \
L /cromwell_root/broad-gp-gotc-pilot/cromwell_execution/PairedEndSingleSampleWorkflow/60d1afe2-dbd4-47e5-9cf5-e2a76d7947cd/call-ScatterIntervalList/glob-cb4648beeaff920acb03de7603c06f98/38scattered.interval_list \
16-02-21 02:29:52,985 cromwell-system-akka.actor.default-dispatcher-14 INFO  - JesBackend [UUID(60d1afe2):HaplotypeCaller:31:3]: Starting call with pre-emptible VM
16-02-21 02:29:52,985 cromwell-system-akka.actor.default-dispatcher-14 INFO  - JES Pipeline [UUID(60d1afe2):HaplotypeCaller:31:3]: Pipeline parameters are:
name=input_bam-0, type=REFERENCE, value=/cromwell_root/broad-gp-gotc-pilot/cromwell_execution/PairedEndSingleSampleWorkflow/60d1afe2-dbd4-47e5-9cf5-e2a76d7947cd/call-GatherBamFiles/VIR_3885.bam}
name=interval_list-0, type=REFERENCE, value=/cromwell_root/broad-gp-gotc-pilot/cromwell_execution/PairedEndSingleSampleWorkflow/60d1afe2-dbd4-47e5-9cf5-e2a76d7947cd/call-ScatterIntervalList/glob-cb4648beeaff920acb03de7603c06f98/38scattered.interval_list}
name=input_bam_index-0, type=REFERENCE, value=/cromwell_root/broad-gp-gotc-pilot/cromwell_execution/PairedEndSingleSampleWorkflow/60d1afe2-dbd4-47e5-9cf5-e2a76d7947cd/call-GatherBamFiles/VIR_3885.bai}
16-02-21 02:29:53,019 cromwell-system-akka.actor.default-dispatcher-14 INFO  - JES Pipeline [UUID(60d1afe2):HaplotypeCaller:31:3]: Pipeline ID is 15929873732439698798
16-02-21 02:29:53,019 cromwell-system-akka.actor.default-dispatcher-14 INFO  - JES Pipeline [UUID(60d1afe2):HaplotypeCaller:31:3]: Project ID: broad-gp-gotc-pilot
16-02-21 02:29:53,019 cromwell-system-akka.actor.default-dispatcher-14 INFO  - JES Run [UUID(60d1afe2):HaplotypeCaller:31:3]: Inputs:
nterval_list-0 -> gs://broad-gp-gotc-pilot/cromwell_execution/PairedEndSingleSampleWorkflow/60d1afe2-dbd4-47e5-9cf5-e2a76d7947cd/call-ScatterIntervalList/glob-cb4648beeaff920acb03de7603c06f98/38scattered.interval_list
nput_bam_index-0 -> gs://broad-gp-gotc-pilot/cromwell_execution/PairedEndSingleSampleWorkflow/60d1afe2-dbd4-47e5-9cf5-e2a76d7947cd/call-GatherBamFiles/VIR_3885.bai
nput_bam-0 -> gs://broad-gp-gotc-pilot/cromwell_execution/PairedEndSingleSampleWorkflow/60d1afe2-dbd4-47e5-9cf5-e2a76d7947cd/call-GatherBamFiles/VIR_3885.bam
xec -> gs://broad-gp-gotc-pilot/cromwell_execution/PairedEndSingleSampleWorkflow/60d1afe2-dbd4-47e5-9cf5-e2a76d7947cd/call-HaplotypeCaller/shard-31/attempt-3/exec.sh
16-02-21 02:29:53,019 cromwell-system-akka.actor.default-dispatcher-14 INFO  - JES Run [UUID(60d1afe2):HaplotypeCaller:31:3]: Outputs:
aplotypeCaller-31-rc.txt -> gs://broad-gp-gotc-pilot/cromwell_execution/PairedEndSingleSampleWorkflow/60d1afe2-dbd4-47e5-9cf5-e2a76d7947cd/call-HaplotypeCaller/shard-31/attempt-3/HaplotypeCaller-31-rc.txt
IR_3885.vcf.gz -> gs://broad-gp-gotc-pilot/cromwell_execution/PairedEndSingleSampleWorkflow/60d1afe2-dbd4-47e5-9cf5-e2a76d7947cd/call-HaplotypeCaller/shard-31/attempt-3/VIR_3885.vcf.gz
IR_3885.vcf.gz.tbi -> gs://broad-gp-gotc-pilot/cromwell_execution/PairedEndSingleSampleWorkflow/60d1afe2-dbd4-47e5-9cf5-e2a76d7947cd/call-HaplotypeCaller/shard-31/attempt-3/VIR_3885.vcf.gz.tbi
onitoring -> gs://broad-gp-gotc-pilot/cromwell_execution/PairedEndSingleSampleWorkflow/60d1afe2-dbd4-47e5-9cf5-e2a76d7947cd/call-HaplotypeCaller/shard-31/attempt-3/monitoring.log
16-02-21 02:29:53,152 cromwell-system-akka.actor.default-dispatcher-14 INFO  - JES Run [UUID(60d1afe2):HaplotypeCaller:31:3]: JES Run ID is operations/EJrSpY2wKhjt8uXd8rD5qIcBIOmt-NysGCoPcHJvZHVjdGlvblF1ZXVl
16-02-21 02:29:53,172 cromwell-system-akka.actor.default-dispatcher-20 INFO  - JES Run [UUID(60d1afe2):HaplotypeCaller:31:3]: Status change from - to Initializing
16-02-21 02:31:30,841 cromwell-system-akka.actor.default-dispatcher-3 INFO  - JES Run [UUID(60d1afe2):HaplotypeCaller:31:3]: Status change from Initializing to Running
16-02-21 02:35:31,061 cromwell-system-akka.actor.default-dispatcher-20 INFO  - JES Run [UUID(60d1afe2):HaplotypeCaller:3:2]: Status change from Running to Success
16-02-21 02:35:31,562 cromwell-system-akka.actor.default-dispatcher-26 INFO  - WorkflowActor [UUID(60d1afe2)]: persisting status of HaplotypeCaller:3:2 to Done.
16-02-21 02:41:36,590 cromwell-system-akka.actor.default-dispatcher-14 INFO  - JES Run [UUID(60d1afe2):HaplotypeCaller:0:2]: Status change from Running to Success
16-02-21 02:56:36,401 cromwell-system-akka.actor.default-dispatcher-17 INFO  - WorkflowActor [UUID(60d1afe2)]: persisting status of HaplotypeCaller:32:2 to Done.
16-02-21 04:22:45,740 cromwell-system-akka.actor.default-dispatcher-12 INFO  - JES Run [UUID(60d1afe2):CollectRawWgsMetrics:2]: Status change from Initializing to Running
16-02-21 05:41:01,717 cromwell-system-akka.actor.default-dispatcher-23 INFO  - JES Run [UUID(60d1afe2):ValidateAggregatedSamFile:3]: Status change from Running to Success
16-02-21 05:41:02,164 cromwell-system-akka.actor.default-dispatcher-13 INFO  - WorkflowActor [UUID(60d1afe2)]: persisting status of ValidateAggregatedSamFile:3 to Done.
16-02-21 08:15:40,399 cromwell-system-akka.actor.default-dispatcher-26 INFO  - JES Run [UUID(60d1afe2):CollectAggregationMetrics]: Status change from Running to Success
16-02-21 08:15:40,910 cromwell-system-akka.actor.default-dispatcher-26 INFO  - WorkflowActor [UUID(60d1afe2)]: persisting status of CollectAggregationMetrics to Done.