Class org.broadinstitute.hellbender.tools.dataflow.pipelines.BaseRecalibratorDataflowIntegrationTest

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[08:10:13] Executing test BaseRecalibratorDataflowIntegrationTest:testBQSR---apiKey AIzaSyDjKyy2KWcEVgtlOlJBdqy4O4oUVMxluE4 --project broad-dsde-dev
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[08:10:49] Executing test BaseRecalibratorDataflowIntegrationTest:testBQSR---runner BLOCKING --apiKey AIzaSyDjKyy2KWcEVgtlOlJBdqy4O4oUVMxluE4 --project broad-dsde-dev --staging gs://hellbender/test/staging/
Dataflow SDK version: 0.4.150727
Submitted job: 2015-09-09_01_11_18-302232699834402856
2015-09-09T08:11:25.384Z: Detail:  (af2e13191d12e06c): Checking required Cloud APIs are enabled.
2015-09-09T08:11:25.773Z: Detail:  (af2e13191d12ea2e): Expanding GroupByKey operations into optimizable parts.
2015-09-09T08:11:25.779Z: Detail:  (af2e13191d12e6b4): Lifting ValueCombiningMappingFns into MergeBucketsMappingFns
2015-09-09T08:11:25.820Z: Detail:  (af2e13191d12e28e): Annotating graph with Autotuner information.
2015-09-09T08:11:25.851Z: Detail:  (af2e13191d12ea38): Fusing adjacent ParDo, Read, Write, and Flatten operations
2015-09-09T08:11:25.859Z: Detail:  (af2e13191d12e6be): Fusing consumer Keys2/Keys into RemoveDuplicateReadVariantPairs/AnonymousParDo3
2015-09-09T08:11:25.861Z: Detail:  (af2e13191d12e344): Fusing consumer KvUUIDVariants into RemoveDuplicateReadVariantPairs/AnonymousParDo3
2015-09-09T08:11:25.863Z: Detail:  (af2e13191d12efca): Fusing consumer Count.Globally4/WithKeys/AddKeys into RemoveDuplicates/Keys/Keys
2015-09-09T08:11:25.866Z: Detail:  (af2e13191d12ec50): Fusing consumer Count.Globally4/Combine.PerKey/GroupByKey+Count.Globally4/Combine.PerKey/Combine.GroupedValues/Partial into Count.Globally4/WithKeys/AddKeys
2015-09-09T08:11:25.868Z: Detail:  (af2e13191d12e8d6): Fusing consumer Count.Globally4/Combine.PerKey/GroupByKey/Reify into Count.Globally4/Combine.PerKey/GroupByKey+Count.Globally4/Combine.PerKey/Combine.GroupedValues/Partial
2015-09-09T08:11:25.870Z: Detail:  (af2e13191d12e55c): Fusing consumer BaseRecalibratorTransform/Combine.Globally/Combine.PerKey/Combine.GroupedValues into BaseRecalibratorTransform/Combine.Globally/Combine.PerKey/GroupByKey/Read
2015-09-09T08:11:25.872Z: Detail:  (af2e13191d12e1e2): Fusing consumer BaseRecalibratorTransform/Combine.Globally/Values/Values into BaseRecalibratorTransform/Combine.Globally/Combine.PerKey/Combine.GroupedValues/Extract
2015-09-09T08:11:25.877Z: Detail:  (af2e13191d12eaee): Fusing consumer BaseRecalibratorTransform/Combine.Globally/Combine.PerKey/Combine.GroupedValues/Extract into BaseRecalibratorTransform/Combine.Globally/Combine.PerKey/Combine.GroupedValues
2015-09-09T08:11:25.882Z: Detail:  (af2e13191d12e3fa): Fusing consumer BaseRecalibratorTransform/Combine.Globally/Combine.PerKey/GroupByKey/Write into BaseRecalibratorTransform/Combine.Globally/Combine.PerKey/GroupByKey/Reify
2015-09-09T08:11:25.889Z: Detail:  (af2e13191d12e98c): Unzipping flatten s99 for input s97.out
2015-09-09T08:11:25.891Z: Detail:  (af2e13191d12e612): Fusing unzipped copy of CoGroupByKey3/GroupByKey/Reify, through flatten , into producer CoGroupByKey3/MakeUnionTable0
2015-09-09T08:11:25.894Z: Detail:  (af2e13191d12e298): Fusing consumer CoGroupByKey3/GroupByKey/Reify into CoGroupByKey3/MakeUnionTable1
2015-09-09T08:11:25.903Z: Detail:  (af2e13191d12e4b0): Unzipping flatten s75 for input s46.out
2015-09-09T08:11:25.906Z: Detail:  (af2e13191d12e136): Fusing unzipped copy of RemoveDuplicates/CreateIndex, through flatten Flatten.FlattenPCollectionList, into producer AddContextDataToRead.StripToUUID/StripToUUID
2015-09-09T08:11:25.908Z: Detail:  (af2e13191d12edbc): Unzipping flatten s75 for input s48.out
2015-09-09T08:11:25.911Z: Detail:  (af2e13191d12ea42): Fusing unzipped copy of RemoveDuplicates/CreateIndex, through flatten , into producer AddContextDataToRead.StripToUUID2/StripToUUID
2015-09-09T08:11:25.913Z: Detail:  (af2e13191d12e6c8): Fusing consumer RemoveDuplicates/CreateIndex into AddContextDataToRead.StripToUUID3/StripToUUID
2015-09-09T08:11:25.915Z: Detail:  (af2e13191d12e34e): Fusing consumer RemoveDuplicates/Combine.PerKey/GroupByKey/Write into RemoveDuplicates/Combine.PerKey/GroupByKey/Reify
2015-09-09T08:11:25.918Z: Detail:  (af2e13191d12efd4): Fusing consumer RemoveDuplicates/Keys/Keys into RemoveDuplicates/Combine.PerKey/Combine.GroupedValues/Extract
2015-09-09T08:11:25.920Z: Detail:  (af2e13191d12ec5a): Fusing consumer RemoveDuplicates/Combine.PerKey/Combine.GroupedValues into RemoveDuplicates/Combine.PerKey/GroupByKey/Read
2015-09-09T08:11:25.922Z: Detail:  (af2e13191d12e8e0): Fusing consumer RemoveDuplicates/Combine.PerKey/GroupByKey/Reify into RemoveDuplicates/Combine.PerKey/GroupByKey+RemoveDuplicates/Combine.PerKey/Combine.GroupedValues/Partial
2015-09-09T08:11:25.925Z: Detail:  (af2e13191d12e566): Fusing consumer Count.Globally4/Values/Values into Count.Globally4/Combine.PerKey/Combine.GroupedValues/Extract
2015-09-09T08:11:25.934Z: Detail:  (af2e13191d12e77e): Unzipping flatten s75-u205 for input s76.out-c203
2015-09-09T08:11:25.937Z: Detail:  (af2e13191d12e404): Fusing unzipped copy of RemoveDuplicates/Combine.PerKey/GroupByKey+RemoveDuplicates/Combine.PerKey/Combine.GroupedValues/Partial, through flatten s75-u205, into producer RemoveDuplicates/CreateIndex
2015-09-09T08:11:25.939Z: Detail:  (af2e13191d12e08a): Unzipping flatten s75-u205 for input s76.out-c207
2015-09-09T08:11:25.942Z: Detail:  (af2e13191d12ed10): Fusing unzipped copy of RemoveDuplicates/Combine.PerKey/GroupByKey+RemoveDuplicates/Combine.PerKey/Combine.GroupedValues/Partial, through flatten , into producer RemoveDuplicates/CreateIndex
2015-09-09T08:11:25.944Z: Detail:  (af2e13191d12e996): Fusing consumer RemoveDuplicates/Combine.PerKey/GroupByKey+RemoveDuplicates/Combine.PerKey/Combine.GroupedValues/Partial into RemoveDuplicates/CreateIndex
2015-09-09T08:11:25.946Z: Detail:  (af2e13191d12e61c): Fusing consumer RemoveDuplicates/Combine.PerKey/Combine.GroupedValues/Extract into RemoveDuplicates/Combine.PerKey/Combine.GroupedValues
2015-09-09T08:11:25.948Z: Detail:  (af2e13191d12e2a2): Fusing consumer BaseRecalibratorTransform/BaseRecalibrator into joinReadwithContextData
2015-09-09T08:11:25.951Z: Detail:  (af2e13191d12ef28): Fusing consumer BaseRecalibratorTransform/Combine.Globally/Combine.PerKey/GroupByKey/Reify into BaseRecalibratorTransform/Combine.Globally/Combine.PerKey/GroupByKey+BaseRecalibratorTransform/Combine.Globally/Combine.PerKey/Combine.GroupedValues/Partial
2015-09-09T08:11:25.953Z: Detail:  (af2e13191d12ebae): Fusing consumer BaseRecalibratorTransform/Combine.Globally/WithKeys/AddKeys into BaseRecalibratorTransform/BaseRecalibrator
2015-09-09T08:11:25.956Z: Detail:  (af2e13191d12e834): Fusing consumer BaseRecalibratorTransform/Combine.Globally/Combine.PerKey/GroupByKey+BaseRecalibratorTransform/Combine.Globally/Combine.PerKey/Combine.GroupedValues/Partial into BaseRecalibratorTransform/Combine.Globally/WithKeys/AddKeys
2015-09-09T08:11:25.958Z: Detail:  (af2e13191d12e4ba): Fusing consumer CoGroupByKey3/ConstructCoGbkResultFn into CoGroupByKey3/GroupByKey/GroupByWindow
2015-09-09T08:11:25.961Z: Detail:  (af2e13191d12e140): Fusing consumer joinReadwithContextData into CoGroupByKey3/ConstructCoGbkResultFn
2015-09-09T08:11:25.963Z: Detail:  (af2e13191d12edc6): Fusing consumer CoGroupByKey3/GroupByKey/GroupByWindow into CoGroupByKey3/GroupByKey/Read
2015-09-09T08:11:25.966Z: Detail:  (af2e13191d12ea4c): Fusing consumer Count.Globally4/Combine.PerKey/Combine.GroupedValues into Count.Globally4/Combine.PerKey/GroupByKey/Read
2015-09-09T08:11:25.968Z: Detail:  (af2e13191d12e6d2): Fusing consumer Count.Globally4/Combine.PerKey/Combine.GroupedValues/Extract into Count.Globally4/Combine.PerKey/Combine.GroupedValues
2015-09-09T08:11:25.977Z: Detail:  (af2e13191d12e8ea): Unzipping flatten s99-u200 for input s100-reify-value71-c198
2015-09-09T08:11:25.980Z: Detail:  (af2e13191d12e570): Fusing unzipped copy of CoGroupByKey3/GroupByKey/Write, through flatten , into producer CoGroupByKey3/GroupByKey/Reify
2015-09-09T08:11:25.982Z: Detail:  (af2e13191d12e1f6): Fusing consumer CoGroupByKey3/GroupByKey/Write into CoGroupByKey3/GroupByKey/Reify
2015-09-09T08:11:25.985Z: Detail:  (af2e13191d12ee7c): Fusing consumer Count.Globally4/Combine.PerKey/GroupByKey/Write into Count.Globally4/Combine.PerKey/GroupByKey/Reify
2015-09-09T08:11:25.987Z: Detail:  (af2e13191d12eb02): Fusing consumer CoGroupByKey2/GroupByKey/Write into CoGroupByKey2/GroupByKey/Reify
2015-09-09T08:11:25.990Z: Detail:  (af2e13191d12e788): Fusing consumer CoGroupByKey2/ConstructCoGbkResultFn into CoGroupByKey2/GroupByKey/GroupByWindow
2015-09-09T08:11:25.992Z: Detail:  (af2e13191d12e40e): Fusing consumer CoGroupByKey2/GroupByKey/GroupByWindow into CoGroupByKey2/GroupByKey/Read
2015-09-09T08:11:25.999Z: Detail:  (af2e13191d12e9a0): Unzipping flatten s92 for input s90.out
2015-09-09T08:11:26.002Z: Detail:  (af2e13191d12e626): Fusing unzipped copy of CoGroupByKey2/GroupByKey/Reify, through flatten , into producer CoGroupByKey2/MakeUnionTable0
2015-09-09T08:11:26.004Z: Detail:  (af2e13191d12e2ac): Fusing consumer kVUUIDReadContextData into CoGroupByKey2/ConstructCoGbkResultFn
2015-09-09T08:11:26.006Z: Detail:  (af2e13191d12ef32): Fusing consumer CoGroupByKey3/MakeUnionTable1 into kVUUIDReadContextData
2015-09-09T08:11:26.016Z: Detail:  (af2e13191d12e4c4): Unzipping flatten s36 for input s34.out
2015-09-09T08:11:26.018Z: Detail:  (af2e13191d12e14a): Fusing unzipped copy of RemoveDuplicateReadVariantPairs/CoGroupByKey2/GroupByKey/Reify, through flatten , into producer RemoveDuplicateReadVariantPairs/CoGroupByKey2/MakeUnionTable0
2015-09-09T08:11:26.025Z: Detail:  (af2e13191d12e6dc): Unzipping flatten s36-u230 for input s37-reify-value125-c228
2015-09-09T08:11:26.028Z: Detail:  (af2e13191d12e362): Fusing unzipped copy of RemoveDuplicateReadVariantPairs/CoGroupByKey2/GroupByKey/Write, through flatten , into producer RemoveDuplicateReadVariantPairs/CoGroupByKey2/GroupByKey/Reify
2015-09-09T08:11:26.030Z: Detail:  (af2e13191d12efe8): Fusing consumer CoGroupByKey2/MakeUnionTable0 into KvUUIDVariants
2015-09-09T08:11:26.032Z: Detail:  (af2e13191d12ec6e): Fusing consumer RemoveDuplicateReadVariantPairs/AnonymousParDo3 into RemoveDuplicateReadVariantPairs/CoGroupByKey2/ConstructCoGbkResultFn
2015-09-09T08:11:26.035Z: Detail:  (af2e13191d12e8f4): Fusing consumer RemoveDuplicateReadVariantPairs/CoGroupByKey2/GroupByKey/GroupByWindow into RemoveDuplicateReadVariantPairs/CoGroupByKey2/GroupByKey/Read
2015-09-09T08:11:26.037Z: Detail:  (af2e13191d12e57a): Fusing consumer RemoveDuplicateReadVariantPairs/CoGroupByKey2/ConstructCoGbkResultFn into RemoveDuplicateReadVariantPairs/CoGroupByKey2/GroupByKey/GroupByWindow
2015-09-09T08:11:26.040Z: Detail:  (af2e13191d12e200): Fusing consumer AddContextDataToRead.StripToUUID3/StripToUUID into Keys2/Keys
2015-09-09T08:11:26.042Z: Detail:  (af2e13191d12ee86): Fusing consumer RemoveDuplicateReadVariantPairs/CoGroupByKey2/GroupByKey/Write into RemoveDuplicateReadVariantPairs/CoGroupByKey2/GroupByKey/Reify
2015-09-09T08:11:26.044Z: Detail:  (af2e13191d12eb0c): Fusing consumer RemoveDuplicateReadVariantPairs/CoGroupByKey2/GroupByKey/Reify into RemoveDuplicateReadVariantPairs/CoGroupByKey2/MakeUnionTable1
2015-09-09T08:11:26.047Z: Detail:  (af2e13191d12e792): Fusing consumer RemoveDuplicateReadVariantPairs/CoGroupByKey/GroupByKey/GroupByWindow into RemoveDuplicateReadVariantPairs/CoGroupByKey/GroupByKey/Read
2015-09-09T08:11:26.053Z: Detail:  (af2e13191d12ed24): Unzipping flatten s28 for input s26.out
2015-09-09T08:11:26.056Z: Detail:  (af2e13191d12e9aa): Fusing unzipped copy of RemoveDuplicateReadVariantPairs/CoGroupByKey/GroupByKey/Reify, through flatten , into producer RemoveDuplicateReadVariantPairs/CoGroupByKey/MakeUnionTable0
2015-09-09T08:11:26.066Z: Detail:  (af2e13191d12ebc2): Unzipping flatten s28-u237 for input s29-reify-value116-c235
2015-09-09T08:11:26.068Z: Detail:  (af2e13191d12e848): Fusing unzipped copy of RemoveDuplicateReadVariantPairs/CoGroupByKey/GroupByKey/Write, through flatten , into producer RemoveDuplicateReadVariantPairs/CoGroupByKey/GroupByKey/Reify
2015-09-09T08:11:26.071Z: Detail:  (af2e13191d12e4ce): Fusing consumer RemoveDuplicateReadVariantPairs/AnonymousParDo2 into RemoveDuplicateReadVariantPairs/CoGroupByKey/ConstructCoGbkResultFn
2015-09-09T08:11:26.073Z: Detail:  (af2e13191d12e154): Fusing consumer RemoveDuplicateReadVariantPairs/CoGroupByKey2/MakeUnionTable1 into RemoveDuplicateReadVariantPairs/AnonymousParDo2
2015-09-09T08:11:26.075Z: Detail:  (af2e13191d12edda): Fusing consumer RemoveDuplicateReadVariantPairs/CoGroupByKey/ConstructCoGbkResultFn into RemoveDuplicateReadVariantPairs/CoGroupByKey/GroupByKey/GroupByWindow
2015-09-09T08:11:26.078Z: Detail:  (af2e13191d12ea60): Fusing consumer RemoveDuplicateReadVariantPairs/ParDo(StripToUUIDs) into AnonymousParDo2
2015-09-09T08:11:26.081Z: Detail:  (af2e13191d12e6e6): Fusing consumer RemoveDuplicateReadVariantPairs/AnonymousParDo into AnonymousParDo2
2015-09-09T08:11:26.083Z: Detail:  (af2e13191d12e36c): Fusing consumer RemoveDuplicateReadVariantPairs/Keys/Keys into AnonymousParDo2
2015-09-09T08:11:26.085Z: Detail:  (af2e13191d12eff2): Fusing consumer RemoveDuplicateReadVariantPairs/CoGroupByKey/GroupByKey/Reify into RemoveDuplicateReadVariantPairs/CoGroupByKey/MakeUnionTable1
2015-09-09T08:11:26.088Z: Detail:  (af2e13191d12ec78): Fusing consumer RemoveDuplicateReadVariantPairs/CoGroupByKey/GroupByKey/Write into RemoveDuplicateReadVariantPairs/CoGroupByKey/GroupByKey/Reify
2015-09-09T08:11:26.090Z: Detail:  (af2e13191d12e8fe): Fusing consumer CoGroupByKey/GroupByKey/GroupByWindow into CoGroupByKey/GroupByKey/Read
2015-09-09T08:11:26.093Z: Detail:  (af2e13191d12e584): Fusing consumer RemoveDuplicateReadVariantPairs/GroupByKey/Write into RemoveDuplicateReadVariantPairs/GroupByKey/Reify
2015-09-09T08:11:26.095Z: Detail:  (af2e13191d12e20a): Fusing consumer RemoveDuplicateReadVariantPairs/RemoveDuplicates/Keys/Keys into RemoveDuplicateReadVariantPairs/RemoveDuplicates/Combine.PerKey/Combine.GroupedValues/Extract
2015-09-09T08:11:26.097Z: Detail:  (af2e13191d12ee90): Fusing consumer RemoveDuplicateReadVariantPairs/GroupByKey/Reify into RemoveDuplicateReadVariantPairs/RemoveDuplicates/Keys/Keys
2015-09-09T08:11:26.100Z: Detail:  (af2e13191d12eb16): Fusing consumer RemoveDuplicateReadVariantPairs/RemoveDuplicates/Combine.PerKey/GroupByKey/Write into RemoveDuplicateReadVariantPairs/RemoveDuplicates/Combine.PerKey/GroupByKey/Reify
2015-09-09T08:11:26.102Z: Detail:  (af2e13191d12e79c): Fusing consumer RemoveDuplicateReadVariantPairs/RemoveDuplicates/Combine.PerKey/Combine.GroupedValues into RemoveDuplicateReadVariantPairs/RemoveDuplicates/Combine.PerKey/GroupByKey/Read
2015-09-09T08:11:26.105Z: Detail:  (af2e13191d12e422): Fusing consumer RemoveDuplicateReadVariantPairs/GroupByKey/GroupByWindow into RemoveDuplicateReadVariantPairs/GroupByKey/Read
2015-09-09T08:11:26.107Z: Detail:  (af2e13191d12e0a8): Fusing consumer RemoveDuplicateReadVariantPairs/RemoveDuplicates/Combine.PerKey/Combine.GroupedValues/Extract into RemoveDuplicateReadVariantPairs/RemoveDuplicates/Combine.PerKey/Combine.GroupedValues
2015-09-09T08:11:26.109Z: Detail:  (af2e13191d12ed2e): Fusing consumer RemoveDuplicateReadVariantPairs/RemoveDuplicates/Combine.PerKey/GroupByKey/Reify into RemoveDuplicateReadVariantPairs/RemoveDuplicates/Combine.PerKey/GroupByKey+RemoveDuplicateReadVariantPairs/RemoveDuplicates/Combine.PerKey/Combine.GroupedValues/Partial
2015-09-09T08:11:26.111Z: Detail:  (af2e13191d12e9b4): Fusing consumer RemoveDuplicateReadVariantPairs/CoGroupByKey/MakeUnionTable0 into RemoveDuplicateReadVariantPairs/GroupByKey/GroupByWindow
2015-09-09T08:11:26.114Z: Detail:  (af2e13191d12e63a): Fusing consumer RemoveDuplicateReadVariantPairs/RemoveDuplicates/Combine.PerKey/GroupByKey+RemoveDuplicateReadVariantPairs/RemoveDuplicates/Combine.PerKey/Combine.GroupedValues/Partial into RemoveDuplicateReadVariantPairs/RemoveDuplicates/CreateIndex
2015-09-09T08:11:26.116Z: Detail:  (af2e13191d12e2c0): Fusing consumer CoGroupByKey/GroupByKey/Write into CoGroupByKey/GroupByKey/Reify
2015-09-09T08:11:26.118Z: Detail:  (af2e13191d12ef46): Fusing consumer RemoveDuplicateReadVariantPairs/RemoveDuplicates/CreateIndex into RemoveDuplicateReadVariantPairs/ParDo(StripToUUIDs)
2015-09-09T08:11:26.121Z: Detail:  (af2e13191d12ebcc): Fusing consumer RemoveDuplicateReadVariantPairs/CoGroupByKey2/MakeUnionTable0 into RemoveDuplicateReadVariantPairs/KeyReadsByUUID/AnonymousParDo
2015-09-09T08:11:26.128Z: Detail:  (af2e13191d12e15e): Unzipping flatten s15 for input s13.out
2015-09-09T08:11:26.131Z: Detail:  (af2e13191d12ede4): Fusing unzipped copy of CoGroupByKey/GroupByKey/Reify, through flatten , into producer CoGroupByKey/MakeUnionTable0
2015-09-09T08:11:26.133Z: Detail:  (af2e13191d12ea6a): Fusing consumer RemoveDuplicateReadVariantPairs/KeyReadsByUUID/AnonymousParDo into RemoveDuplicateReadVariantPairs/Keys/Keys
2015-09-09T08:11:26.136Z: Detail:  (af2e13191d12e6f0): Fusing consumer AnonymousParDo2 into CoGroupByKey/ConstructCoGbkResultFn
2015-09-09T08:11:26.138Z: Detail:  (af2e13191d12e376): Fusing consumer CoGroupByKey/ConstructCoGbkResultFn into CoGroupByKey/GroupByKey/GroupByWindow
2015-09-09T08:11:26.140Z: Detail:  (af2e13191d12effc): Fusing consumer RemoveDuplicateReadVariantPairs/CoGroupByKey/MakeUnionTable1 into RemoveDuplicateReadVariantPairs/AnonymousParDo
2015-09-09T08:11:26.145Z: Detail:  (af2e13191d12e908): Fusing consumer CoGroupByKey/MakeUnionTable0 into KeyVariantByOverlappingVariantShard/KeyVariantByVariantShard
2015-09-09T08:11:26.154Z: Detail:  (af2e13191d12eb20): Fusing consumer Count.Globally/WithKeys/AddKeys into AddContextDataToRead.StripToUUID/StripToUUID
2015-09-09T08:11:26.157Z: Detail:  (af2e13191d12e7a6): Fusing consumer Count.Globally2/WithKeys/AddKeys into AddContextDataToRead.StripToUUID/StripToUUID
2015-09-09T08:11:26.159Z: Detail:  (af2e13191d12e42c): Fusing consumer Count.Globally3/WithKeys/AddKeys into AddContextDataToRead.StripToUUID/StripToUUID
2015-09-09T08:11:26.161Z: Detail:  (af2e13191d12e0b2): Fusing consumer KeyReadsByOverlappingVariantShard/KeyReadByVariantShard into DataflowReadFilter/CountingAndReadFilter
2015-09-09T08:11:26.164Z: Detail:  (af2e13191d12ed38): Fusing consumer KeyReadsByRefShard/KeyReadByRefShard into DataflowReadFilter/CountingAndReadFilter
2015-09-09T08:11:26.166Z: Detail:  (af2e13191d12e9be): Fusing consumer AddContextDataToRead.StripToUUID/StripToUUID into DataflowReadFilter/CountingAndReadFilter
2015-09-09T08:11:26.169Z: Detail:  (af2e13191d12e644): Fusing consumer KeyReadsByUUID/AnonymousParDo into DataflowReadFilter/CountingAndReadFilter
2015-09-09T08:11:26.171Z: Detail:  (af2e13191d12e2ca): Fusing consumer Keys/Keys into PairReadWithRefBases/AnonymousParDo
2015-09-09T08:11:26.173Z: Detail:  (af2e13191d12ef50): Fusing consumer KvUUIDRefBases into PairReadWithRefBases/AnonymousParDo
2015-09-09T08:11:26.176Z: Detail:  (af2e13191d12ebd6): Fusing consumer CoGroupByKey/GroupByKey/Reify into CoGroupByKey/MakeUnionTable1
2015-09-09T08:11:26.178Z: Detail:  (af2e13191d12e85c): Fusing consumer CoGroupByKey2/GroupByKey/Reify into CoGroupByKey2/MakeUnionTable1
2015-09-09T08:11:26.181Z: Detail:  (af2e13191d12e4e2): Fusing consumer Count.Globally3/Values/Values into Count.Globally3/Combine.PerKey/Combine.GroupedValues/Extract
2015-09-09T08:11:26.185Z: Detail:  (af2e13191d12edee): Fusing consumer CoGroupByKey2/MakeUnionTable1 into KvUUIDRefBases
2015-09-09T08:11:26.188Z: Detail:  (af2e13191d12ea74): Fusing consumer Count.Globally/Combine.PerKey/Combine.GroupedValues/Extract into Count.Globally/Combine.PerKey/Combine.GroupedValues
2015-09-09T08:11:26.190Z: Detail:  (af2e13191d12e6fa): Fusing consumer PairReadWithRefBases/AnonymousParDo into AnonymousParDo3
2015-09-09T08:11:26.192Z: Detail:  (af2e13191d12e380): Fusing consumer Count.Globally3/Combine.PerKey/GroupByKey+Count.Globally3/Combine.PerKey/Combine.GroupedValues/Partial into Count.Globally3/WithKeys/AddKeys
2015-09-09T08:11:26.195Z: Detail:  (af2e13191d12e006): Fusing consumer KeyReadsByRefShard/GroupByKey/GroupByWindow into KeyReadsByRefShard/GroupByKey/Read
2015-09-09T08:11:26.197Z: Detail:  (af2e13191d12ec8c): Fusing consumer Count.Globally/Values/Values into Count.Globally/Combine.PerKey/Combine.GroupedValues/Extract
2015-09-09T08:11:26.200Z: Detail:  (af2e13191d12e912): Fusing consumer AnonymousParDo3 into KeyReadsByRefShard/GroupByKey/GroupByWindow
2015-09-09T08:11:26.202Z: Detail:  (af2e13191d12e598): Fusing consumer Count.Globally3/Combine.PerKey/GroupByKey/Reify into Count.Globally3/Combine.PerKey/GroupByKey+Count.Globally3/Combine.PerKey/Combine.GroupedValues/Partial
2015-09-09T08:11:26.205Z: Detail:  (af2e13191d12e21e): Fusing consumer Count.Globally/Combine.PerKey/GroupByKey/Write into Count.Globally/Combine.PerKey/GroupByKey/Reify
2015-09-09T08:11:26.207Z: Detail:  (af2e13191d12eea4): Fusing consumer KeyReadsByRefShard/GroupByKey/Write into KeyReadsByRefShard/GroupByKey/Reify
2015-09-09T08:11:26.210Z: Detail:  (af2e13191d12eb2a): Fusing consumer Count.Globally2/Combine.PerKey/GroupByKey/Reify into Count.Globally2/Combine.PerKey/GroupByKey+Count.Globally2/Combine.PerKey/Combine.GroupedValues/Partial
2015-09-09T08:11:26.212Z: Detail:  (af2e13191d12e7b0): Fusing consumer CoGroupByKey3/MakeUnionTable0 into KeyReadsByUUID/AnonymousParDo
2015-09-09T08:11:26.214Z: Detail:  (af2e13191d12e436): Fusing consumer KeyReadsByRefShard/GroupByKey/Reify into KeyReadsByRefShard/KeyReadByRefShard
2015-09-09T08:11:26.216Z: Detail:  (af2e13191d12e0bc): Fusing consumer AnonymousParDo into GoogleGenomicsReadToGATKRead/AnonymousParDo
2015-09-09T08:11:26.219Z: Detail:  (af2e13191d12ed42): Fusing consumer Count.Globally/Combine.PerKey/GroupByKey+Count.Globally/Combine.PerKey/Combine.GroupedValues/Partial into Count.Globally/WithKeys/AddKeys
2015-09-09T08:11:26.222Z: Detail:  (af2e13191d12e9c8): Fusing consumer GoogleGenomicsReadToGATKRead/AnonymousParDo into ParDo(Read)
2015-09-09T08:11:26.224Z: Detail:  (af2e13191d12e64e): Fusing consumer CoGroupByKey/MakeUnionTable1 into KeyReadsByOverlappingVariantShard/KeyReadByVariantShard
2015-09-09T08:11:26.226Z: Detail:  (af2e13191d12e2d4): Fusing consumer Count.Globally2/Values/Values into Count.Globally2/Combine.PerKey/Combine.GroupedValues/Extract
2015-09-09T08:11:26.230Z: Detail:  (af2e13191d12ebe0): Fusing consumer Count.Globally2/Combine.PerKey/GroupByKey+Count.Globally2/Combine.PerKey/Combine.GroupedValues/Partial into Count.Globally2/WithKeys/AddKeys
2015-09-09T08:11:26.234Z: Detail:  (af2e13191d12e4ec): Fusing consumer Count.Globally3/Combine.PerKey/GroupByKey/Write into Count.Globally3/Combine.PerKey/GroupByKey/Reify
2015-09-09T08:11:26.238Z: Detail:  (af2e13191d12edf8): Fusing consumer Count.Globally/Combine.PerKey/Combine.GroupedValues into Count.Globally/Combine.PerKey/GroupByKey/Read
2015-09-09T08:11:26.241Z: Detail:  (af2e13191d12ea7e): Fusing consumer AddContextDataToRead.StripToUUID2/StripToUUID into Keys/Keys
2015-09-09T08:11:26.242Z: Detail:  (af2e13191d12e704): Fusing consumer Count.Globally/Combine.PerKey/GroupByKey/Reify into Count.Globally/Combine.PerKey/GroupByKey+Count.Globally/Combine.PerKey/Combine.GroupedValues/Partial
2015-09-09T08:11:26.245Z: Detail:  (af2e13191d12e38a): Fusing consumer Count.Globally2/Combine.PerKey/Combine.GroupedValues/Extract into Count.Globally2/Combine.PerKey/Combine.GroupedValues
2015-09-09T08:11:26.247Z: Detail:  (af2e13191d12e010): Fusing consumer DataflowReadFilter/CountingAndReadFilter into AnonymousParDo
2015-09-09T08:11:26.249Z: Detail:  (af2e13191d12ec96): Fusing consumer Count.Globally2/Combine.PerKey/GroupByKey/Write into Count.Globally2/Combine.PerKey/GroupByKey/Reify
2015-09-09T08:11:26.251Z: Detail:  (af2e13191d12e91c): Fusing consumer Count.Globally3/Combine.PerKey/Combine.GroupedValues/Extract into Count.Globally3/Combine.PerKey/Combine.GroupedValues
2015-09-09T08:11:26.253Z: Detail:  (af2e13191d12e5a2): Fusing consumer Count.Globally2/Combine.PerKey/Combine.GroupedValues into Count.Globally2/Combine.PerKey/GroupByKey/Read
2015-09-09T08:11:26.255Z: Detail:  (af2e13191d12e228): Fusing consumer Count.Globally3/Combine.PerKey/Combine.GroupedValues into Count.Globally3/Combine.PerKey/GroupByKey/Read
2015-09-09T08:11:26.257Z: Detail:  (af2e13191d12eeae): Fusing consumer AnonymousParDo4 into BaseRecalibratorTransform/addQuantizationInfo
2015-09-09T08:11:26.266Z: Detail:  (af2e13191d12e0c6): Fusing consumer save to gs://hellbender/test/staging/temp-ds-recaltables.sj into AnonymousParDo4
2015-09-09T08:11:26.278Z: Detail:  (af2e13191d12ebea): Fusing consumer BaseRecalibratorTransform/addQuantizationInfo into BaseRecalibratorTransform/finalizeRecalTables
2015-09-09T08:11:26.280Z: Detail:  (af2e13191d12e870): Fusing consumer assertSameReads into Count.Globally4/ProduceDefault
2015-09-09T08:11:26.282Z: Detail:  (af2e13191d12e4f6): Fusing consumer BaseRecalibratorTransform/finalizeRecalTables into BaseRecalibratorTransform/Combine.Globally/ProduceDefault
2015-09-09T08:11:26.767Z: Detail:  (af2e13191d12ef12): Adding StepResource setup and teardown to workflow graph.
2015-09-09T08:11:27.725Z: Basic:  (1d93c5f64cc8c805): Starting 3 workers...
2015-09-09T08:11:27.765Z: Basic:  S07: (7d0828eb69e8f396): Executing operation Count.Globally2/Combine.PerKey/GroupByKey/Create
2015-09-09T08:11:27.765Z: Basic:  S41: (85a0e2784da51ec6): Executing operation View.AsSingleton2/View.CreatePCollectionView
2015-09-09T08:11:27.765Z: Basic:  S40: (70d23817853d17e0): Executing operation View.AsSingleton/View.CreatePCollectionView
2015-09-09T08:11:27.765Z: Basic:  S06: (b66ca6c2c7bdb3f4): Executing operation Count.Globally/Combine.PerKey/GroupByKey/Create
2015-09-09T08:11:27.765Z: Basic:  S08: (36be21d30e4a2662): Executing operation Count.Globally3/Combine.PerKey/GroupByKey/Create
2015-09-09T08:11:27.765Z: Basic:  S01: (bc15f59c21e74efa): Executing operation KeyReadsByRefShard/GroupByKey/Create
2015-09-09T08:11:27.765Z: Basic:  S02: (7b60673a5259e656): Executing operation View ReferenceDataflowSource as singleton/View.CreatePCollectionView
2015-09-09T08:11:27.765Z: Basic:  S05: (cdbc35d52107057e): Executing operation CoGroupByKey/GroupByKey/Create
2015-09-09T08:11:27.881Z: Basic:  S03: (270ab46fb9347c10): Executing operation CoGroupByKey2/GroupByKey/Create
2015-09-09T08:11:27.886Z: Basic:  S09: (85a0e2784da519fc): Executing operation RemoveDuplicates/Combine.PerKey/GroupByKey/Create
2015-09-09T08:11:27.886Z: Basic:  S24: (e6a110fee568977a): Executing operation KeyVariantByOverlappingVariantShard/KeyVariantByVariantShard+CoGroupByKey/MakeUnionTable0+CoGroupByKey/GroupByKey/Reify+CoGroupByKey/GroupByKey/Write
2015-09-09T08:11:28.480Z: Basic:  S04: (1d93c5f64cc8c9b3): Executing operation CoGroupByKey3/GroupByKey/Create
2015-09-09T08:11:29.088Z: Basic:  S10: (53354dfb3bce0d9b): Executing operation ParDo(Read)+GoogleGenomicsReadToGATKRead/AnonymousParDo+AnonymousParDo+DataflowReadFilter/CountingAndReadFilter+KeyReadsByOverlappingVariantShard/KeyReadByVariantShard+KeyReadsByRefShard/KeyReadByRefShard+AddContextDataToRead.StripToUUID/StripToUUID+RemoveDuplicates/CreateIndex+RemoveDuplicates/Combine.PerKey/GroupByKey+RemoveDuplicates/Combine.PerKey/Combine.GroupedValues/Partial+RemoveDuplicates/Combine.PerKey/GroupByKey/Reify+RemoveDuplicates/Combine.PerKey/GroupByKey/Write+Count.Globally/WithKeys/AddKeys+Count.Globally2/WithKeys/AddKeys+Count.Globally3/WithKeys/AddKeys+KeyReadsByUUID/AnonymousParDo+Count.Globally3/Combine.PerKey/GroupByKey+Count.Globally3/Combine.PerKey/Combine.GroupedValues/Partial+Count.Globally3/Combine.PerKey/GroupByKey/Reify+CoGroupByKey3/MakeUnionTable0+CoGroupByKey3/GroupByKey/Reify+CoGroupByKey3/GroupByKey/Write+KeyReadsByRefShard/GroupByKey/Reify+KeyReadsByRefShard/GroupByKey/Write+Count.Globally/Combine.PerKey/GroupByKey+Count.Globally/Combine.PerKey/Combine.GroupedValues/Partial+CoGroupByKey/MakeUnionTable1+CoGroupByKey/GroupByKey/Reify+CoGroupByKey/GroupByKey/Write+Count.Globally2/Combine.PerKey/GroupByKey+Count.Globally2/Combine.PerKey/Combine.GroupedValues/Partial+Count.Globally2/Combine.PerKey/GroupByKey/Reify+Count.Globally3/Combine.PerKey/GroupByKey/Write+Count.Globally/Combine.PerKey/GroupByKey/Reify+Count.Globally/Combine.PerKey/GroupByKey/Write+Count.Globally2/Combine.PerKey/GroupByKey/Write
2015-09-09T08:12:19.062Z: Detail:  (3c0a865f357e614c): Workers have started successfully.
2015-09-09T08:12:46.737Z: Basic:  S26: (c1c701a525a7489): Executing operation RemoveDuplicateReadVariantPairs/CoGroupByKey/GroupByKey/Create
2015-09-09T08:12:46.748Z: Basic:  S25: (80268a0d55f2cc55): Executing operation RemoveDuplicateReadVariantPairs/RemoveDuplicates/Combine.PerKey/GroupByKey/Create
2015-09-09T08:12:46.754Z: Basic:  S15: (40948608ebc443e9): Executing operation Count.Globally2/Combine.PerKey/GroupByKey/Read+Count.Globally2/Combine.PerKey/Combine.GroupedValues+Count.Globally2/Combine.PerKey/Combine.GroupedValues/Extract+Count.Globally2/Values/Values
2015-09-09T08:12:46.754Z: Basic:  S11: (a3dbcf0371b4ae91): Executing operation Count.Globally/Combine.PerKey/GroupByKey/Read+Count.Globally/Combine.PerKey/Combine.GroupedValues+Count.Globally/Combine.PerKey/Combine.GroupedValues/Extract+Count.Globally/Values/Values
2015-09-09T08:12:46.754Z: Basic:  S19: (3f2456a52eb552ad): Executing operation Count.Globally3/Combine.PerKey/GroupByKey/Read+Count.Globally3/Combine.PerKey/Combine.GroupedValues+Count.Globally3/Combine.PerKey/Combine.GroupedValues/Extract+Count.Globally3/Values/Values
2015-09-09T08:12:46.755Z: Basic:  S23: (1c86bff6d29c6635): Executing operation KeyReadsByRefShard/GroupByKey/Read+KeyReadsByRefShard/GroupByKey/GroupByWindow+AnonymousParDo3+PairReadWithRefBases/AnonymousParDo+Keys/Keys+KvUUIDRefBases+CoGroupByKey2/MakeUnionTable1+CoGroupByKey2/GroupByKey/Reify+CoGroupByKey2/GroupByKey/Write+AddContextDataToRead.StripToUUID2/StripToUUID+RemoveDuplicates/CreateIndex+RemoveDuplicates/Combine.PerKey/GroupByKey+RemoveDuplicates/Combine.PerKey/Combine.GroupedValues/Partial+RemoveDuplicates/Combine.PerKey/GroupByKey/Reify+RemoveDuplicates/Combine.PerKey/GroupByKey/Write
2015-09-09T08:12:47.329Z: Basic:  S27: (d7305c954f3952f3): Executing operation RemoveDuplicateReadVariantPairs/CoGroupByKey2/GroupByKey/Create
2015-09-09T08:12:48.493Z: Basic:  S28: (ea69c63bc05dc24): Executing operation CoGroupByKey/GroupByKey/Read+CoGroupByKey/GroupByKey/GroupByWindow+CoGroupByKey/ConstructCoGbkResultFn+AnonymousParDo2+RemoveDuplicateReadVariantPairs/ParDo(StripToUUIDs)+RemoveDuplicateReadVariantPairs/AnonymousParDo+RemoveDuplicateReadVariantPairs/Keys/Keys+RemoveDuplicateReadVariantPairs/RemoveDuplicates/CreateIndex+RemoveDuplicateReadVariantPairs/RemoveDuplicates/Combine.PerKey/GroupByKey+RemoveDuplicateReadVariantPairs/RemoveDuplicates/Combine.PerKey/Combine.GroupedValues/Partial+RemoveDuplicateReadVariantPairs/RemoveDuplicates/Combine.PerKey/GroupByKey/Reify+RemoveDuplicateReadVariantPairs/RemoveDuplicates/Combine.PerKey/GroupByKey/Write+RemoveDuplicateReadVariantPairs/KeyReadsByUUID/AnonymousParDo+RemoveDuplicateReadVariantPairs/CoGroupByKey2/MakeUnionTable0+RemoveDuplicateReadVariantPairs/CoGroupByKey2/GroupByKey/Reify+RemoveDuplicateReadVariantPairs/CoGroupByKey2/GroupByKey/Write+RemoveDuplicateReadVariantPairs/CoGroupByKey/MakeUnionTable1+RemoveDuplicateReadVariantPairs/CoGroupByKey/GroupByKey/Reify+RemoveDuplicateReadVariantPairs/CoGroupByKey/GroupByKey/Write
2015-09-09T08:12:50.796Z: Basic:  S20: (c1c701a525a736a): Executing operation Count.Globally3/View.AsIterable/View.CreatePCollectionView
2015-09-09T08:12:50.844Z: Basic:  S21: (1c86bff6d29c6a0b): Executing operation Count.Globally3/ProduceDefault
2015-09-09T08:12:52.942Z: Basic:  S29: (40948608ebc44496): Executing operation RemoveDuplicateReadVariantPairs/GroupByKey/Create
2015-09-09T08:12:53.510Z: Basic:  S30: (603c5c4a71158b81): Executing operation RemoveDuplicateReadVariantPairs/RemoveDuplicates/Combine.PerKey/GroupByKey/Read+RemoveDuplicateReadVariantPairs/RemoveDuplicates/Combine.PerKey/Combine.GroupedValues+RemoveDuplicateReadVariantPairs/RemoveDuplicates/Combine.PerKey/Combine.GroupedValues/Extract+RemoveDuplicateReadVariantPairs/RemoveDuplicates/Keys/Keys+RemoveDuplicateReadVariantPairs/GroupByKey/Reify+RemoveDuplicateReadVariantPairs/GroupByKey/Write
2015-09-09T08:12:53.822Z: Basic:  S12: (b6322df7e738bdfe): Executing operation Count.Globally/View.AsIterable/View.CreatePCollectionView
2015-09-09T08:12:53.890Z: Basic:  S13: (c1c701a525a724b): Executing operation Count.Globally/ProduceDefault
2015-09-09T08:12:54.076Z: Basic:  S31: (85a0e2784da51b1c): Executing operation RemoveDuplicateReadVariantPairs/GroupByKey/Read+RemoveDuplicateReadVariantPairs/GroupByKey/GroupByWindow+RemoveDuplicateReadVariantPairs/CoGroupByKey/MakeUnionTable0+RemoveDuplicateReadVariantPairs/CoGroupByKey/GroupByKey/Reify+RemoveDuplicateReadVariantPairs/CoGroupByKey/GroupByKey/Write
2015-09-09T08:12:54.456Z: Basic:  S16: (ea69c63bc05d887): Executing operation Count.Globally2/View.AsIterable/View.CreatePCollectionView
2015-09-09T08:12:54.538Z: Basic:  S17: (d7305c954f3951b9): Executing operation Count.Globally2/ProduceDefault
2015-09-09T08:12:54.556Z: Basic:  S32: (ee8b03b78713ef73): Executing operation RemoveDuplicateReadVariantPairs/CoGroupByKey/GroupByKey/Read+RemoveDuplicateReadVariantPairs/CoGroupByKey/GroupByKey/GroupByWindow+RemoveDuplicateReadVariantPairs/CoGroupByKey/ConstructCoGbkResultFn+RemoveDuplicateReadVariantPairs/AnonymousParDo2+RemoveDuplicateReadVariantPairs/CoGroupByKey2/MakeUnionTable1+RemoveDuplicateReadVariantPairs/CoGroupByKey2/GroupByKey/Reify+RemoveDuplicateReadVariantPairs/CoGroupByKey2/GroupByKey/Write
2015-09-09T08:12:54.772Z: Basic:  S22: (1c86bff6d29c6abc): Executing operation View.AsSingleton5/View.CreatePCollectionView
2015-09-09T08:12:55.119Z: Basic:  S33: (b6322df7e738ba87): Executing operation RemoveDuplicateReadVariantPairs/CoGroupByKey2/GroupByKey/Read+RemoveDuplicateReadVariantPairs/CoGroupByKey2/GroupByKey/GroupByWindow+RemoveDuplicateReadVariantPairs/CoGroupByKey2/ConstructCoGbkResultFn+RemoveDuplicateReadVariantPairs/AnonymousParDo3+Keys2/Keys+KvUUIDVariants+CoGroupByKey2/MakeUnionTable0+CoGroupByKey2/GroupByKey/Reify+CoGroupByKey2/GroupByKey/Write+AddContextDataToRead.StripToUUID3/StripToUUID+RemoveDuplicates/CreateIndex+RemoveDuplicates/Combine.PerKey/GroupByKey+RemoveDuplicates/Combine.PerKey/Combine.GroupedValues/Partial+RemoveDuplicates/Combine.PerKey/GroupByKey/Reify+RemoveDuplicates/Combine.PerKey/GroupByKey/Write
2015-09-09T08:12:55.698Z: Basic:  S39: (367b995363fd2d2f): Executing operation CoGroupByKey2/GroupByKey/Read+CoGroupByKey2/GroupByKey/GroupByWindow+CoGroupByKey2/ConstructCoGbkResultFn+kVUUIDReadContextData+CoGroupByKey3/MakeUnionTable1+CoGroupByKey3/GroupByKey/Reify+CoGroupByKey3/GroupByKey/Write
2015-09-09T08:12:55.712Z: Basic:  S34: (468a67effcdbefce): Executing operation Count.Globally4/Combine.PerKey/GroupByKey/Create
2015-09-09T08:12:56.336Z: Basic:  S35: (270ab46fb9347ee4): Executing operation RemoveDuplicates/Combine.PerKey/GroupByKey/Read+RemoveDuplicates/Combine.PerKey/Combine.GroupedValues+RemoveDuplicates/Combine.PerKey/Combine.GroupedValues/Extract+RemoveDuplicates/Keys/Keys+Count.Globally4/WithKeys/AddKeys+Count.Globally4/Combine.PerKey/GroupByKey+Count.Globally4/Combine.PerKey/Combine.GroupedValues/Partial+Count.Globally4/Combine.PerKey/GroupByKey/Reify+Count.Globally4/Combine.PerKey/GroupByKey/Write
2015-09-09T08:12:56.976Z: Basic:  S36: (c1c701a525a70fd): Executing operation Count.Globally4/Combine.PerKey/GroupByKey/Read+Count.Globally4/Combine.PerKey/Combine.GroupedValues+Count.Globally4/Combine.PerKey/Combine.GroupedValues/Extract+Count.Globally4/Values/Values
2015-09-09T08:12:57.169Z: Basic:  S42: (80268a0d55f2c889): Executing operation BaseRecalibratorTransform/Combine.Globally/Combine.PerKey/GroupByKey/Create
2015-09-09T08:12:57.758Z: Basic:  S18: (b6322df7e738bf55): Executing operation View.AsSingleton4/View.CreatePCollectionView
2015-09-09T08:12:57.812Z: Basic:  S43: (5d5740d15277ea32): Executing operation CoGroupByKey3/GroupByKey/Read+CoGroupByKey3/GroupByKey/GroupByWindow+CoGroupByKey3/ConstructCoGbkResultFn+joinReadwithContextData+BaseRecalibratorTransform/BaseRecalibrator+BaseRecalibratorTransform/Combine.Globally/WithKeys/AddKeys+BaseRecalibratorTransform/Combine.Globally/Combine.PerKey/GroupByKey+BaseRecalibratorTransform/Combine.Globally/Combine.PerKey/Combine.GroupedValues/Partial+BaseRecalibratorTransform/Combine.Globally/Combine.PerKey/GroupByKey/Reify+BaseRecalibratorTransform/Combine.Globally/Combine.PerKey/GroupByKey/Write
2015-09-09T08:12:57.933Z: Basic:  S14: (270ab46fb934785f): Executing operation View.AsSingleton3/View.CreatePCollectionView
2015-09-09T08:13:00.894Z: Basic:  S44: (a3dbcf0371b4adc0): Executing operation BaseRecalibratorTransform/Combine.Globally/Combine.PerKey/GroupByKey/Read+BaseRecalibratorTransform/Combine.Globally/Combine.PerKey/Combine.GroupedValues+BaseRecalibratorTransform/Combine.Globally/Combine.PerKey/Combine.GroupedValues/Extract+BaseRecalibratorTransform/Combine.Globally/Values/Values
2015-09-09T08:13:04.766Z: Basic:  S37: (d7305c954f3954ce): Executing operation Count.Globally4/View.AsIterable/View.CreatePCollectionView
2015-09-09T08:13:04.848Z: Basic:  S38: (85a0e2784da51723): Executing operation Count.Globally4/ProduceDefault+assertSameReads
2015-09-09T08:13:05.757Z: Basic:  S45: (5d5740d15277e51b): Executing operation BaseRecalibratorTransform/Combine.Globally/View.AsIterable/View.CreatePCollectionView
2015-09-09T08:13:05.847Z: Basic:  S46: (c1c701a525a7773): Executing operation BaseRecalibratorTransform/Combine.Globally/ProduceDefault+BaseRecalibratorTransform/finalizeRecalTables+BaseRecalibratorTransform/addQuantizationInfo+AnonymousParDo4+save to gs://hellbender/test/staging/temp-ds-recaltables.sj
2015-09-09T08:13:20.156Z: Basic:  (93121ca90a85db7b): Stopping worker pool...
2015-09-09T08:14:00.344Z: Basic:  (93121ca90a85d208): Worker pool stopped.
2015-09-09T08:14:00.482Z: Detail:  (5d5740d15277e839): Cleaning up.
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[08:14:12] Executing test BaseRecalibratorDataflowIntegrationTest:testBQSRFailWithIncompatibleReference
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[08:14:14] Executing test BaseRecalibratorDataflowIntegrationTest:testBQSRFailWithoutDBSNP
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[08:14:14] Executing test BaseRecalibratorDataflowIntegrationTest:testBQSR---apiKey AIzaSyDjKyy2KWcEVgtlOlJBdqy4O4oUVMxluE4 --project broad-dsde-dev 
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[08:14:40] Executing test BaseRecalibratorDataflowIntegrationTest:testBQSR---apiKey AIzaSyDjKyy2KWcEVgtlOlJBdqy4O4oUVMxluE4 --project broad-dsde-dev -knownSites src/test/resources/org/broadinstitute/hellbender/tools/BQSR/bqsr.fakeSitesForTesting.b37.chr17.vcf
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[08:15:04] Executing test BaseRecalibratorDataflowIntegrationTest:testBQSR---apiKey AIzaSyDjKyy2KWcEVgtlOlJBdqy4O4oUVMxluE4 --project broad-dsde-dev --indels_context_size 4
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[08:15:30] Executing test BaseRecalibratorDataflowIntegrationTest:testBQSR---apiKey AIzaSyDjKyy2KWcEVgtlOlJBdqy4O4oUVMxluE4 --project broad-dsde-dev --low_quality_tail 5
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[08:15:53] Executing test BaseRecalibratorDataflowIntegrationTest:testBQSR---apiKey AIzaSyDjKyy2KWcEVgtlOlJBdqy4O4oUVMxluE4 --project broad-dsde-dev --quantizing_levels 6
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[08:16:19] Executing test BaseRecalibratorDataflowIntegrationTest:testBQSR---apiKey AIzaSyDjKyy2KWcEVgtlOlJBdqy4O4oUVMxluE4 --project broad-dsde-dev --mismatches_context_size 4

[September 9, 2015 8:10:14 AM UTC] org.broadinstitute.hellbender.tools.dataflow.pipelines.BaseRecalibratorDataflow  --RECAL_TABLE_FILE /tmp/walktest.tmp_param.02478576192541456575.tmp --sort_by_all_columns true --input gs://hellbender/test/resources/org/broadinstitute/hellbender/tools/BQSR/CEUTrio.HiSeq.WGS.b37.ch20.1m-1m1k.NA12878.bam --reference gg://reference/EOSsjdnTicvzwAE --baseRecalibrationKnownVariants src/test/resources/org/broadinstitute/hellbender/tools/BQSR/dbsnp_132.b37.excluding_sites_after_129.chr17_69k_70k.vcf --project broad-dsde-dev --apiKey *********** --VERBOSITY ERROR  --run_without_dbsnp_potentially_ruining_quality false --solid_recal_mode SET_Q_ZERO --solid_nocall_strategy THROW_EXCEPTION --mismatches_context_size 2 --indels_context_size 3 --maximum_cycle_value 500 --mismatches_default_quality -1 --insertions_default_quality 45 --deletions_default_quality 45 --low_quality_tail 2 --quantizing_levels 16 --interval_set_rule UNION --interval_padding 0 --bqsrBAQGapOpenPenalty 40.0 --preserve_qscores_less_than 6 --useOriginalQualities false --defaultBaseQualities -1 --runner LOCAL --numWorkers 0 --help false --version false --QUIET false
[September 9, 2015 8:10:14 AM UTC] Executing as travis@testing-worker-linux-docker-75fb849c-3212-linux-2 on Linux 3.13.0-40-generic amd64; Java HotSpot(TM) 64-Bit Server VM 1.8.0_31-b13; Version: Version:null JdkDeflater
Sep 09, 2015 8:10:14 AM com.google.cloud.dataflow.sdk.runners.DirectPipelineRunner <init>
INFO: DirectPipelineRunner using random seed -1797979452473677200.
Sep 09, 2015 8:10:14 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coders for genomics classes
Sep 09, 2015 8:10:14 AM org.reflections.Reflections scan
INFO: Reflections took 254 ms to scan 250 urls, producing 79 keys and 156 values 
Sep 09, 2015 8:10:14 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for SearchVariantsResponse
Sep 09, 2015 8:10:14 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for ImportVariantsRequest
Sep 09, 2015 8:10:14 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for ExperimentalCreateJobResponse
Sep 09, 2015 8:10:14 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for SearchVariantSetsRequest
Sep 09, 2015 8:10:14 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for VariantSet
Sep 09, 2015 8:10:14 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for ExportVariantSetResponse
Sep 09, 2015 8:10:14 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for KeyValue
Sep 09, 2015 8:10:14 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for ListCoverageBucketsResponse
Sep 09, 2015 8:10:14 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for AlignReadGroupSetsResponse
Sep 09, 2015 8:10:14 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for ImportVariantsResponse
Sep 09, 2015 8:10:14 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for SearchReferenceSetsResponse
Sep 09, 2015 8:10:14 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for ReadGroupProgram
Sep 09, 2015 8:10:14 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for SearchCallSetsResponse
Sep 09, 2015 8:10:14 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for Reference
Sep 09, 2015 8:10:14 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for ExternalId
Sep 09, 2015 8:10:14 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for SearchReadsRequest
Sep 09, 2015 8:10:14 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for ExportVariantSetRequest
Sep 09, 2015 8:10:14 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for CallSet
Sep 09, 2015 8:10:14 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for JobRequest
Sep 09, 2015 8:10:14 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for Metadata
Sep 09, 2015 8:10:14 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for ReferenceSet
Sep 09, 2015 8:10:14 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for CallReadGroupSetsResponse
Sep 09, 2015 8:10:14 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for FastqMetadata
Sep 09, 2015 8:10:14 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for SearchVariantsRequest
Sep 09, 2015 8:10:14 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for SearchAnnotationSetsRequest
Sep 09, 2015 8:10:14 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for SearchReadGroupSetsRequest
Sep 09, 2015 8:10:14 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for CoverageBucket
Sep 09, 2015 8:10:14 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for SearchJobsResponse
Sep 09, 2015 8:10:14 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for ImportReadGroupSetsRequest
Sep 09, 2015 8:10:14 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for TranscriptCodingSequence
Sep 09, 2015 8:10:14 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for Variant
Sep 09, 2015 8:10:14 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for SearchReadGroupSetsResponse
Sep 09, 2015 8:10:14 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for SearchAnnotationsRequest
Sep 09, 2015 8:10:14 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for SearchVariantSetsResponse
Sep 09, 2015 8:10:14 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for InterleavedFastqSource
Sep 09, 2015 8:10:14 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for BatchCreateAnnotationsRequest
Sep 09, 2015 8:10:14 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for SearchReferencesRequest
Sep 09, 2015 8:10:14 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for SearchJobsRequest
Sep 09, 2015 8:10:14 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for AlignReadGroupSetsRequest
Sep 09, 2015 8:10:14 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for Job
Sep 09, 2015 8:10:14 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for TranscriptExon
Sep 09, 2015 8:10:14 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for SearchReferenceSetsRequest
Sep 09, 2015 8:10:14 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for QueryRange
Sep 09, 2015 8:10:14 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for LinearAlignment
Sep 09, 2015 8:10:14 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for Position
Sep 09, 2015 8:10:14 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for Annotation
Sep 09, 2015 8:10:14 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for SearchReadsResponse
Sep 09, 2015 8:10:14 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for ExperimentalCreateJobRequest
Sep 09, 2015 8:10:14 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for AnnotationSet
Sep 09, 2015 8:10:14 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for Dataset
Sep 09, 2015 8:10:14 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for Read
Sep 09, 2015 8:10:14 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for Call
Sep 09, 2015 8:10:14 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for ReadGroupExperiment
Sep 09, 2015 8:10:14 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for VariantAnnotationCondition
Sep 09, 2015 8:10:14 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for ReadGroup
Sep 09, 2015 8:10:14 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for VariantAnnotation
Sep 09, 2015 8:10:14 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for Int32Value
Sep 09, 2015 8:10:14 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for ExportReadGroupSetsRequest
Sep 09, 2015 8:10:14 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for ReferenceBound
Sep 09, 2015 8:10:14 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for ImportReadGroupSetsResponse
Sep 09, 2015 8:10:14 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for MergeVariantsRequest
Sep 09, 2015 8:10:14 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for CigarUnit
Sep 09, 2015 8:10:14 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for SearchAnnotationsResponse
Sep 09, 2015 8:10:14 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for BatchAnnotationsResponseEntry
Sep 09, 2015 8:10:14 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for CallReadGroupSetsRequest
Sep 09, 2015 8:10:14 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for ListBasesResponse
Sep 09, 2015 8:10:14 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for SearchReferencesResponse
Sep 09, 2015 8:10:14 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for PairedFastqSource
Sep 09, 2015 8:10:14 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for BatchAnnotationsResponse
Sep 09, 2015 8:10:14 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for SearchCallSetsRequest
Sep 09, 2015 8:10:14 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for RangePosition
Sep 09, 2015 8:10:14 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for Transcript
Sep 09, 2015 8:10:14 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for BatchAnnotationsResponseEntryStatus
Sep 09, 2015 8:10:14 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for ExportReadGroupSetsResponse
Sep 09, 2015 8:10:14 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for SearchAnnotationSetsResponse
Sep 09, 2015 8:10:14 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for ListDatasetsResponse
Sep 09, 2015 8:10:14 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for ReadGroupSet
Sep 09, 2015 8:10:14 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for Range
Sep 09, 2015 8:10:14 AM com.google.cloud.genomics.dataflow.utils.GCSOptions$Methods createStorageClient
INFO: Creating storgae client for DataflowCommandLineProgram
Sep 09, 2015 8:10:14 AM com.google.cloud.genomics.dataflow.readers.bam.SeekableGCSStream <init>
INFO: Creating SeekableGCSStream: gs://hellbender/test/resources/org/broadinstitute/hellbender/tools/BQSR/CEUTrio.HiSeq.WGS.b37.ch20.1m-1m1k.NA12878.bam.bai
Sep 09, 2015 8:10:14 AM com.google.cloud.genomics.dataflow.readers.bam.SeekableGCSStream uriToStorageObject
INFO: uriToStorageObject hellbender/test/resources/org/broadinstitute/hellbender/tools/BQSR/CEUTrio.HiSeq.WGS.b37.ch20.1m-1m1k.NA12878.bam.bai=hellbender:test/resources/org/broadinstitute/hellbender/tools/BQSR/CEUTrio.HiSeq.WGS.b37.ch20.1m-1m1k.NA12878.bam.bai
Sep 09, 2015 8:10:14 AM com.google.cloud.genomics.dataflow.readers.bam.SeekableGCSStream <init>
INFO: Creating SeekableGCSStream: gs://hellbender/test/resources/org/broadinstitute/hellbender/tools/BQSR/CEUTrio.HiSeq.WGS.b37.ch20.1m-1m1k.NA12878.bam
Sep 09, 2015 8:10:14 AM com.google.cloud.genomics.dataflow.readers.bam.SeekableGCSStream uriToStorageObject
INFO: uriToStorageObject hellbender/test/resources/org/broadinstitute/hellbender/tools/BQSR/CEUTrio.HiSeq.WGS.b37.ch20.1m-1m1k.NA12878.bam=hellbender:test/resources/org/broadinstitute/hellbender/tools/BQSR/CEUTrio.HiSeq.WGS.b37.ch20.1m-1m1k.NA12878.bam
Sep 09, 2015 8:10:14 AM com.google.cloud.genomics.dataflow.readers.bam.BAMIO openBAMFile
INFO: getReadsFromBAMFile - got input resources
Sep 09, 2015 8:10:14 AM com.google.cloud.genomics.dataflow.readers.bam.Sharder process
INFO: Processing BAM file gs://hellbender/test/resources/org/broadinstitute/hellbender/tools/BQSR/CEUTrio.HiSeq.WGS.b37.ch20.1m-1m1k.NA12878.bam
Sep 09, 2015 8:10:14 AM com.google.cloud.genomics.dataflow.readers.bam.SeekableGCSStream <init>
INFO: Creating SeekableGCSStream: gs://hellbender/test/resources/org/broadinstitute/hellbender/tools/BQSR/CEUTrio.HiSeq.WGS.b37.ch20.1m-1m1k.NA12878.bam.bai
Sep 09, 2015 8:10:14 AM com.google.cloud.genomics.dataflow.readers.bam.SeekableGCSStream uriToStorageObject
INFO: uriToStorageObject hellbender/test/resources/org/broadinstitute/hellbender/tools/BQSR/CEUTrio.HiSeq.WGS.b37.ch20.1m-1m1k.NA12878.bam.bai=hellbender:test/resources/org/broadinstitute/hellbender/tools/BQSR/CEUTrio.HiSeq.WGS.b37.ch20.1m-1m1k.NA12878.bam.bai
Sep 09, 2015 8:10:14 AM com.google.cloud.genomics.dataflow.readers.bam.SeekableGCSStream <init>
INFO: Creating SeekableGCSStream: gs://hellbender/test/resources/org/broadinstitute/hellbender/tools/BQSR/CEUTrio.HiSeq.WGS.b37.ch20.1m-1m1k.NA12878.bam
Sep 09, 2015 8:10:14 AM com.google.cloud.genomics.dataflow.readers.bam.SeekableGCSStream uriToStorageObject
INFO: uriToStorageObject hellbender/test/resources/org/broadinstitute/hellbender/tools/BQSR/CEUTrio.HiSeq.WGS.b37.ch20.1m-1m1k.NA12878.bam=hellbender:test/resources/org/broadinstitute/hellbender/tools/BQSR/CEUTrio.HiSeq.WGS.b37.ch20.1m-1m1k.NA12878.bam
Sep 09, 2015 8:10:14 AM com.google.cloud.genomics.dataflow.readers.bam.BAMIO openBAMFile
INFO: getReadsFromBAMFile - got input resources
Sep 09, 2015 8:10:15 AM com.google.cloud.genomics.dataflow.readers.bam.Sharder openFile
INFO: Has index = true
Sep 09, 2015 8:10:15 AM com.google.cloud.genomics.dataflow.readers.bam.Sharder processHeader
INFO: All references = false
Sep 09, 2015 8:10:15 AM com.google.cloud.genomics.dataflow.readers.bam.Sharder processHeader
INFO: BAM has index = true
Sep 09, 2015 8:10:15 AM com.google.cloud.genomics.dataflow.readers.bam.Sharder processHeader
INFO: BAM has browseable index = true
Sep 09, 2015 8:10:15 AM com.google.cloud.genomics.dataflow.readers.bam.Sharder processHeader
INFO: Class for index = htsjdk.samtools.CachingBAMFileIndex
Sep 09, 2015 8:10:16 AM com.google.cloud.genomics.dataflow.readers.bam.Sharder createShardsForReference
INFO: Outputting last shard of size 16383, 538459 bytes
Sep 09, 2015 8:10:21 AM com.google.cloud.dataflow.sdk.Pipeline applyInternal
WARNING: Transform Create.Values2 does not have a stable unique name. This will prevent reloading of pipelines.
Sep 09, 2015 8:10:22 AM com.google.cloud.dataflow.sdk.Pipeline applyInternal
WARNING: Transform Create.Values3 does not have a stable unique name. This will prevent reloading of pipelines.
Sep 09, 2015 8:10:22 AM com.google.cloud.dataflow.sdk.Pipeline applyInternal
WARNING: Transform View.AsSingleton2 does not have a stable unique name. This will prevent reloading of pipelines.
Sep 09, 2015 8:10:22 AM com.google.cloud.dataflow.sdk.Pipeline applyInternal
WARNING: Transform Create.Values4 does not have a stable unique name. This will prevent reloading of pipelines.
Sep 09, 2015 8:10:22 AM com.google.cloud.dataflow.sdk.Pipeline applyInternal
WARNING: Transform AnonymousParDo2 does not have a stable unique name. This will prevent reloading of pipelines.
Sep 09, 2015 8:10:22 AM com.google.cloud.dataflow.sdk.Pipeline applyInternal
WARNING: Transform RemoveDuplicateReadVariantPairs/AnonymousParDo2 does not have a stable unique name. This will prevent reloading of pipelines.
Sep 09, 2015 8:10:22 AM com.google.cloud.dataflow.sdk.Pipeline applyInternal
WARNING: Transform RemoveDuplicateReadVariantPairs/CoGroupByKey2 does not have a stable unique name. This will prevent reloading of pipelines.
Sep 09, 2015 8:10:22 AM com.google.cloud.dataflow.sdk.Pipeline applyInternal
WARNING: Transform RemoveDuplicateReadVariantPairs/AnonymousParDo3 does not have a stable unique name. This will prevent reloading of pipelines.
Sep 09, 2015 8:10:22 AM com.google.cloud.dataflow.sdk.Pipeline applyInternal
WARNING: Transform AnonymousParDo3 does not have a stable unique name. This will prevent reloading of pipelines.
Sep 09, 2015 8:10:22 AM com.google.cloud.dataflow.sdk.Pipeline applyInternal
WARNING: Transform AddContextDataToRead.StripToUUID2 does not have a stable unique name. This will prevent reloading of pipelines.
Sep 09, 2015 8:10:22 AM com.google.cloud.dataflow.sdk.Pipeline applyInternal
WARNING: Transform Keys2 does not have a stable unique name. This will prevent reloading of pipelines.
Sep 09, 2015 8:10:22 AM com.google.cloud.dataflow.sdk.Pipeline applyInternal
WARNING: Transform AddContextDataToRead.StripToUUID3 does not have a stable unique name. This will prevent reloading of pipelines.
Sep 09, 2015 8:10:22 AM com.google.cloud.dataflow.sdk.Pipeline applyInternal
WARNING: Transform View.AsSingleton3 does not have a stable unique name. This will prevent reloading of pipelines.
Sep 09, 2015 8:10:22 AM com.google.cloud.dataflow.sdk.Pipeline applyInternal
WARNING: Transform Count.Globally2 does not have a stable unique name. This will prevent reloading of pipelines.
Sep 09, 2015 8:10:22 AM com.google.cloud.dataflow.sdk.Pipeline applyInternal
WARNING: Transform View.AsSingleton4 does not have a stable unique name. This will prevent reloading of pipelines.
Sep 09, 2015 8:10:22 AM com.google.cloud.dataflow.sdk.Pipeline applyInternal
WARNING: Transform Count.Globally3 does not have a stable unique name. This will prevent reloading of pipelines.
Sep 09, 2015 8:10:22 AM com.google.cloud.dataflow.sdk.Pipeline applyInternal
WARNING: Transform View.AsSingleton5 does not have a stable unique name. This will prevent reloading of pipelines.
Sep 09, 2015 8:10:22 AM com.google.cloud.dataflow.sdk.Pipeline applyInternal
WARNING: Transform Count.Globally4 does not have a stable unique name. This will prevent reloading of pipelines.
Sep 09, 2015 8:10:22 AM com.google.cloud.dataflow.sdk.Pipeline applyInternal
WARNING: Transform CoGroupByKey2 does not have a stable unique name. This will prevent reloading of pipelines.
Sep 09, 2015 8:10:22 AM com.google.cloud.dataflow.sdk.Pipeline applyInternal
WARNING: Transform CoGroupByKey3 does not have a stable unique name. This will prevent reloading of pipelines.
Sep 09, 2015 8:10:22 AM com.google.cloud.dataflow.sdk.Pipeline applyInternal
WARNING: Transform AnonymousParDo4 does not have a stable unique name. This will prevent reloading of pipelines.
Sep 09, 2015 8:10:22 AM com.google.cloud.dataflow.sdk.runners.DirectPipelineRunner run
INFO: Executing pipeline using the DirectPipelineRunner.
Sep 09, 2015 8:10:23 AM com.google.cloud.genomics.dataflow.readers.bam.Reader openFile
INFO: Processing shard gs://hellbender/test/resources/org/broadinstitute/hellbender/tools/BQSR/CEUTrio.HiSeq.WGS.b37.ch20.1m-1m1k.NA12878.bam: 20:999425:63025521, locus size = 62026096, span size = 538459
Sep 09, 2015 8:10:23 AM com.google.cloud.genomics.dataflow.readers.bam.SeekableGCSStream <init>
INFO: Creating SeekableGCSStream: gs://hellbender/test/resources/org/broadinstitute/hellbender/tools/BQSR/CEUTrio.HiSeq.WGS.b37.ch20.1m-1m1k.NA12878.bam.bai
Sep 09, 2015 8:10:23 AM com.google.cloud.genomics.dataflow.readers.bam.SeekableGCSStream uriToStorageObject
INFO: uriToStorageObject hellbender/test/resources/org/broadinstitute/hellbender/tools/BQSR/CEUTrio.HiSeq.WGS.b37.ch20.1m-1m1k.NA12878.bam.bai=hellbender:test/resources/org/broadinstitute/hellbender/tools/BQSR/CEUTrio.HiSeq.WGS.b37.ch20.1m-1m1k.NA12878.bam.bai
Sep 09, 2015 8:10:23 AM com.google.cloud.genomics.dataflow.readers.bam.SeekableGCSStream <init>
INFO: Creating SeekableGCSStream: gs://hellbender/test/resources/org/broadinstitute/hellbender/tools/BQSR/CEUTrio.HiSeq.WGS.b37.ch20.1m-1m1k.NA12878.bam
Sep 09, 2015 8:10:23 AM com.google.cloud.genomics.dataflow.readers.bam.SeekableGCSStream uriToStorageObject
INFO: uriToStorageObject hellbender/test/resources/org/broadinstitute/hellbender/tools/BQSR/CEUTrio.HiSeq.WGS.b37.ch20.1m-1m1k.NA12878.bam=hellbender:test/resources/org/broadinstitute/hellbender/tools/BQSR/CEUTrio.HiSeq.WGS.b37.ch20.1m-1m1k.NA12878.bam
Sep 09, 2015 8:10:23 AM com.google.cloud.genomics.dataflow.readers.bam.BAMIO openBAMFile
INFO: getReadsFromBAMFile - got input resources
Sep 09, 2015 8:10:23 AM com.google.cloud.genomics.dataflow.readers.bam.Reader openFile
INFO: Processing span
Sep 09, 2015 8:10:23 AM com.google.cloud.genomics.dataflow.readers.bam.Reader dumpStats
INFO: Processed 1497 in 559.6 ms. Speed: 2677 reads/sec, skipped other sequences 13, skippedBefore 0, skipped after 0
Sep 09, 2015 8:10:44 AM com.google.cloud.dataflow.sdk.runners.DirectPipelineRunner run
INFO: Pipeline execution complete.
[September 9, 2015 8:10:48 AM UTC] org.broadinstitute.hellbender.tools.dataflow.pipelines.BaseRecalibratorDataflow done. Elapsed time: 0.58 minutes.
Runtime.totalMemory()=1296564224
[September 9, 2015 8:10:49 AM UTC] org.broadinstitute.hellbender.tools.dataflow.pipelines.BaseRecalibratorDataflow  --RECAL_TABLE_FILE /tmp/walktest.tmp_param.019932303570288076.tmp --sort_by_all_columns true --input gs://hellbender/test/resources/org/broadinstitute/hellbender/tools/BQSR/CEUTrio.HiSeq.WGS.b37.ch20.1m-1m1k.NA12878.bam --reference gg://reference/EOSsjdnTicvzwAE --baseRecalibrationKnownVariants src/test/resources/org/broadinstitute/hellbender/tools/BQSR/dbsnp_132.b37.excluding_sites_after_129.chr17_69k_70k.vcf --runner BLOCKING --project broad-dsde-dev --staging gs://hellbender/test/staging/ --apiKey *********** --VERBOSITY ERROR  --run_without_dbsnp_potentially_ruining_quality false --solid_recal_mode SET_Q_ZERO --solid_nocall_strategy THROW_EXCEPTION --mismatches_context_size 2 --indels_context_size 3 --maximum_cycle_value 500 --mismatches_default_quality -1 --insertions_default_quality 45 --deletions_default_quality 45 --low_quality_tail 2 --quantizing_levels 16 --interval_set_rule UNION --interval_padding 0 --bqsrBAQGapOpenPenalty 40.0 --preserve_qscores_less_than 6 --useOriginalQualities false --defaultBaseQualities -1 --numWorkers 0 --help false --version false --QUIET false
[September 9, 2015 8:10:49 AM UTC] Executing as travis@testing-worker-linux-docker-75fb849c-3212-linux-2 on Linux 3.13.0-40-generic amd64; Java HotSpot(TM) 64-Bit Server VM 1.8.0_31-b13; Version: Version:null JdkDeflater
Sep 09, 2015 8:10:49 AM com.google.cloud.dataflow.sdk.runners.DataflowPipelineRunner fromOptions
INFO: PipelineOptions.filesToStage was not specified. Defaulting to files from the classpath: will stage 241 files. Enable logging at DEBUG level to see which files will be staged.
Sep 09, 2015 8:10:49 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coders for genomics classes
Sep 09, 2015 8:10:49 AM org.reflections.Reflections scan
INFO: Reflections took 138 ms to scan 250 urls, producing 79 keys and 156 values 
Sep 09, 2015 8:10:49 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for SearchVariantsResponse
Sep 09, 2015 8:10:49 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for ImportVariantsRequest
Sep 09, 2015 8:10:49 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for ExperimentalCreateJobResponse
Sep 09, 2015 8:10:49 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for SearchVariantSetsRequest
Sep 09, 2015 8:10:49 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for VariantSet
Sep 09, 2015 8:10:49 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for ExportVariantSetResponse
Sep 09, 2015 8:10:49 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for KeyValue
Sep 09, 2015 8:10:49 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for ListCoverageBucketsResponse
Sep 09, 2015 8:10:49 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for AlignReadGroupSetsResponse
Sep 09, 2015 8:10:49 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for ImportVariantsResponse
Sep 09, 2015 8:10:49 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for SearchReferenceSetsResponse
Sep 09, 2015 8:10:49 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for ReadGroupProgram
Sep 09, 2015 8:10:49 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for SearchCallSetsResponse
Sep 09, 2015 8:10:49 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for Reference
Sep 09, 2015 8:10:49 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for ExternalId
Sep 09, 2015 8:10:49 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for SearchReadsRequest
Sep 09, 2015 8:10:49 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for ExportVariantSetRequest
Sep 09, 2015 8:10:49 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for CallSet
Sep 09, 2015 8:10:49 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for JobRequest
Sep 09, 2015 8:10:49 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for Metadata
Sep 09, 2015 8:10:49 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for ReferenceSet
Sep 09, 2015 8:10:49 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for CallReadGroupSetsResponse
Sep 09, 2015 8:10:49 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for FastqMetadata
Sep 09, 2015 8:10:49 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for SearchVariantsRequest
Sep 09, 2015 8:10:49 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for SearchAnnotationSetsRequest
Sep 09, 2015 8:10:49 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for SearchReadGroupSetsRequest
Sep 09, 2015 8:10:49 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for CoverageBucket
Sep 09, 2015 8:10:49 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for SearchJobsResponse
Sep 09, 2015 8:10:49 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for ImportReadGroupSetsRequest
Sep 09, 2015 8:10:49 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for TranscriptCodingSequence
Sep 09, 2015 8:10:49 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for Variant
Sep 09, 2015 8:10:49 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for SearchReadGroupSetsResponse
Sep 09, 2015 8:10:49 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for SearchAnnotationsRequest
Sep 09, 2015 8:10:49 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for SearchVariantSetsResponse
Sep 09, 2015 8:10:49 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for InterleavedFastqSource
Sep 09, 2015 8:10:49 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for BatchCreateAnnotationsRequest
Sep 09, 2015 8:10:49 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for SearchReferencesRequest
Sep 09, 2015 8:10:49 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for SearchJobsRequest
Sep 09, 2015 8:10:49 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for AlignReadGroupSetsRequest
Sep 09, 2015 8:10:49 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for Job
Sep 09, 2015 8:10:49 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for TranscriptExon
Sep 09, 2015 8:10:49 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for SearchReferenceSetsRequest
Sep 09, 2015 8:10:49 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for QueryRange
Sep 09, 2015 8:10:49 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for LinearAlignment
Sep 09, 2015 8:10:49 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for Position
Sep 09, 2015 8:10:49 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for Annotation
Sep 09, 2015 8:10:49 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for SearchReadsResponse
Sep 09, 2015 8:10:49 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for ExperimentalCreateJobRequest
Sep 09, 2015 8:10:49 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for AnnotationSet
Sep 09, 2015 8:10:49 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for Dataset
Sep 09, 2015 8:10:49 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for Read
Sep 09, 2015 8:10:49 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for Call
Sep 09, 2015 8:10:49 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for ReadGroupExperiment
Sep 09, 2015 8:10:49 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for VariantAnnotationCondition
Sep 09, 2015 8:10:49 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for ReadGroup
Sep 09, 2015 8:10:49 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for VariantAnnotation
Sep 09, 2015 8:10:49 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for Int32Value
Sep 09, 2015 8:10:49 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for ExportReadGroupSetsRequest
Sep 09, 2015 8:10:49 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for ReferenceBound
Sep 09, 2015 8:10:49 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for ImportReadGroupSetsResponse
Sep 09, 2015 8:10:49 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for MergeVariantsRequest
Sep 09, 2015 8:10:49 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for CigarUnit
Sep 09, 2015 8:10:49 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for SearchAnnotationsResponse
Sep 09, 2015 8:10:49 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for BatchAnnotationsResponseEntry
Sep 09, 2015 8:10:49 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for CallReadGroupSetsRequest
Sep 09, 2015 8:10:49 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for ListBasesResponse
Sep 09, 2015 8:10:49 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for SearchReferencesResponse
Sep 09, 2015 8:10:49 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for PairedFastqSource
Sep 09, 2015 8:10:49 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for BatchAnnotationsResponse
Sep 09, 2015 8:10:49 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for SearchCallSetsRequest
Sep 09, 2015 8:10:49 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for RangePosition
Sep 09, 2015 8:10:49 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for Transcript
Sep 09, 2015 8:10:49 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for BatchAnnotationsResponseEntryStatus
Sep 09, 2015 8:10:49 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for ExportReadGroupSetsResponse
Sep 09, 2015 8:10:49 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for SearchAnnotationSetsResponse
Sep 09, 2015 8:10:49 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for ListDatasetsResponse
Sep 09, 2015 8:10:49 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for ReadGroupSet
Sep 09, 2015 8:10:49 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for Range
Sep 09, 2015 8:10:49 AM com.google.cloud.genomics.dataflow.utils.GCSOptions$Methods createStorageClient
INFO: Creating storgae client for DataflowCommandLineProgram
Sep 09, 2015 8:10:49 AM com.google.cloud.genomics.dataflow.readers.bam.SeekableGCSStream <init>
INFO: Creating SeekableGCSStream: gs://hellbender/test/resources/org/broadinstitute/hellbender/tools/BQSR/CEUTrio.HiSeq.WGS.b37.ch20.1m-1m1k.NA12878.bam.bai
Sep 09, 2015 8:10:49 AM com.google.cloud.genomics.dataflow.readers.bam.SeekableGCSStream uriToStorageObject
INFO: uriToStorageObject hellbender/test/resources/org/broadinstitute/hellbender/tools/BQSR/CEUTrio.HiSeq.WGS.b37.ch20.1m-1m1k.NA12878.bam.bai=hellbender:test/resources/org/broadinstitute/hellbender/tools/BQSR/CEUTrio.HiSeq.WGS.b37.ch20.1m-1m1k.NA12878.bam.bai
Sep 09, 2015 8:10:49 AM com.google.cloud.genomics.dataflow.readers.bam.SeekableGCSStream <init>
INFO: Creating SeekableGCSStream: gs://hellbender/test/resources/org/broadinstitute/hellbender/tools/BQSR/CEUTrio.HiSeq.WGS.b37.ch20.1m-1m1k.NA12878.bam
Sep 09, 2015 8:10:49 AM com.google.cloud.genomics.dataflow.readers.bam.SeekableGCSStream uriToStorageObject
INFO: uriToStorageObject hellbender/test/resources/org/broadinstitute/hellbender/tools/BQSR/CEUTrio.HiSeq.WGS.b37.ch20.1m-1m1k.NA12878.bam=hellbender:test/resources/org/broadinstitute/hellbender/tools/BQSR/CEUTrio.HiSeq.WGS.b37.ch20.1m-1m1k.NA12878.bam
Sep 09, 2015 8:10:49 AM com.google.cloud.genomics.dataflow.readers.bam.BAMIO openBAMFile
INFO: getReadsFromBAMFile - got input resources
Sep 09, 2015 8:10:49 AM com.google.cloud.genomics.dataflow.readers.bam.Sharder process
INFO: Processing BAM file gs://hellbender/test/resources/org/broadinstitute/hellbender/tools/BQSR/CEUTrio.HiSeq.WGS.b37.ch20.1m-1m1k.NA12878.bam
Sep 09, 2015 8:10:49 AM com.google.cloud.genomics.dataflow.readers.bam.SeekableGCSStream <init>
INFO: Creating SeekableGCSStream: gs://hellbender/test/resources/org/broadinstitute/hellbender/tools/BQSR/CEUTrio.HiSeq.WGS.b37.ch20.1m-1m1k.NA12878.bam.bai
Sep 09, 2015 8:10:49 AM com.google.cloud.genomics.dataflow.readers.bam.SeekableGCSStream uriToStorageObject
INFO: uriToStorageObject hellbender/test/resources/org/broadinstitute/hellbender/tools/BQSR/CEUTrio.HiSeq.WGS.b37.ch20.1m-1m1k.NA12878.bam.bai=hellbender:test/resources/org/broadinstitute/hellbender/tools/BQSR/CEUTrio.HiSeq.WGS.b37.ch20.1m-1m1k.NA12878.bam.bai
Sep 09, 2015 8:10:49 AM com.google.cloud.genomics.dataflow.readers.bam.SeekableGCSStream <init>
INFO: Creating SeekableGCSStream: gs://hellbender/test/resources/org/broadinstitute/hellbender/tools/BQSR/CEUTrio.HiSeq.WGS.b37.ch20.1m-1m1k.NA12878.bam
Sep 09, 2015 8:10:49 AM com.google.cloud.genomics.dataflow.readers.bam.SeekableGCSStream uriToStorageObject
INFO: uriToStorageObject hellbender/test/resources/org/broadinstitute/hellbender/tools/BQSR/CEUTrio.HiSeq.WGS.b37.ch20.1m-1m1k.NA12878.bam=hellbender:test/resources/org/broadinstitute/hellbender/tools/BQSR/CEUTrio.HiSeq.WGS.b37.ch20.1m-1m1k.NA12878.bam
Sep 09, 2015 8:10:49 AM com.google.cloud.genomics.dataflow.readers.bam.BAMIO openBAMFile
INFO: getReadsFromBAMFile - got input resources
Sep 09, 2015 8:10:50 AM com.google.cloud.genomics.dataflow.readers.bam.Sharder openFile
INFO: Has index = true
Sep 09, 2015 8:10:50 AM com.google.cloud.genomics.dataflow.readers.bam.Sharder processHeader
INFO: All references = false
Sep 09, 2015 8:10:50 AM com.google.cloud.genomics.dataflow.readers.bam.Sharder processHeader
INFO: BAM has index = true
Sep 09, 2015 8:10:50 AM com.google.cloud.genomics.dataflow.readers.bam.Sharder processHeader
INFO: BAM has browseable index = true
Sep 09, 2015 8:10:50 AM com.google.cloud.genomics.dataflow.readers.bam.Sharder processHeader
INFO: Class for index = htsjdk.samtools.CachingBAMFileIndex
Sep 09, 2015 8:10:51 AM com.google.cloud.genomics.dataflow.readers.bam.Sharder createShardsForReference
INFO: Outputting last shard of size 16383, 538459 bytes
Sep 09, 2015 8:10:56 AM com.google.cloud.dataflow.sdk.Pipeline applyInternal
WARNING: Transform Create.Values2 does not have a stable unique name. This will prevent reloading of pipelines.
Sep 09, 2015 8:10:57 AM com.google.cloud.dataflow.sdk.Pipeline applyInternal
WARNING: Transform Create.Values3 does not have a stable unique name. This will prevent reloading of pipelines.
Sep 09, 2015 8:10:57 AM com.google.cloud.dataflow.sdk.Pipeline applyInternal
WARNING: Transform View.AsSingleton2 does not have a stable unique name. This will prevent reloading of pipelines.
Sep 09, 2015 8:10:57 AM com.google.cloud.dataflow.sdk.Pipeline applyInternal
WARNING: Transform Create.Values4 does not have a stable unique name. This will prevent reloading of pipelines.
Sep 09, 2015 8:10:57 AM com.google.cloud.dataflow.sdk.Pipeline applyInternal
WARNING: Transform AnonymousParDo2 does not have a stable unique name. This will prevent reloading of pipelines.
Sep 09, 2015 8:10:57 AM com.google.cloud.dataflow.sdk.Pipeline applyInternal
WARNING: Transform RemoveDuplicateReadVariantPairs/AnonymousParDo2 does not have a stable unique name. This will prevent reloading of pipelines.
Sep 09, 2015 8:10:57 AM com.google.cloud.dataflow.sdk.Pipeline applyInternal
WARNING: Transform RemoveDuplicateReadVariantPairs/CoGroupByKey2 does not have a stable unique name. This will prevent reloading of pipelines.
Sep 09, 2015 8:10:57 AM com.google.cloud.dataflow.sdk.Pipeline applyInternal
WARNING: Transform RemoveDuplicateReadVariantPairs/AnonymousParDo3 does not have a stable unique name. This will prevent reloading of pipelines.
Sep 09, 2015 8:10:57 AM com.google.cloud.dataflow.sdk.Pipeline applyInternal
WARNING: Transform AnonymousParDo3 does not have a stable unique name. This will prevent reloading of pipelines.
Sep 09, 2015 8:10:57 AM com.google.cloud.dataflow.sdk.Pipeline applyInternal
WARNING: Transform AddContextDataToRead.StripToUUID2 does not have a stable unique name. This will prevent reloading of pipelines.
Sep 09, 2015 8:10:57 AM com.google.cloud.dataflow.sdk.Pipeline applyInternal
WARNING: Transform Keys2 does not have a stable unique name. This will prevent reloading of pipelines.
Sep 09, 2015 8:10:57 AM com.google.cloud.dataflow.sdk.Pipeline applyInternal
WARNING: Transform AddContextDataToRead.StripToUUID3 does not have a stable unique name. This will prevent reloading of pipelines.
Sep 09, 2015 8:10:57 AM com.google.cloud.dataflow.sdk.Pipeline applyInternal
WARNING: Transform View.AsSingleton3 does not have a stable unique name. This will prevent reloading of pipelines.
Sep 09, 2015 8:10:57 AM com.google.cloud.dataflow.sdk.Pipeline applyInternal
WARNING: Transform Count.Globally2 does not have a stable unique name. This will prevent reloading of pipelines.
Sep 09, 2015 8:10:57 AM com.google.cloud.dataflow.sdk.Pipeline applyInternal
WARNING: Transform View.AsSingleton4 does not have a stable unique name. This will prevent reloading of pipelines.
Sep 09, 2015 8:10:57 AM com.google.cloud.dataflow.sdk.Pipeline applyInternal
WARNING: Transform Count.Globally3 does not have a stable unique name. This will prevent reloading of pipelines.
Sep 09, 2015 8:10:57 AM com.google.cloud.dataflow.sdk.Pipeline applyInternal
WARNING: Transform View.AsSingleton5 does not have a stable unique name. This will prevent reloading of pipelines.
Sep 09, 2015 8:10:57 AM com.google.cloud.dataflow.sdk.Pipeline applyInternal
WARNING: Transform Count.Globally4 does not have a stable unique name. This will prevent reloading of pipelines.
Sep 09, 2015 8:10:57 AM com.google.cloud.dataflow.sdk.Pipeline applyInternal
WARNING: Transform CoGroupByKey2 does not have a stable unique name. This will prevent reloading of pipelines.
Sep 09, 2015 8:10:57 AM com.google.cloud.dataflow.sdk.Pipeline applyInternal
WARNING: Transform CoGroupByKey3 does not have a stable unique name. This will prevent reloading of pipelines.
Sep 09, 2015 8:10:57 AM com.google.cloud.dataflow.sdk.Pipeline applyInternal
WARNING: Transform AnonymousParDo4 does not have a stable unique name. This will prevent reloading of pipelines.
Sep 09, 2015 8:10:57 AM com.google.cloud.dataflow.sdk.runners.DataflowPipelineRunner run
INFO: Executing pipeline on the Dataflow Service, which will have billing implications related to Google Compute Engine usage and other Google Cloud Services.
Sep 09, 2015 8:10:57 AM com.google.cloud.dataflow.sdk.util.PackageUtil stageClasspathElements
INFO: Uploading 241 files from PipelineOptions.filesToStage to staging location to prepare for execution.
Sep 09, 2015 8:11:17 AM com.google.cloud.dataflow.sdk.util.PackageUtil stageClasspathElements
INFO: Uploading PipelineOptions.filesToStage complete: 0 files newly uploaded, 241 files cached
Sep 09, 2015 8:11:18 AM com.google.cloud.dataflow.sdk.runners.DataflowPipelineRunner run
INFO: To access the Dataflow monitoring console, please navigate to https://console.developers.google.com/project/broad-dsde-dev/dataflow/job/2015-09-09_01_11_18-302232699834402856
Sep 09, 2015 8:11:18 AM com.google.cloud.dataflow.sdk.runners.DataflowPipelineRunner run
INFO: To cancel the job using the 'gcloud' tool, run:
> gcloud alpha dataflow jobs --project=broad-dsde-dev cancel 2015-09-09_01_11_18-302232699834402856
Sep 09, 2015 8:14:04 AM com.google.cloud.dataflow.sdk.runners.BlockingDataflowPipelineRunner run
INFO: Job finished with status DONE
[September 9, 2015 8:14:12 AM UTC] org.broadinstitute.hellbender.tools.dataflow.pipelines.BaseRecalibratorDataflow done. Elapsed time: 3.39 minutes.
Runtime.totalMemory()=1321730048
[September 9, 2015 8:14:12 AM UTC] org.broadinstitute.hellbender.tools.dataflow.pipelines.BaseRecalibratorDataflow  --RECAL_TABLE_FILE /tmp/walktest.tmp_param.05338751133662250033.tmp --sort_by_all_columns true --input src/test/resources/org/broadinstitute/hellbender/tools/BQSR/NA12878.chr17_69k_70k.dictFix.bam --reference gg://reference/EMWV_ZfLxrDY-wE --baseRecalibrationKnownVariants src/test/resources/org/broadinstitute/hellbender/tools/BQSR/dbsnp_132.b37.excluding_sites_after_129.chr17_69k_70k.vcf --project broad-dsde-dev --apiKey *********** --VERBOSITY ERROR  --run_without_dbsnp_potentially_ruining_quality false --solid_recal_mode SET_Q_ZERO --solid_nocall_strategy THROW_EXCEPTION --mismatches_context_size 2 --indels_context_size 3 --maximum_cycle_value 500 --mismatches_default_quality -1 --insertions_default_quality 45 --deletions_default_quality 45 --low_quality_tail 2 --quantizing_levels 16 --interval_set_rule UNION --interval_padding 0 --bqsrBAQGapOpenPenalty 40.0 --preserve_qscores_less_than 6 --useOriginalQualities false --defaultBaseQualities -1 --runner LOCAL --numWorkers 0 --help false --version false --QUIET false
[September 9, 2015 8:14:12 AM UTC] Executing as travis@testing-worker-linux-docker-75fb849c-3212-linux-2 on Linux 3.13.0-40-generic amd64; Java HotSpot(TM) 64-Bit Server VM 1.8.0_31-b13; Version: Version:null JdkDeflater
Sep 09, 2015 8:14:12 AM com.google.cloud.dataflow.sdk.runners.DirectPipelineRunner <init>
INFO: DirectPipelineRunner using random seed -4186392981047174541.
Sep 09, 2015 8:14:12 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coders for genomics classes
Sep 09, 2015 8:14:12 AM org.reflections.Reflections scan
INFO: Reflections took 197 ms to scan 250 urls, producing 79 keys and 156 values 
Sep 09, 2015 8:14:12 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for SearchVariantsResponse
Sep 09, 2015 8:14:12 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for ImportVariantsRequest
Sep 09, 2015 8:14:12 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for ExperimentalCreateJobResponse
Sep 09, 2015 8:14:12 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for SearchVariantSetsRequest
Sep 09, 2015 8:14:12 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for VariantSet
Sep 09, 2015 8:14:12 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for ExportVariantSetResponse
Sep 09, 2015 8:14:12 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for KeyValue
Sep 09, 2015 8:14:12 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for ListCoverageBucketsResponse
Sep 09, 2015 8:14:12 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for AlignReadGroupSetsResponse
Sep 09, 2015 8:14:12 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for ImportVariantsResponse
Sep 09, 2015 8:14:12 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for SearchReferenceSetsResponse
Sep 09, 2015 8:14:12 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for ReadGroupProgram
Sep 09, 2015 8:14:12 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for SearchCallSetsResponse
Sep 09, 2015 8:14:12 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for Reference
Sep 09, 2015 8:14:12 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for ExternalId
Sep 09, 2015 8:14:12 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for SearchReadsRequest
Sep 09, 2015 8:14:12 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for ExportVariantSetRequest
Sep 09, 2015 8:14:12 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for CallSet
Sep 09, 2015 8:14:12 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for JobRequest
Sep 09, 2015 8:14:12 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for Metadata
Sep 09, 2015 8:14:12 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for ReferenceSet
Sep 09, 2015 8:14:12 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for CallReadGroupSetsResponse
Sep 09, 2015 8:14:12 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for FastqMetadata
Sep 09, 2015 8:14:12 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for SearchVariantsRequest
Sep 09, 2015 8:14:12 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for SearchAnnotationSetsRequest
Sep 09, 2015 8:14:12 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for SearchReadGroupSetsRequest
Sep 09, 2015 8:14:12 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for CoverageBucket
Sep 09, 2015 8:14:12 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for SearchJobsResponse
Sep 09, 2015 8:14:12 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for ImportReadGroupSetsRequest
Sep 09, 2015 8:14:12 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for TranscriptCodingSequence
Sep 09, 2015 8:14:12 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for Variant
Sep 09, 2015 8:14:12 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for SearchReadGroupSetsResponse
Sep 09, 2015 8:14:12 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for SearchAnnotationsRequest
Sep 09, 2015 8:14:12 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for SearchVariantSetsResponse
Sep 09, 2015 8:14:12 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for InterleavedFastqSource
Sep 09, 2015 8:14:12 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for BatchCreateAnnotationsRequest
Sep 09, 2015 8:14:12 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for SearchReferencesRequest
Sep 09, 2015 8:14:12 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for SearchJobsRequest
Sep 09, 2015 8:14:12 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for AlignReadGroupSetsRequest
Sep 09, 2015 8:14:12 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for Job
Sep 09, 2015 8:14:12 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for TranscriptExon
Sep 09, 2015 8:14:12 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for SearchReferenceSetsRequest
Sep 09, 2015 8:14:12 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for QueryRange
Sep 09, 2015 8:14:13 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for LinearAlignment
Sep 09, 2015 8:14:13 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for Position
Sep 09, 2015 8:14:13 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for Annotation
Sep 09, 2015 8:14:13 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for SearchReadsResponse
Sep 09, 2015 8:14:13 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for ExperimentalCreateJobRequest
Sep 09, 2015 8:14:13 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for AnnotationSet
Sep 09, 2015 8:14:13 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for Dataset
Sep 09, 2015 8:14:13 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for Read
Sep 09, 2015 8:14:13 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for Call
Sep 09, 2015 8:14:13 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for ReadGroupExperiment
Sep 09, 2015 8:14:13 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for VariantAnnotationCondition
Sep 09, 2015 8:14:13 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for ReadGroup
Sep 09, 2015 8:14:13 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for VariantAnnotation
Sep 09, 2015 8:14:13 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for Int32Value
Sep 09, 2015 8:14:13 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for ExportReadGroupSetsRequest
Sep 09, 2015 8:14:13 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for ReferenceBound
Sep 09, 2015 8:14:13 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for ImportReadGroupSetsResponse
Sep 09, 2015 8:14:13 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for MergeVariantsRequest
Sep 09, 2015 8:14:13 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for CigarUnit
Sep 09, 2015 8:14:13 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for SearchAnnotationsResponse
Sep 09, 2015 8:14:13 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for BatchAnnotationsResponseEntry
Sep 09, 2015 8:14:13 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for CallReadGroupSetsRequest
Sep 09, 2015 8:14:13 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for ListBasesResponse
Sep 09, 2015 8:14:13 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for SearchReferencesResponse
Sep 09, 2015 8:14:13 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for PairedFastqSource
Sep 09, 2015 8:14:13 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for BatchAnnotationsResponse
Sep 09, 2015 8:14:13 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for SearchCallSetsRequest
Sep 09, 2015 8:14:13 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for RangePosition
Sep 09, 2015 8:14:13 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for Transcript
Sep 09, 2015 8:14:13 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for BatchAnnotationsResponseEntryStatus
Sep 09, 2015 8:14:13 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for ExportReadGroupSetsResponse
Sep 09, 2015 8:14:13 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for SearchAnnotationSetsResponse
Sep 09, 2015 8:14:13 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for ListDatasetsResponse
Sep 09, 2015 8:14:13 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for ReadGroupSet
Sep 09, 2015 8:14:13 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for Range
Sep 09, 2015 8:14:13 AM com.google.cloud.dataflow.sdk.Pipeline applyInternal
WARNING: Transform Create.Values2 does not have a stable unique name. This will prevent reloading of pipelines.
[September 9, 2015 8:14:14 AM UTC] org.broadinstitute.hellbender.tools.dataflow.pipelines.BaseRecalibratorDataflow done. Elapsed time: 0.03 minutes.
Runtime.totalMemory()=1324351488
[September 9, 2015 8:14:14 AM UTC] org.broadinstitute.hellbender.tools.dataflow.pipelines.BaseRecalibratorDataflow  --RECAL_TABLE_FILE /tmp/walktest.tmp_param.04079323296833201535.tmp --sort_by_all_columns true --input src/test/resources/org/broadinstitute/hellbender/tools/BQSR/CEUTrio.HiSeq.WGS.b37.ch20.1m-1m1k.NA12878.bam --reference gg://reference/EOSsjdnTicvzwAE --baseRecalibrationKnownVariants src/test/resources/org/broadinstitute/hellbender/tools/BQSR/dbsnp_132.b37.excluding_sites_after_129.chr17_69k_70k.vcf --project broad-dsde-dev --apiKey *********** --VERBOSITY ERROR  --run_without_dbsnp_potentially_ruining_quality false --solid_recal_mode SET_Q_ZERO --solid_nocall_strategy THROW_EXCEPTION --mismatches_context_size 2 --indels_context_size 3 --maximum_cycle_value 500 --mismatches_default_quality -1 --insertions_default_quality 45 --deletions_default_quality 45 --low_quality_tail 2 --quantizing_levels 16 --interval_set_rule UNION --interval_padding 0 --bqsrBAQGapOpenPenalty 40.0 --preserve_qscores_less_than 6 --useOriginalQualities false --defaultBaseQualities -1 --runner LOCAL --numWorkers 0 --help false --version false --QUIET false
[September 9, 2015 8:14:14 AM UTC] Executing as travis@testing-worker-linux-docker-75fb849c-3212-linux-2 on Linux 3.13.0-40-generic amd64; Java HotSpot(TM) 64-Bit Server VM 1.8.0_31-b13; Version: Version:null JdkDeflater
Sep 09, 2015 8:14:14 AM com.google.cloud.dataflow.sdk.runners.DirectPipelineRunner <init>
INFO: DirectPipelineRunner using random seed 3670379152225313036.
Sep 09, 2015 8:14:14 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coders for genomics classes
Sep 09, 2015 8:14:14 AM org.reflections.Reflections scan
INFO: Reflections took 136 ms to scan 250 urls, producing 79 keys and 156 values 
Sep 09, 2015 8:14:14 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for SearchVariantsResponse
Sep 09, 2015 8:14:14 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for ImportVariantsRequest
Sep 09, 2015 8:14:14 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for ExperimentalCreateJobResponse
Sep 09, 2015 8:14:14 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for SearchVariantSetsRequest
Sep 09, 2015 8:14:14 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for VariantSet
Sep 09, 2015 8:14:14 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for ExportVariantSetResponse
Sep 09, 2015 8:14:14 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for KeyValue
Sep 09, 2015 8:14:14 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for ListCoverageBucketsResponse
Sep 09, 2015 8:14:14 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for AlignReadGroupSetsResponse
Sep 09, 2015 8:14:14 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for ImportVariantsResponse
Sep 09, 2015 8:14:14 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for SearchReferenceSetsResponse
Sep 09, 2015 8:14:14 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for ReadGroupProgram
Sep 09, 2015 8:14:14 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for SearchCallSetsResponse
Sep 09, 2015 8:14:14 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for Reference
Sep 09, 2015 8:14:14 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for ExternalId
Sep 09, 2015 8:14:14 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for SearchReadsRequest
Sep 09, 2015 8:14:14 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for ExportVariantSetRequest
Sep 09, 2015 8:14:14 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for CallSet
Sep 09, 2015 8:14:14 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for JobRequest
Sep 09, 2015 8:14:14 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for Metadata
Sep 09, 2015 8:14:14 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for ReferenceSet
Sep 09, 2015 8:14:14 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for CallReadGroupSetsResponse
Sep 09, 2015 8:14:14 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for FastqMetadata
Sep 09, 2015 8:14:14 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for SearchVariantsRequest
Sep 09, 2015 8:14:14 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for SearchAnnotationSetsRequest
Sep 09, 2015 8:14:14 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for SearchReadGroupSetsRequest
Sep 09, 2015 8:14:14 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for CoverageBucket
Sep 09, 2015 8:14:14 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for SearchJobsResponse
Sep 09, 2015 8:14:14 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for ImportReadGroupSetsRequest
Sep 09, 2015 8:14:14 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for TranscriptCodingSequence
Sep 09, 2015 8:14:14 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for Variant
Sep 09, 2015 8:14:14 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for SearchReadGroupSetsResponse
Sep 09, 2015 8:14:14 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for SearchAnnotationsRequest
Sep 09, 2015 8:14:14 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for SearchVariantSetsResponse
Sep 09, 2015 8:14:14 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for InterleavedFastqSource
Sep 09, 2015 8:14:14 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for BatchCreateAnnotationsRequest
Sep 09, 2015 8:14:14 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for SearchReferencesRequest
Sep 09, 2015 8:14:14 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for SearchJobsRequest
Sep 09, 2015 8:14:14 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for AlignReadGroupSetsRequest
Sep 09, 2015 8:14:14 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for Job
Sep 09, 2015 8:14:14 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for TranscriptExon
Sep 09, 2015 8:14:14 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for SearchReferenceSetsRequest
Sep 09, 2015 8:14:14 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for QueryRange
Sep 09, 2015 8:14:14 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for LinearAlignment
Sep 09, 2015 8:14:14 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for Position
Sep 09, 2015 8:14:14 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for Annotation
Sep 09, 2015 8:14:14 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for SearchReadsResponse
Sep 09, 2015 8:14:14 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for ExperimentalCreateJobRequest
Sep 09, 2015 8:14:14 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for AnnotationSet
Sep 09, 2015 8:14:14 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for Dataset
Sep 09, 2015 8:14:14 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for Read
Sep 09, 2015 8:14:14 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for Call
Sep 09, 2015 8:14:14 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for ReadGroupExperiment
Sep 09, 2015 8:14:14 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for VariantAnnotationCondition
Sep 09, 2015 8:14:14 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for ReadGroup
Sep 09, 2015 8:14:14 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for VariantAnnotation
Sep 09, 2015 8:14:14 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for Int32Value
Sep 09, 2015 8:14:14 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for ExportReadGroupSetsRequest
Sep 09, 2015 8:14:14 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for ReferenceBound
Sep 09, 2015 8:14:14 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for ImportReadGroupSetsResponse
Sep 09, 2015 8:14:14 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for MergeVariantsRequest
Sep 09, 2015 8:14:14 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for CigarUnit
Sep 09, 2015 8:14:14 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for SearchAnnotationsResponse
Sep 09, 2015 8:14:14 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for BatchAnnotationsResponseEntry
Sep 09, 2015 8:14:14 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for CallReadGroupSetsRequest
Sep 09, 2015 8:14:14 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for ListBasesResponse
Sep 09, 2015 8:14:14 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for SearchReferencesResponse
Sep 09, 2015 8:14:14 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for PairedFastqSource
Sep 09, 2015 8:14:14 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for BatchAnnotationsResponse
Sep 09, 2015 8:14:14 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for SearchCallSetsRequest
Sep 09, 2015 8:14:14 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for RangePosition
Sep 09, 2015 8:14:14 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for Transcript
Sep 09, 2015 8:14:14 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for BatchAnnotationsResponseEntryStatus
Sep 09, 2015 8:14:14 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for ExportReadGroupSetsResponse
Sep 09, 2015 8:14:14 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for SearchAnnotationSetsResponse
Sep 09, 2015 8:14:14 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for ListDatasetsResponse
Sep 09, 2015 8:14:14 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for ReadGroupSet
Sep 09, 2015 8:14:14 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for Range
Sep 09, 2015 8:14:14 AM com.google.cloud.dataflow.sdk.Pipeline applyInternal
WARNING: Transform Create.Values2 does not have a stable unique name. This will prevent reloading of pipelines.
Sep 09, 2015 8:14:15 AM com.google.cloud.dataflow.sdk.Pipeline applyInternal
WARNING: Transform Create.Values3 does not have a stable unique name. This will prevent reloading of pipelines.
Sep 09, 2015 8:14:15 AM com.google.cloud.dataflow.sdk.Pipeline applyInternal
WARNING: Transform View.AsSingleton2 does not have a stable unique name. This will prevent reloading of pipelines.
Sep 09, 2015 8:14:15 AM com.google.cloud.dataflow.sdk.Pipeline applyInternal
WARNING: Transform Create.Values4 does not have a stable unique name. This will prevent reloading of pipelines.
Sep 09, 2015 8:14:15 AM com.google.cloud.dataflow.sdk.Pipeline applyInternal
WARNING: Transform AnonymousParDo2 does not have a stable unique name. This will prevent reloading of pipelines.
Sep 09, 2015 8:14:15 AM com.google.cloud.dataflow.sdk.Pipeline applyInternal
WARNING: Transform RemoveDuplicateReadVariantPairs/AnonymousParDo2 does not have a stable unique name. This will prevent reloading of pipelines.
Sep 09, 2015 8:14:15 AM com.google.cloud.dataflow.sdk.Pipeline applyInternal
WARNING: Transform RemoveDuplicateReadVariantPairs/CoGroupByKey2 does not have a stable unique name. This will prevent reloading of pipelines.
Sep 09, 2015 8:14:15 AM com.google.cloud.dataflow.sdk.Pipeline applyInternal
WARNING: Transform RemoveDuplicateReadVariantPairs/AnonymousParDo3 does not have a stable unique name. This will prevent reloading of pipelines.
Sep 09, 2015 8:14:15 AM com.google.cloud.dataflow.sdk.Pipeline applyInternal
WARNING: Transform AnonymousParDo3 does not have a stable unique name. This will prevent reloading of pipelines.
Sep 09, 2015 8:14:15 AM com.google.cloud.dataflow.sdk.Pipeline applyInternal
WARNING: Transform AddContextDataToRead.StripToUUID2 does not have a stable unique name. This will prevent reloading of pipelines.
Sep 09, 2015 8:14:15 AM com.google.cloud.dataflow.sdk.Pipeline applyInternal
WARNING: Transform Keys2 does not have a stable unique name. This will prevent reloading of pipelines.
Sep 09, 2015 8:14:15 AM com.google.cloud.dataflow.sdk.Pipeline applyInternal
WARNING: Transform AddContextDataToRead.StripToUUID3 does not have a stable unique name. This will prevent reloading of pipelines.
Sep 09, 2015 8:14:15 AM com.google.cloud.dataflow.sdk.Pipeline applyInternal
WARNING: Transform View.AsSingleton3 does not have a stable unique name. This will prevent reloading of pipelines.
Sep 09, 2015 8:14:15 AM com.google.cloud.dataflow.sdk.Pipeline applyInternal
WARNING: Transform Count.Globally2 does not have a stable unique name. This will prevent reloading of pipelines.
Sep 09, 2015 8:14:15 AM com.google.cloud.dataflow.sdk.Pipeline applyInternal
WARNING: Transform View.AsSingleton4 does not have a stable unique name. This will prevent reloading of pipelines.
Sep 09, 2015 8:14:15 AM com.google.cloud.dataflow.sdk.Pipeline applyInternal
WARNING: Transform Count.Globally3 does not have a stable unique name. This will prevent reloading of pipelines.
Sep 09, 2015 8:14:16 AM com.google.cloud.dataflow.sdk.Pipeline applyInternal
WARNING: Transform View.AsSingleton5 does not have a stable unique name. This will prevent reloading of pipelines.
Sep 09, 2015 8:14:16 AM com.google.cloud.dataflow.sdk.Pipeline applyInternal
WARNING: Transform Count.Globally4 does not have a stable unique name. This will prevent reloading of pipelines.
Sep 09, 2015 8:14:16 AM com.google.cloud.dataflow.sdk.Pipeline applyInternal
WARNING: Transform CoGroupByKey2 does not have a stable unique name. This will prevent reloading of pipelines.
Sep 09, 2015 8:14:16 AM com.google.cloud.dataflow.sdk.Pipeline applyInternal
WARNING: Transform CoGroupByKey3 does not have a stable unique name. This will prevent reloading of pipelines.
Sep 09, 2015 8:14:16 AM com.google.cloud.dataflow.sdk.Pipeline applyInternal
WARNING: Transform AnonymousParDo4 does not have a stable unique name. This will prevent reloading of pipelines.
Sep 09, 2015 8:14:16 AM com.google.cloud.dataflow.sdk.runners.DirectPipelineRunner run
INFO: Executing pipeline using the DirectPipelineRunner.
Sep 09, 2015 8:14:35 AM com.google.cloud.dataflow.sdk.runners.DirectPipelineRunner run
INFO: Pipeline execution complete.
[September 9, 2015 8:14:40 AM UTC] org.broadinstitute.hellbender.tools.dataflow.pipelines.BaseRecalibratorDataflow done. Elapsed time: 0.43 minutes.
Runtime.totalMemory()=1403518976
[September 9, 2015 8:14:40 AM UTC] org.broadinstitute.hellbender.tools.dataflow.pipelines.BaseRecalibratorDataflow  --knownSites /home/travis/build/broadinstitute/hellbender/src/test/resources/org/broadinstitute/hellbender/tools/BQSR/bqsr.fakeSitesForTesting.b37.chr17.vcf --RECAL_TABLE_FILE /tmp/walktest.tmp_param.02614253070718609175.tmp --sort_by_all_columns true --input src/test/resources/org/broadinstitute/hellbender/tools/BQSR/CEUTrio.HiSeq.WGS.b37.ch20.1m-1m1k.NA12878.bam --reference gg://reference/EOSsjdnTicvzwAE --baseRecalibrationKnownVariants src/test/resources/org/broadinstitute/hellbender/tools/BQSR/dbsnp_132.b37.excluding_sites_after_129.chr17_69k_70k.vcf --project broad-dsde-dev --apiKey *********** --VERBOSITY ERROR  --run_without_dbsnp_potentially_ruining_quality false --solid_recal_mode SET_Q_ZERO --solid_nocall_strategy THROW_EXCEPTION --mismatches_context_size 2 --indels_context_size 3 --maximum_cycle_value 500 --mismatches_default_quality -1 --insertions_default_quality 45 --deletions_default_quality 45 --low_quality_tail 2 --quantizing_levels 16 --interval_set_rule UNION --interval_padding 0 --bqsrBAQGapOpenPenalty 40.0 --preserve_qscores_less_than 6 --useOriginalQualities false --defaultBaseQualities -1 --runner LOCAL --numWorkers 0 --help false --version false --QUIET false
[September 9, 2015 8:14:40 AM UTC] Executing as travis@testing-worker-linux-docker-75fb849c-3212-linux-2 on Linux 3.13.0-40-generic amd64; Java HotSpot(TM) 64-Bit Server VM 1.8.0_31-b13; Version: Version:null JdkDeflater
Sep 09, 2015 8:14:40 AM com.google.cloud.dataflow.sdk.runners.DirectPipelineRunner <init>
INFO: DirectPipelineRunner using random seed -2727454312687046635.
Sep 09, 2015 8:14:40 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coders for genomics classes
Sep 09, 2015 8:14:40 AM org.reflections.Reflections scan
INFO: Reflections took 141 ms to scan 250 urls, producing 79 keys and 156 values 
Sep 09, 2015 8:14:40 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for SearchVariantsResponse
Sep 09, 2015 8:14:40 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for ImportVariantsRequest
Sep 09, 2015 8:14:40 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for ExperimentalCreateJobResponse
Sep 09, 2015 8:14:40 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for SearchVariantSetsRequest
Sep 09, 2015 8:14:40 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for VariantSet
Sep 09, 2015 8:14:40 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for ExportVariantSetResponse
Sep 09, 2015 8:14:40 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for KeyValue
Sep 09, 2015 8:14:40 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for ListCoverageBucketsResponse
Sep 09, 2015 8:14:40 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for AlignReadGroupSetsResponse
Sep 09, 2015 8:14:40 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for ImportVariantsResponse
Sep 09, 2015 8:14:40 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for SearchReferenceSetsResponse
Sep 09, 2015 8:14:40 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for ReadGroupProgram
Sep 09, 2015 8:14:40 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for SearchCallSetsResponse
Sep 09, 2015 8:14:40 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for Reference
Sep 09, 2015 8:14:40 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for ExternalId
Sep 09, 2015 8:14:40 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for SearchReadsRequest
Sep 09, 2015 8:14:40 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for ExportVariantSetRequest
Sep 09, 2015 8:14:40 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for CallSet
Sep 09, 2015 8:14:40 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for JobRequest
Sep 09, 2015 8:14:40 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for Metadata
Sep 09, 2015 8:14:40 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for ReferenceSet
Sep 09, 2015 8:14:40 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for CallReadGroupSetsResponse
Sep 09, 2015 8:14:40 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for FastqMetadata
Sep 09, 2015 8:14:40 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for SearchVariantsRequest
Sep 09, 2015 8:14:40 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for SearchAnnotationSetsRequest
Sep 09, 2015 8:14:40 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for SearchReadGroupSetsRequest
Sep 09, 2015 8:14:40 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for CoverageBucket
Sep 09, 2015 8:14:40 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for SearchJobsResponse
Sep 09, 2015 8:14:40 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for ImportReadGroupSetsRequest
Sep 09, 2015 8:14:40 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for TranscriptCodingSequence
Sep 09, 2015 8:14:40 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for Variant
Sep 09, 2015 8:14:40 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for SearchReadGroupSetsResponse
Sep 09, 2015 8:14:40 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for SearchAnnotationsRequest
Sep 09, 2015 8:14:40 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for SearchVariantSetsResponse
Sep 09, 2015 8:14:40 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for InterleavedFastqSource
Sep 09, 2015 8:14:40 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for BatchCreateAnnotationsRequest
Sep 09, 2015 8:14:40 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for SearchReferencesRequest
Sep 09, 2015 8:14:40 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for SearchJobsRequest
Sep 09, 2015 8:14:40 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for AlignReadGroupSetsRequest
Sep 09, 2015 8:14:40 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for Job
Sep 09, 2015 8:14:40 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for TranscriptExon
Sep 09, 2015 8:14:40 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for SearchReferenceSetsRequest
Sep 09, 2015 8:14:40 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for QueryRange
Sep 09, 2015 8:14:40 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for LinearAlignment
Sep 09, 2015 8:14:40 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for Position
Sep 09, 2015 8:14:40 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for Annotation
Sep 09, 2015 8:14:40 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for SearchReadsResponse
Sep 09, 2015 8:14:40 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for ExperimentalCreateJobRequest
Sep 09, 2015 8:14:40 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for AnnotationSet
Sep 09, 2015 8:14:40 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for Dataset
Sep 09, 2015 8:14:40 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for Read
Sep 09, 2015 8:14:40 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for Call
Sep 09, 2015 8:14:40 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for ReadGroupExperiment
Sep 09, 2015 8:14:40 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for VariantAnnotationCondition
Sep 09, 2015 8:14:40 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for ReadGroup
Sep 09, 2015 8:14:40 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for VariantAnnotation
Sep 09, 2015 8:14:40 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for Int32Value
Sep 09, 2015 8:14:40 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for ExportReadGroupSetsRequest
Sep 09, 2015 8:14:40 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for ReferenceBound
Sep 09, 2015 8:14:40 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for ImportReadGroupSetsResponse
Sep 09, 2015 8:14:40 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for MergeVariantsRequest
Sep 09, 2015 8:14:40 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for CigarUnit
Sep 09, 2015 8:14:40 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for SearchAnnotationsResponse
Sep 09, 2015 8:14:40 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for BatchAnnotationsResponseEntry
Sep 09, 2015 8:14:40 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for CallReadGroupSetsRequest
Sep 09, 2015 8:14:40 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for ListBasesResponse
Sep 09, 2015 8:14:40 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for SearchReferencesResponse
Sep 09, 2015 8:14:40 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for PairedFastqSource
Sep 09, 2015 8:14:40 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for BatchAnnotationsResponse
Sep 09, 2015 8:14:40 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for SearchCallSetsRequest
Sep 09, 2015 8:14:40 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for RangePosition
Sep 09, 2015 8:14:40 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for Transcript
Sep 09, 2015 8:14:40 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for BatchAnnotationsResponseEntryStatus
Sep 09, 2015 8:14:40 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for ExportReadGroupSetsResponse
Sep 09, 2015 8:14:40 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for SearchAnnotationSetsResponse
Sep 09, 2015 8:14:40 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for ListDatasetsResponse
Sep 09, 2015 8:14:40 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for ReadGroupSet
Sep 09, 2015 8:14:40 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for Range
Sep 09, 2015 8:14:40 AM com.google.cloud.dataflow.sdk.Pipeline applyInternal
WARNING: Transform Create.Values2 does not have a stable unique name. This will prevent reloading of pipelines.
Sep 09, 2015 8:14:40 AM com.google.cloud.dataflow.sdk.Pipeline applyInternal
WARNING: Transform Create.Values3 does not have a stable unique name. This will prevent reloading of pipelines.
Sep 09, 2015 8:14:40 AM com.google.cloud.dataflow.sdk.Pipeline applyInternal
WARNING: Transform View.AsSingleton2 does not have a stable unique name. This will prevent reloading of pipelines.
Sep 09, 2015 8:14:40 AM com.google.cloud.dataflow.sdk.Pipeline applyInternal
WARNING: Transform Create.Values4 does not have a stable unique name. This will prevent reloading of pipelines.
Sep 09, 2015 8:14:40 AM com.google.cloud.dataflow.sdk.Pipeline applyInternal
WARNING: Transform AnonymousParDo2 does not have a stable unique name. This will prevent reloading of pipelines.
Sep 09, 2015 8:14:40 AM com.google.cloud.dataflow.sdk.Pipeline applyInternal
WARNING: Transform RemoveDuplicateReadVariantPairs/AnonymousParDo2 does not have a stable unique name. This will prevent reloading of pipelines.
Sep 09, 2015 8:14:40 AM com.google.cloud.dataflow.sdk.Pipeline applyInternal
WARNING: Transform RemoveDuplicateReadVariantPairs/CoGroupByKey2 does not have a stable unique name. This will prevent reloading of pipelines.
Sep 09, 2015 8:14:40 AM com.google.cloud.dataflow.sdk.Pipeline applyInternal
WARNING: Transform RemoveDuplicateReadVariantPairs/AnonymousParDo3 does not have a stable unique name. This will prevent reloading of pipelines.
Sep 09, 2015 8:14:40 AM com.google.cloud.dataflow.sdk.Pipeline applyInternal
WARNING: Transform AnonymousParDo3 does not have a stable unique name. This will prevent reloading of pipelines.
Sep 09, 2015 8:14:40 AM com.google.cloud.dataflow.sdk.Pipeline applyInternal
WARNING: Transform AddContextDataToRead.StripToUUID2 does not have a stable unique name. This will prevent reloading of pipelines.
Sep 09, 2015 8:14:40 AM com.google.cloud.dataflow.sdk.Pipeline applyInternal
WARNING: Transform Keys2 does not have a stable unique name. This will prevent reloading of pipelines.
Sep 09, 2015 8:14:40 AM com.google.cloud.dataflow.sdk.Pipeline applyInternal
WARNING: Transform AddContextDataToRead.StripToUUID3 does not have a stable unique name. This will prevent reloading of pipelines.
Sep 09, 2015 8:14:40 AM com.google.cloud.dataflow.sdk.Pipeline applyInternal
WARNING: Transform View.AsSingleton3 does not have a stable unique name. This will prevent reloading of pipelines.
Sep 09, 2015 8:14:40 AM com.google.cloud.dataflow.sdk.Pipeline applyInternal
WARNING: Transform Count.Globally2 does not have a stable unique name. This will prevent reloading of pipelines.
Sep 09, 2015 8:14:40 AM com.google.cloud.dataflow.sdk.Pipeline applyInternal
WARNING: Transform View.AsSingleton4 does not have a stable unique name. This will prevent reloading of pipelines.
Sep 09, 2015 8:14:40 AM com.google.cloud.dataflow.sdk.Pipeline applyInternal
WARNING: Transform Count.Globally3 does not have a stable unique name. This will prevent reloading of pipelines.
Sep 09, 2015 8:14:40 AM com.google.cloud.dataflow.sdk.Pipeline applyInternal
WARNING: Transform View.AsSingleton5 does not have a stable unique name. This will prevent reloading of pipelines.
Sep 09, 2015 8:14:40 AM com.google.cloud.dataflow.sdk.Pipeline applyInternal
WARNING: Transform Count.Globally4 does not have a stable unique name. This will prevent reloading of pipelines.
Sep 09, 2015 8:14:40 AM com.google.cloud.dataflow.sdk.Pipeline applyInternal
WARNING: Transform CoGroupByKey2 does not have a stable unique name. This will prevent reloading of pipelines.
Sep 09, 2015 8:14:40 AM com.google.cloud.dataflow.sdk.Pipeline applyInternal
WARNING: Transform CoGroupByKey3 does not have a stable unique name. This will prevent reloading of pipelines.
Sep 09, 2015 8:14:40 AM com.google.cloud.dataflow.sdk.Pipeline applyInternal
WARNING: Transform AnonymousParDo4 does not have a stable unique name. This will prevent reloading of pipelines.
Sep 09, 2015 8:14:40 AM com.google.cloud.dataflow.sdk.runners.DirectPipelineRunner run
INFO: Executing pipeline using the DirectPipelineRunner.
Sep 09, 2015 8:14:59 AM com.google.cloud.dataflow.sdk.runners.DirectPipelineRunner run
INFO: Pipeline execution complete.
[September 9, 2015 8:15:04 AM UTC] org.broadinstitute.hellbender.tools.dataflow.pipelines.BaseRecalibratorDataflow done. Elapsed time: 0.40 minutes.
Runtime.totalMemory()=1418723328
[September 9, 2015 8:15:04 AM UTC] org.broadinstitute.hellbender.tools.dataflow.pipelines.BaseRecalibratorDataflow  --RECAL_TABLE_FILE /tmp/walktest.tmp_param.043157368816636792.tmp --indels_context_size 4 --sort_by_all_columns true --input src/test/resources/org/broadinstitute/hellbender/tools/BQSR/CEUTrio.HiSeq.WGS.b37.ch20.1m-1m1k.NA12878.bam --reference gg://reference/EOSsjdnTicvzwAE --baseRecalibrationKnownVariants src/test/resources/org/broadinstitute/hellbender/tools/BQSR/dbsnp_132.b37.excluding_sites_after_129.chr17_69k_70k.vcf --project broad-dsde-dev --apiKey *********** --VERBOSITY ERROR  --run_without_dbsnp_potentially_ruining_quality false --solid_recal_mode SET_Q_ZERO --solid_nocall_strategy THROW_EXCEPTION --mismatches_context_size 2 --maximum_cycle_value 500 --mismatches_default_quality -1 --insertions_default_quality 45 --deletions_default_quality 45 --low_quality_tail 2 --quantizing_levels 16 --interval_set_rule UNION --interval_padding 0 --bqsrBAQGapOpenPenalty 40.0 --preserve_qscores_less_than 6 --useOriginalQualities false --defaultBaseQualities -1 --runner LOCAL --numWorkers 0 --help false --version false --QUIET false
[September 9, 2015 8:15:04 AM UTC] Executing as travis@testing-worker-linux-docker-75fb849c-3212-linux-2 on Linux 3.13.0-40-generic amd64; Java HotSpot(TM) 64-Bit Server VM 1.8.0_31-b13; Version: Version:null JdkDeflater
Sep 09, 2015 8:15:04 AM com.google.cloud.dataflow.sdk.runners.DirectPipelineRunner <init>
INFO: DirectPipelineRunner using random seed -276727199516704869.
Sep 09, 2015 8:15:04 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coders for genomics classes
Sep 09, 2015 8:15:04 AM org.reflections.Reflections scan
INFO: Reflections took 172 ms to scan 250 urls, producing 79 keys and 156 values 
Sep 09, 2015 8:15:04 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for SearchVariantsResponse
Sep 09, 2015 8:15:04 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for ImportVariantsRequest
Sep 09, 2015 8:15:04 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for ExperimentalCreateJobResponse
Sep 09, 2015 8:15:04 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for SearchVariantSetsRequest
Sep 09, 2015 8:15:04 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for VariantSet
Sep 09, 2015 8:15:04 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for ExportVariantSetResponse
Sep 09, 2015 8:15:04 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for KeyValue
Sep 09, 2015 8:15:04 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for ListCoverageBucketsResponse
Sep 09, 2015 8:15:04 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for AlignReadGroupSetsResponse
Sep 09, 2015 8:15:04 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for ImportVariantsResponse
Sep 09, 2015 8:15:04 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for SearchReferenceSetsResponse
Sep 09, 2015 8:15:04 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for ReadGroupProgram
Sep 09, 2015 8:15:04 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for SearchCallSetsResponse
Sep 09, 2015 8:15:04 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for Reference
Sep 09, 2015 8:15:04 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for ExternalId
Sep 09, 2015 8:15:04 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for SearchReadsRequest
Sep 09, 2015 8:15:04 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for ExportVariantSetRequest
Sep 09, 2015 8:15:04 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for CallSet
Sep 09, 2015 8:15:04 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for JobRequest
Sep 09, 2015 8:15:04 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for Metadata
Sep 09, 2015 8:15:04 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for ReferenceSet
Sep 09, 2015 8:15:04 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for CallReadGroupSetsResponse
Sep 09, 2015 8:15:04 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for FastqMetadata
Sep 09, 2015 8:15:04 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for SearchVariantsRequest
Sep 09, 2015 8:15:04 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for SearchAnnotationSetsRequest
Sep 09, 2015 8:15:04 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for SearchReadGroupSetsRequest
Sep 09, 2015 8:15:04 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for CoverageBucket
Sep 09, 2015 8:15:04 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for SearchJobsResponse
Sep 09, 2015 8:15:04 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for ImportReadGroupSetsRequest
Sep 09, 2015 8:15:04 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for TranscriptCodingSequence
Sep 09, 2015 8:15:04 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for Variant
Sep 09, 2015 8:15:04 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for SearchReadGroupSetsResponse
Sep 09, 2015 8:15:04 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for SearchAnnotationsRequest
Sep 09, 2015 8:15:04 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for SearchVariantSetsResponse
Sep 09, 2015 8:15:04 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for InterleavedFastqSource
Sep 09, 2015 8:15:04 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for BatchCreateAnnotationsRequest
Sep 09, 2015 8:15:04 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for SearchReferencesRequest
Sep 09, 2015 8:15:04 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for SearchJobsRequest
Sep 09, 2015 8:15:04 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for AlignReadGroupSetsRequest
Sep 09, 2015 8:15:04 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for Job
Sep 09, 2015 8:15:04 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for TranscriptExon
Sep 09, 2015 8:15:04 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for SearchReferenceSetsRequest
Sep 09, 2015 8:15:04 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for QueryRange
Sep 09, 2015 8:15:04 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for LinearAlignment
Sep 09, 2015 8:15:04 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for Position
Sep 09, 2015 8:15:04 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for Annotation
Sep 09, 2015 8:15:04 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for SearchReadsResponse
Sep 09, 2015 8:15:04 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for ExperimentalCreateJobRequest
Sep 09, 2015 8:15:04 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for AnnotationSet
Sep 09, 2015 8:15:04 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for Dataset
Sep 09, 2015 8:15:04 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for Read
Sep 09, 2015 8:15:04 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for Call
Sep 09, 2015 8:15:04 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for ReadGroupExperiment
Sep 09, 2015 8:15:04 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for VariantAnnotationCondition
Sep 09, 2015 8:15:04 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for ReadGroup
Sep 09, 2015 8:15:04 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for VariantAnnotation
Sep 09, 2015 8:15:04 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for Int32Value
Sep 09, 2015 8:15:04 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for ExportReadGroupSetsRequest
Sep 09, 2015 8:15:04 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for ReferenceBound
Sep 09, 2015 8:15:04 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for ImportReadGroupSetsResponse
Sep 09, 2015 8:15:04 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for MergeVariantsRequest
Sep 09, 2015 8:15:04 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for CigarUnit
Sep 09, 2015 8:15:04 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for SearchAnnotationsResponse
Sep 09, 2015 8:15:04 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for BatchAnnotationsResponseEntry
Sep 09, 2015 8:15:04 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for CallReadGroupSetsRequest
Sep 09, 2015 8:15:04 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for ListBasesResponse
Sep 09, 2015 8:15:04 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for SearchReferencesResponse
Sep 09, 2015 8:15:04 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for PairedFastqSource
Sep 09, 2015 8:15:04 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for BatchAnnotationsResponse
Sep 09, 2015 8:15:04 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for SearchCallSetsRequest
Sep 09, 2015 8:15:04 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for RangePosition
Sep 09, 2015 8:15:04 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for Transcript
Sep 09, 2015 8:15:04 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for BatchAnnotationsResponseEntryStatus
Sep 09, 2015 8:15:04 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for ExportReadGroupSetsResponse
Sep 09, 2015 8:15:04 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for SearchAnnotationSetsResponse
Sep 09, 2015 8:15:04 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for ListDatasetsResponse
Sep 09, 2015 8:15:04 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for ReadGroupSet
Sep 09, 2015 8:15:04 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for Range
Sep 09, 2015 8:15:04 AM com.google.cloud.dataflow.sdk.Pipeline applyInternal
WARNING: Transform Create.Values2 does not have a stable unique name. This will prevent reloading of pipelines.
Sep 09, 2015 8:15:06 AM com.google.cloud.dataflow.sdk.Pipeline applyInternal
WARNING: Transform Create.Values3 does not have a stable unique name. This will prevent reloading of pipelines.
Sep 09, 2015 8:15:06 AM com.google.cloud.dataflow.sdk.Pipeline applyInternal
WARNING: Transform View.AsSingleton2 does not have a stable unique name. This will prevent reloading of pipelines.
Sep 09, 2015 8:15:06 AM com.google.cloud.dataflow.sdk.Pipeline applyInternal
WARNING: Transform Create.Values4 does not have a stable unique name. This will prevent reloading of pipelines.
Sep 09, 2015 8:15:06 AM com.google.cloud.dataflow.sdk.Pipeline applyInternal
WARNING: Transform AnonymousParDo2 does not have a stable unique name. This will prevent reloading of pipelines.
Sep 09, 2015 8:15:06 AM com.google.cloud.dataflow.sdk.Pipeline applyInternal
WARNING: Transform RemoveDuplicateReadVariantPairs/AnonymousParDo2 does not have a stable unique name. This will prevent reloading of pipelines.
Sep 09, 2015 8:15:06 AM com.google.cloud.dataflow.sdk.Pipeline applyInternal
WARNING: Transform RemoveDuplicateReadVariantPairs/CoGroupByKey2 does not have a stable unique name. This will prevent reloading of pipelines.
Sep 09, 2015 8:15:06 AM com.google.cloud.dataflow.sdk.Pipeline applyInternal
WARNING: Transform RemoveDuplicateReadVariantPairs/AnonymousParDo3 does not have a stable unique name. This will prevent reloading of pipelines.
Sep 09, 2015 8:15:06 AM com.google.cloud.dataflow.sdk.Pipeline applyInternal
WARNING: Transform AnonymousParDo3 does not have a stable unique name. This will prevent reloading of pipelines.
Sep 09, 2015 8:15:06 AM com.google.cloud.dataflow.sdk.Pipeline applyInternal
WARNING: Transform AddContextDataToRead.StripToUUID2 does not have a stable unique name. This will prevent reloading of pipelines.
Sep 09, 2015 8:15:06 AM com.google.cloud.dataflow.sdk.Pipeline applyInternal
WARNING: Transform Keys2 does not have a stable unique name. This will prevent reloading of pipelines.
Sep 09, 2015 8:15:06 AM com.google.cloud.dataflow.sdk.Pipeline applyInternal
WARNING: Transform AddContextDataToRead.StripToUUID3 does not have a stable unique name. This will prevent reloading of pipelines.
Sep 09, 2015 8:15:06 AM com.google.cloud.dataflow.sdk.Pipeline applyInternal
WARNING: Transform View.AsSingleton3 does not have a stable unique name. This will prevent reloading of pipelines.
Sep 09, 2015 8:15:06 AM com.google.cloud.dataflow.sdk.Pipeline applyInternal
WARNING: Transform Count.Globally2 does not have a stable unique name. This will prevent reloading of pipelines.
Sep 09, 2015 8:15:06 AM com.google.cloud.dataflow.sdk.Pipeline applyInternal
WARNING: Transform View.AsSingleton4 does not have a stable unique name. This will prevent reloading of pipelines.
Sep 09, 2015 8:15:06 AM com.google.cloud.dataflow.sdk.Pipeline applyInternal
WARNING: Transform Count.Globally3 does not have a stable unique name. This will prevent reloading of pipelines.
Sep 09, 2015 8:15:06 AM com.google.cloud.dataflow.sdk.Pipeline applyInternal
WARNING: Transform View.AsSingleton5 does not have a stable unique name. This will prevent reloading of pipelines.
Sep 09, 2015 8:15:06 AM com.google.cloud.dataflow.sdk.Pipeline applyInternal
WARNING: Transform Count.Globally4 does not have a stable unique name. This will prevent reloading of pipelines.
Sep 09, 2015 8:15:06 AM com.google.cloud.dataflow.sdk.Pipeline applyInternal
WARNING: Transform CoGroupByKey2 does not have a stable unique name. This will prevent reloading of pipelines.
Sep 09, 2015 8:15:06 AM com.google.cloud.dataflow.sdk.Pipeline applyInternal
WARNING: Transform CoGroupByKey3 does not have a stable unique name. This will prevent reloading of pipelines.
Sep 09, 2015 8:15:06 AM com.google.cloud.dataflow.sdk.Pipeline applyInternal
WARNING: Transform AnonymousParDo4 does not have a stable unique name. This will prevent reloading of pipelines.
Sep 09, 2015 8:15:06 AM com.google.cloud.dataflow.sdk.runners.DirectPipelineRunner run
INFO: Executing pipeline using the DirectPipelineRunner.
Sep 09, 2015 8:15:25 AM com.google.cloud.dataflow.sdk.runners.DirectPipelineRunner run
INFO: Pipeline execution complete.
[September 9, 2015 8:15:30 AM UTC] org.broadinstitute.hellbender.tools.dataflow.pipelines.BaseRecalibratorDataflow done. Elapsed time: 0.43 minutes.
Runtime.totalMemory()=1421344768
[September 9, 2015 8:15:30 AM UTC] org.broadinstitute.hellbender.tools.dataflow.pipelines.BaseRecalibratorDataflow  --RECAL_TABLE_FILE /tmp/walktest.tmp_param.0550446583665724377.tmp --low_quality_tail 5 --sort_by_all_columns true --input src/test/resources/org/broadinstitute/hellbender/tools/BQSR/CEUTrio.HiSeq.WGS.b37.ch20.1m-1m1k.NA12878.bam --reference gg://reference/EOSsjdnTicvzwAE --baseRecalibrationKnownVariants src/test/resources/org/broadinstitute/hellbender/tools/BQSR/dbsnp_132.b37.excluding_sites_after_129.chr17_69k_70k.vcf --project broad-dsde-dev --apiKey *********** --VERBOSITY ERROR  --run_without_dbsnp_potentially_ruining_quality false --solid_recal_mode SET_Q_ZERO --solid_nocall_strategy THROW_EXCEPTION --mismatches_context_size 2 --indels_context_size 3 --maximum_cycle_value 500 --mismatches_default_quality -1 --insertions_default_quality 45 --deletions_default_quality 45 --quantizing_levels 16 --interval_set_rule UNION --interval_padding 0 --bqsrBAQGapOpenPenalty 40.0 --preserve_qscores_less_than 6 --useOriginalQualities false --defaultBaseQualities -1 --runner LOCAL --numWorkers 0 --help false --version false --QUIET false
[September 9, 2015 8:15:30 AM UTC] Executing as travis@testing-worker-linux-docker-75fb849c-3212-linux-2 on Linux 3.13.0-40-generic amd64; Java HotSpot(TM) 64-Bit Server VM 1.8.0_31-b13; Version: Version:null JdkDeflater
Sep 09, 2015 8:15:30 AM com.google.cloud.dataflow.sdk.runners.DirectPipelineRunner <init>
INFO: DirectPipelineRunner using random seed -7657396563155665927.
Sep 09, 2015 8:15:30 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coders for genomics classes
Sep 09, 2015 8:15:30 AM org.reflections.Reflections scan
INFO: Reflections took 138 ms to scan 250 urls, producing 79 keys and 156 values 
Sep 09, 2015 8:15:30 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for SearchVariantsResponse
Sep 09, 2015 8:15:30 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for ImportVariantsRequest
Sep 09, 2015 8:15:30 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for ExperimentalCreateJobResponse
Sep 09, 2015 8:15:30 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for SearchVariantSetsRequest
Sep 09, 2015 8:15:30 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for VariantSet
Sep 09, 2015 8:15:30 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for ExportVariantSetResponse
Sep 09, 2015 8:15:30 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for KeyValue
Sep 09, 2015 8:15:30 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for ListCoverageBucketsResponse
Sep 09, 2015 8:15:30 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for AlignReadGroupSetsResponse
Sep 09, 2015 8:15:30 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for ImportVariantsResponse
Sep 09, 2015 8:15:30 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for SearchReferenceSetsResponse
Sep 09, 2015 8:15:30 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for ReadGroupProgram
Sep 09, 2015 8:15:30 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for SearchCallSetsResponse
Sep 09, 2015 8:15:30 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for Reference
Sep 09, 2015 8:15:30 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for ExternalId
Sep 09, 2015 8:15:30 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for SearchReadsRequest
Sep 09, 2015 8:15:30 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for ExportVariantSetRequest
Sep 09, 2015 8:15:30 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for CallSet
Sep 09, 2015 8:15:30 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for JobRequest
Sep 09, 2015 8:15:30 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for Metadata
Sep 09, 2015 8:15:30 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for ReferenceSet
Sep 09, 2015 8:15:30 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for CallReadGroupSetsResponse
Sep 09, 2015 8:15:30 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for FastqMetadata
Sep 09, 2015 8:15:30 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for SearchVariantsRequest
Sep 09, 2015 8:15:30 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for SearchAnnotationSetsRequest
Sep 09, 2015 8:15:30 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for SearchReadGroupSetsRequest
Sep 09, 2015 8:15:30 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for CoverageBucket
Sep 09, 2015 8:15:30 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for SearchJobsResponse
Sep 09, 2015 8:15:30 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for ImportReadGroupSetsRequest
Sep 09, 2015 8:15:30 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for TranscriptCodingSequence
Sep 09, 2015 8:15:30 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for Variant
Sep 09, 2015 8:15:30 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for SearchReadGroupSetsResponse
Sep 09, 2015 8:15:30 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for SearchAnnotationsRequest
Sep 09, 2015 8:15:30 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for SearchVariantSetsResponse
Sep 09, 2015 8:15:30 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for InterleavedFastqSource
Sep 09, 2015 8:15:30 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for BatchCreateAnnotationsRequest
Sep 09, 2015 8:15:30 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for SearchReferencesRequest
Sep 09, 2015 8:15:30 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for SearchJobsRequest
Sep 09, 2015 8:15:30 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for AlignReadGroupSetsRequest
Sep 09, 2015 8:15:30 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for Job
Sep 09, 2015 8:15:30 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for TranscriptExon
Sep 09, 2015 8:15:30 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for SearchReferenceSetsRequest
Sep 09, 2015 8:15:30 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for QueryRange
Sep 09, 2015 8:15:30 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for LinearAlignment
Sep 09, 2015 8:15:30 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for Position
Sep 09, 2015 8:15:30 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for Annotation
Sep 09, 2015 8:15:30 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for SearchReadsResponse
Sep 09, 2015 8:15:30 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for ExperimentalCreateJobRequest
Sep 09, 2015 8:15:30 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for AnnotationSet
Sep 09, 2015 8:15:30 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for Dataset
Sep 09, 2015 8:15:30 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for Read
Sep 09, 2015 8:15:30 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for Call
Sep 09, 2015 8:15:30 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for ReadGroupExperiment
Sep 09, 2015 8:15:30 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for VariantAnnotationCondition
Sep 09, 2015 8:15:30 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for ReadGroup
Sep 09, 2015 8:15:30 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for VariantAnnotation
Sep 09, 2015 8:15:30 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for Int32Value
Sep 09, 2015 8:15:30 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for ExportReadGroupSetsRequest
Sep 09, 2015 8:15:30 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for ReferenceBound
Sep 09, 2015 8:15:30 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for ImportReadGroupSetsResponse
Sep 09, 2015 8:15:30 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for MergeVariantsRequest
Sep 09, 2015 8:15:30 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for CigarUnit
Sep 09, 2015 8:15:30 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for SearchAnnotationsResponse
Sep 09, 2015 8:15:30 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for BatchAnnotationsResponseEntry
Sep 09, 2015 8:15:30 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for CallReadGroupSetsRequest
Sep 09, 2015 8:15:30 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for ListBasesResponse
Sep 09, 2015 8:15:30 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for SearchReferencesResponse
Sep 09, 2015 8:15:30 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for PairedFastqSource
Sep 09, 2015 8:15:30 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for BatchAnnotationsResponse
Sep 09, 2015 8:15:30 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for SearchCallSetsRequest
Sep 09, 2015 8:15:30 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for RangePosition
Sep 09, 2015 8:15:30 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for Transcript
Sep 09, 2015 8:15:30 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for BatchAnnotationsResponseEntryStatus
Sep 09, 2015 8:15:30 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for ExportReadGroupSetsResponse
Sep 09, 2015 8:15:30 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for SearchAnnotationSetsResponse
Sep 09, 2015 8:15:30 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for ListDatasetsResponse
Sep 09, 2015 8:15:30 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for ReadGroupSet
Sep 09, 2015 8:15:30 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for Range
Sep 09, 2015 8:15:30 AM com.google.cloud.dataflow.sdk.Pipeline applyInternal
WARNING: Transform Create.Values2 does not have a stable unique name. This will prevent reloading of pipelines.
Sep 09, 2015 8:15:32 AM com.google.cloud.dataflow.sdk.Pipeline applyInternal
WARNING: Transform Create.Values3 does not have a stable unique name. This will prevent reloading of pipelines.
Sep 09, 2015 8:15:32 AM com.google.cloud.dataflow.sdk.Pipeline applyInternal
WARNING: Transform View.AsSingleton2 does not have a stable unique name. This will prevent reloading of pipelines.
Sep 09, 2015 8:15:32 AM com.google.cloud.dataflow.sdk.Pipeline applyInternal
WARNING: Transform Create.Values4 does not have a stable unique name. This will prevent reloading of pipelines.
Sep 09, 2015 8:15:32 AM com.google.cloud.dataflow.sdk.Pipeline applyInternal
WARNING: Transform AnonymousParDo2 does not have a stable unique name. This will prevent reloading of pipelines.
Sep 09, 2015 8:15:32 AM com.google.cloud.dataflow.sdk.Pipeline applyInternal
WARNING: Transform RemoveDuplicateReadVariantPairs/AnonymousParDo2 does not have a stable unique name. This will prevent reloading of pipelines.
Sep 09, 2015 8:15:32 AM com.google.cloud.dataflow.sdk.Pipeline applyInternal
WARNING: Transform RemoveDuplicateReadVariantPairs/CoGroupByKey2 does not have a stable unique name. This will prevent reloading of pipelines.
Sep 09, 2015 8:15:32 AM com.google.cloud.dataflow.sdk.Pipeline applyInternal
WARNING: Transform RemoveDuplicateReadVariantPairs/AnonymousParDo3 does not have a stable unique name. This will prevent reloading of pipelines.
Sep 09, 2015 8:15:32 AM com.google.cloud.dataflow.sdk.Pipeline applyInternal
WARNING: Transform AnonymousParDo3 does not have a stable unique name. This will prevent reloading of pipelines.
Sep 09, 2015 8:15:32 AM com.google.cloud.dataflow.sdk.Pipeline applyInternal
WARNING: Transform AddContextDataToRead.StripToUUID2 does not have a stable unique name. This will prevent reloading of pipelines.
Sep 09, 2015 8:15:32 AM com.google.cloud.dataflow.sdk.Pipeline applyInternal
WARNING: Transform Keys2 does not have a stable unique name. This will prevent reloading of pipelines.
Sep 09, 2015 8:15:32 AM com.google.cloud.dataflow.sdk.Pipeline applyInternal
WARNING: Transform AddContextDataToRead.StripToUUID3 does not have a stable unique name. This will prevent reloading of pipelines.
Sep 09, 2015 8:15:32 AM com.google.cloud.dataflow.sdk.Pipeline applyInternal
WARNING: Transform View.AsSingleton3 does not have a stable unique name. This will prevent reloading of pipelines.
Sep 09, 2015 8:15:32 AM com.google.cloud.dataflow.sdk.Pipeline applyInternal
WARNING: Transform Count.Globally2 does not have a stable unique name. This will prevent reloading of pipelines.
Sep 09, 2015 8:15:32 AM com.google.cloud.dataflow.sdk.Pipeline applyInternal
WARNING: Transform View.AsSingleton4 does not have a stable unique name. This will prevent reloading of pipelines.
Sep 09, 2015 8:15:32 AM com.google.cloud.dataflow.sdk.Pipeline applyInternal
WARNING: Transform Count.Globally3 does not have a stable unique name. This will prevent reloading of pipelines.
Sep 09, 2015 8:15:32 AM com.google.cloud.dataflow.sdk.Pipeline applyInternal
WARNING: Transform View.AsSingleton5 does not have a stable unique name. This will prevent reloading of pipelines.
Sep 09, 2015 8:15:32 AM com.google.cloud.dataflow.sdk.Pipeline applyInternal
WARNING: Transform Count.Globally4 does not have a stable unique name. This will prevent reloading of pipelines.
Sep 09, 2015 8:15:32 AM com.google.cloud.dataflow.sdk.Pipeline applyInternal
WARNING: Transform CoGroupByKey2 does not have a stable unique name. This will prevent reloading of pipelines.
Sep 09, 2015 8:15:32 AM com.google.cloud.dataflow.sdk.Pipeline applyInternal
WARNING: Transform CoGroupByKey3 does not have a stable unique name. This will prevent reloading of pipelines.
Sep 09, 2015 8:15:32 AM com.google.cloud.dataflow.sdk.Pipeline applyInternal
WARNING: Transform AnonymousParDo4 does not have a stable unique name. This will prevent reloading of pipelines.
Sep 09, 2015 8:15:32 AM com.google.cloud.dataflow.sdk.runners.DirectPipelineRunner run
INFO: Executing pipeline using the DirectPipelineRunner.
Sep 09, 2015 8:15:48 AM com.google.cloud.dataflow.sdk.runners.DirectPipelineRunner run
INFO: Pipeline execution complete.
[September 9, 2015 8:15:53 AM UTC] org.broadinstitute.hellbender.tools.dataflow.pipelines.BaseRecalibratorDataflow done. Elapsed time: 0.38 minutes.
Runtime.totalMemory()=1496842240
[September 9, 2015 8:15:53 AM UTC] org.broadinstitute.hellbender.tools.dataflow.pipelines.BaseRecalibratorDataflow  --RECAL_TABLE_FILE /tmp/walktest.tmp_param.04161860272704820551.tmp --quantizing_levels 6 --sort_by_all_columns true --input src/test/resources/org/broadinstitute/hellbender/tools/BQSR/CEUTrio.HiSeq.WGS.b37.ch20.1m-1m1k.NA12878.bam --reference gg://reference/EOSsjdnTicvzwAE --baseRecalibrationKnownVariants src/test/resources/org/broadinstitute/hellbender/tools/BQSR/dbsnp_132.b37.excluding_sites_after_129.chr17_69k_70k.vcf --project broad-dsde-dev --apiKey *********** --VERBOSITY ERROR  --run_without_dbsnp_potentially_ruining_quality false --solid_recal_mode SET_Q_ZERO --solid_nocall_strategy THROW_EXCEPTION --mismatches_context_size 2 --indels_context_size 3 --maximum_cycle_value 500 --mismatches_default_quality -1 --insertions_default_quality 45 --deletions_default_quality 45 --low_quality_tail 2 --interval_set_rule UNION --interval_padding 0 --bqsrBAQGapOpenPenalty 40.0 --preserve_qscores_less_than 6 --useOriginalQualities false --defaultBaseQualities -1 --runner LOCAL --numWorkers 0 --help false --version false --QUIET false
[September 9, 2015 8:15:53 AM UTC] Executing as travis@testing-worker-linux-docker-75fb849c-3212-linux-2 on Linux 3.13.0-40-generic amd64; Java HotSpot(TM) 64-Bit Server VM 1.8.0_31-b13; Version: Version:null JdkDeflater
Sep 09, 2015 8:15:53 AM com.google.cloud.dataflow.sdk.runners.DirectPipelineRunner <init>
INFO: DirectPipelineRunner using random seed 1835310172353948517.
Sep 09, 2015 8:15:53 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coders for genomics classes
Sep 09, 2015 8:15:53 AM org.reflections.Reflections scan
INFO: Reflections took 136 ms to scan 250 urls, producing 79 keys and 156 values 
Sep 09, 2015 8:15:53 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for SearchVariantsResponse
Sep 09, 2015 8:15:53 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for ImportVariantsRequest
Sep 09, 2015 8:15:53 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for ExperimentalCreateJobResponse
Sep 09, 2015 8:15:53 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for SearchVariantSetsRequest
Sep 09, 2015 8:15:53 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for VariantSet
Sep 09, 2015 8:15:53 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for ExportVariantSetResponse
Sep 09, 2015 8:15:53 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for KeyValue
Sep 09, 2015 8:15:53 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for ListCoverageBucketsResponse
Sep 09, 2015 8:15:53 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for AlignReadGroupSetsResponse
Sep 09, 2015 8:15:53 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for ImportVariantsResponse
Sep 09, 2015 8:15:53 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for SearchReferenceSetsResponse
Sep 09, 2015 8:15:53 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for ReadGroupProgram
Sep 09, 2015 8:15:53 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for SearchCallSetsResponse
Sep 09, 2015 8:15:53 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for Reference
Sep 09, 2015 8:15:53 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for ExternalId
Sep 09, 2015 8:15:53 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for SearchReadsRequest
Sep 09, 2015 8:15:53 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for ExportVariantSetRequest
Sep 09, 2015 8:15:53 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for CallSet
Sep 09, 2015 8:15:53 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for JobRequest
Sep 09, 2015 8:15:53 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for Metadata
Sep 09, 2015 8:15:53 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for ReferenceSet
Sep 09, 2015 8:15:53 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for CallReadGroupSetsResponse
Sep 09, 2015 8:15:53 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for FastqMetadata
Sep 09, 2015 8:15:53 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for SearchVariantsRequest
Sep 09, 2015 8:15:53 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for SearchAnnotationSetsRequest
Sep 09, 2015 8:15:53 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for SearchReadGroupSetsRequest
Sep 09, 2015 8:15:53 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for CoverageBucket
Sep 09, 2015 8:15:53 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for SearchJobsResponse
Sep 09, 2015 8:15:53 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for ImportReadGroupSetsRequest
Sep 09, 2015 8:15:53 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for TranscriptCodingSequence
Sep 09, 2015 8:15:53 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for Variant
Sep 09, 2015 8:15:53 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for SearchReadGroupSetsResponse
Sep 09, 2015 8:15:53 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for SearchAnnotationsRequest
Sep 09, 2015 8:15:53 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for SearchVariantSetsResponse
Sep 09, 2015 8:15:53 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for InterleavedFastqSource
Sep 09, 2015 8:15:53 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for BatchCreateAnnotationsRequest
Sep 09, 2015 8:15:53 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for SearchReferencesRequest
Sep 09, 2015 8:15:53 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for SearchJobsRequest
Sep 09, 2015 8:15:53 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for AlignReadGroupSetsRequest
Sep 09, 2015 8:15:53 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for Job
Sep 09, 2015 8:15:53 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for TranscriptExon
Sep 09, 2015 8:15:53 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for SearchReferenceSetsRequest
Sep 09, 2015 8:15:53 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for QueryRange
Sep 09, 2015 8:15:53 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for LinearAlignment
Sep 09, 2015 8:15:53 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for Position
Sep 09, 2015 8:15:53 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for Annotation
Sep 09, 2015 8:15:53 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for SearchReadsResponse
Sep 09, 2015 8:15:53 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for ExperimentalCreateJobRequest
Sep 09, 2015 8:15:53 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for AnnotationSet
Sep 09, 2015 8:15:53 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for Dataset
Sep 09, 2015 8:15:53 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for Read
Sep 09, 2015 8:15:53 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for Call
Sep 09, 2015 8:15:53 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for ReadGroupExperiment
Sep 09, 2015 8:15:53 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for VariantAnnotationCondition
Sep 09, 2015 8:15:53 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for ReadGroup
Sep 09, 2015 8:15:53 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for VariantAnnotation
Sep 09, 2015 8:15:53 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for Int32Value
Sep 09, 2015 8:15:53 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for ExportReadGroupSetsRequest
Sep 09, 2015 8:15:53 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for ReferenceBound
Sep 09, 2015 8:15:53 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for ImportReadGroupSetsResponse
Sep 09, 2015 8:15:53 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for MergeVariantsRequest
Sep 09, 2015 8:15:53 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for CigarUnit
Sep 09, 2015 8:15:53 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for SearchAnnotationsResponse
Sep 09, 2015 8:15:53 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for BatchAnnotationsResponseEntry
Sep 09, 2015 8:15:53 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for CallReadGroupSetsRequest
Sep 09, 2015 8:15:53 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for ListBasesResponse
Sep 09, 2015 8:15:53 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for SearchReferencesResponse
Sep 09, 2015 8:15:53 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for PairedFastqSource
Sep 09, 2015 8:15:53 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for BatchAnnotationsResponse
Sep 09, 2015 8:15:53 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for SearchCallSetsRequest
Sep 09, 2015 8:15:53 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for RangePosition
Sep 09, 2015 8:15:53 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for Transcript
Sep 09, 2015 8:15:53 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for BatchAnnotationsResponseEntryStatus
Sep 09, 2015 8:15:53 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for ExportReadGroupSetsResponse
Sep 09, 2015 8:15:53 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for SearchAnnotationSetsResponse
Sep 09, 2015 8:15:53 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for ListDatasetsResponse
Sep 09, 2015 8:15:53 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for ReadGroupSet
Sep 09, 2015 8:15:53 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for Range
Sep 09, 2015 8:15:53 AM com.google.cloud.dataflow.sdk.Pipeline applyInternal
WARNING: Transform Create.Values2 does not have a stable unique name. This will prevent reloading of pipelines.
Sep 09, 2015 8:15:53 AM com.google.cloud.dataflow.sdk.Pipeline applyInternal
WARNING: Transform Create.Values3 does not have a stable unique name. This will prevent reloading of pipelines.
Sep 09, 2015 8:15:53 AM com.google.cloud.dataflow.sdk.Pipeline applyInternal
WARNING: Transform View.AsSingleton2 does not have a stable unique name. This will prevent reloading of pipelines.
Sep 09, 2015 8:15:53 AM com.google.cloud.dataflow.sdk.Pipeline applyInternal
WARNING: Transform Create.Values4 does not have a stable unique name. This will prevent reloading of pipelines.
Sep 09, 2015 8:15:53 AM com.google.cloud.dataflow.sdk.Pipeline applyInternal
WARNING: Transform AnonymousParDo2 does not have a stable unique name. This will prevent reloading of pipelines.
Sep 09, 2015 8:15:53 AM com.google.cloud.dataflow.sdk.Pipeline applyInternal
WARNING: Transform RemoveDuplicateReadVariantPairs/AnonymousParDo2 does not have a stable unique name. This will prevent reloading of pipelines.
Sep 09, 2015 8:15:53 AM com.google.cloud.dataflow.sdk.Pipeline applyInternal
WARNING: Transform RemoveDuplicateReadVariantPairs/CoGroupByKey2 does not have a stable unique name. This will prevent reloading of pipelines.
Sep 09, 2015 8:15:53 AM com.google.cloud.dataflow.sdk.Pipeline applyInternal
WARNING: Transform RemoveDuplicateReadVariantPairs/AnonymousParDo3 does not have a stable unique name. This will prevent reloading of pipelines.
Sep 09, 2015 8:15:53 AM com.google.cloud.dataflow.sdk.Pipeline applyInternal
WARNING: Transform AnonymousParDo3 does not have a stable unique name. This will prevent reloading of pipelines.
Sep 09, 2015 8:15:53 AM com.google.cloud.dataflow.sdk.Pipeline applyInternal
WARNING: Transform AddContextDataToRead.StripToUUID2 does not have a stable unique name. This will prevent reloading of pipelines.
Sep 09, 2015 8:15:53 AM com.google.cloud.dataflow.sdk.Pipeline applyInternal
WARNING: Transform Keys2 does not have a stable unique name. This will prevent reloading of pipelines.
Sep 09, 2015 8:15:53 AM com.google.cloud.dataflow.sdk.Pipeline applyInternal
WARNING: Transform AddContextDataToRead.StripToUUID3 does not have a stable unique name. This will prevent reloading of pipelines.
Sep 09, 2015 8:15:53 AM com.google.cloud.dataflow.sdk.Pipeline applyInternal
WARNING: Transform View.AsSingleton3 does not have a stable unique name. This will prevent reloading of pipelines.
Sep 09, 2015 8:15:53 AM com.google.cloud.dataflow.sdk.Pipeline applyInternal
WARNING: Transform Count.Globally2 does not have a stable unique name. This will prevent reloading of pipelines.
Sep 09, 2015 8:15:53 AM com.google.cloud.dataflow.sdk.Pipeline applyInternal
WARNING: Transform View.AsSingleton4 does not have a stable unique name. This will prevent reloading of pipelines.
Sep 09, 2015 8:15:53 AM com.google.cloud.dataflow.sdk.Pipeline applyInternal
WARNING: Transform Count.Globally3 does not have a stable unique name. This will prevent reloading of pipelines.
Sep 09, 2015 8:15:53 AM com.google.cloud.dataflow.sdk.Pipeline applyInternal
WARNING: Transform View.AsSingleton5 does not have a stable unique name. This will prevent reloading of pipelines.
Sep 09, 2015 8:15:53 AM com.google.cloud.dataflow.sdk.Pipeline applyInternal
WARNING: Transform Count.Globally4 does not have a stable unique name. This will prevent reloading of pipelines.
Sep 09, 2015 8:15:53 AM com.google.cloud.dataflow.sdk.Pipeline applyInternal
WARNING: Transform CoGroupByKey2 does not have a stable unique name. This will prevent reloading of pipelines.
Sep 09, 2015 8:15:53 AM com.google.cloud.dataflow.sdk.Pipeline applyInternal
WARNING: Transform CoGroupByKey3 does not have a stable unique name. This will prevent reloading of pipelines.
Sep 09, 2015 8:15:53 AM com.google.cloud.dataflow.sdk.Pipeline applyInternal
WARNING: Transform AnonymousParDo4 does not have a stable unique name. This will prevent reloading of pipelines.
Sep 09, 2015 8:15:53 AM com.google.cloud.dataflow.sdk.runners.DirectPipelineRunner run
INFO: Executing pipeline using the DirectPipelineRunner.
Sep 09, 2015 8:16:14 AM com.google.cloud.dataflow.sdk.runners.DirectPipelineRunner run
INFO: Pipeline execution complete.
[September 9, 2015 8:16:19 AM UTC] org.broadinstitute.hellbender.tools.dataflow.pipelines.BaseRecalibratorDataflow done. Elapsed time: 0.44 minutes.
Runtime.totalMemory()=1701838848
[September 9, 2015 8:16:19 AM UTC] org.broadinstitute.hellbender.tools.dataflow.pipelines.BaseRecalibratorDataflow  --RECAL_TABLE_FILE /tmp/walktest.tmp_param.05809810738604115770.tmp --mismatches_context_size 4 --sort_by_all_columns true --input src/test/resources/org/broadinstitute/hellbender/tools/BQSR/CEUTrio.HiSeq.WGS.b37.ch20.1m-1m1k.NA12878.bam --reference gg://reference/EOSsjdnTicvzwAE --baseRecalibrationKnownVariants src/test/resources/org/broadinstitute/hellbender/tools/BQSR/dbsnp_132.b37.excluding_sites_after_129.chr17_69k_70k.vcf --project broad-dsde-dev --apiKey *********** --VERBOSITY ERROR  --run_without_dbsnp_potentially_ruining_quality false --solid_recal_mode SET_Q_ZERO --solid_nocall_strategy THROW_EXCEPTION --indels_context_size 3 --maximum_cycle_value 500 --mismatches_default_quality -1 --insertions_default_quality 45 --deletions_default_quality 45 --low_quality_tail 2 --quantizing_levels 16 --interval_set_rule UNION --interval_padding 0 --bqsrBAQGapOpenPenalty 40.0 --preserve_qscores_less_than 6 --useOriginalQualities false --defaultBaseQualities -1 --runner LOCAL --numWorkers 0 --help false --version false --QUIET false
[September 9, 2015 8:16:19 AM UTC] Executing as travis@testing-worker-linux-docker-75fb849c-3212-linux-2 on Linux 3.13.0-40-generic amd64; Java HotSpot(TM) 64-Bit Server VM 1.8.0_31-b13; Version: Version:null JdkDeflater
Sep 09, 2015 8:16:19 AM com.google.cloud.dataflow.sdk.runners.DirectPipelineRunner <init>
INFO: DirectPipelineRunner using random seed 1497070226050510126.
Sep 09, 2015 8:16:19 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coders for genomics classes
Sep 09, 2015 8:16:20 AM org.reflections.Reflections scan
INFO: Reflections took 146 ms to scan 250 urls, producing 79 keys and 156 values 
Sep 09, 2015 8:16:20 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for SearchVariantsResponse
Sep 09, 2015 8:16:20 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for ImportVariantsRequest
Sep 09, 2015 8:16:20 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for ExperimentalCreateJobResponse
Sep 09, 2015 8:16:20 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for SearchVariantSetsRequest
Sep 09, 2015 8:16:20 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for VariantSet
Sep 09, 2015 8:16:20 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for ExportVariantSetResponse
Sep 09, 2015 8:16:20 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for KeyValue
Sep 09, 2015 8:16:20 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for ListCoverageBucketsResponse
Sep 09, 2015 8:16:20 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for AlignReadGroupSetsResponse
Sep 09, 2015 8:16:20 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for ImportVariantsResponse
Sep 09, 2015 8:16:20 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for SearchReferenceSetsResponse
Sep 09, 2015 8:16:20 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for ReadGroupProgram
Sep 09, 2015 8:16:20 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for SearchCallSetsResponse
Sep 09, 2015 8:16:20 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for Reference
Sep 09, 2015 8:16:20 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for ExternalId
Sep 09, 2015 8:16:20 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for SearchReadsRequest
Sep 09, 2015 8:16:20 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for ExportVariantSetRequest
Sep 09, 2015 8:16:20 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for CallSet
Sep 09, 2015 8:16:20 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for JobRequest
Sep 09, 2015 8:16:20 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for Metadata
Sep 09, 2015 8:16:20 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for ReferenceSet
Sep 09, 2015 8:16:20 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for CallReadGroupSetsResponse
Sep 09, 2015 8:16:20 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for FastqMetadata
Sep 09, 2015 8:16:20 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for SearchVariantsRequest
Sep 09, 2015 8:16:20 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for SearchAnnotationSetsRequest
Sep 09, 2015 8:16:20 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for SearchReadGroupSetsRequest
Sep 09, 2015 8:16:20 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for CoverageBucket
Sep 09, 2015 8:16:20 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for SearchJobsResponse
Sep 09, 2015 8:16:20 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for ImportReadGroupSetsRequest
Sep 09, 2015 8:16:20 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for TranscriptCodingSequence
Sep 09, 2015 8:16:20 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for Variant
Sep 09, 2015 8:16:20 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for SearchReadGroupSetsResponse
Sep 09, 2015 8:16:20 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for SearchAnnotationsRequest
Sep 09, 2015 8:16:20 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for SearchVariantSetsResponse
Sep 09, 2015 8:16:20 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for InterleavedFastqSource
Sep 09, 2015 8:16:20 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for BatchCreateAnnotationsRequest
Sep 09, 2015 8:16:20 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for SearchReferencesRequest
Sep 09, 2015 8:16:20 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for SearchJobsRequest
Sep 09, 2015 8:16:20 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for AlignReadGroupSetsRequest
Sep 09, 2015 8:16:20 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for Job
Sep 09, 2015 8:16:20 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for TranscriptExon
Sep 09, 2015 8:16:20 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for SearchReferenceSetsRequest
Sep 09, 2015 8:16:20 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for QueryRange
Sep 09, 2015 8:16:20 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for LinearAlignment
Sep 09, 2015 8:16:20 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for Position
Sep 09, 2015 8:16:20 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for Annotation
Sep 09, 2015 8:16:20 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for SearchReadsResponse
Sep 09, 2015 8:16:20 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for ExperimentalCreateJobRequest
Sep 09, 2015 8:16:20 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for AnnotationSet
Sep 09, 2015 8:16:20 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for Dataset
Sep 09, 2015 8:16:20 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for Read
Sep 09, 2015 8:16:20 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for Call
Sep 09, 2015 8:16:20 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for ReadGroupExperiment
Sep 09, 2015 8:16:20 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for VariantAnnotationCondition
Sep 09, 2015 8:16:20 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for ReadGroup
Sep 09, 2015 8:16:20 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for VariantAnnotation
Sep 09, 2015 8:16:20 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for Int32Value
Sep 09, 2015 8:16:20 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for ExportReadGroupSetsRequest
Sep 09, 2015 8:16:20 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for ReferenceBound
Sep 09, 2015 8:16:20 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for ImportReadGroupSetsResponse
Sep 09, 2015 8:16:20 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for MergeVariantsRequest
Sep 09, 2015 8:16:20 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for CigarUnit
Sep 09, 2015 8:16:20 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for SearchAnnotationsResponse
Sep 09, 2015 8:16:20 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for BatchAnnotationsResponseEntry
Sep 09, 2015 8:16:20 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for CallReadGroupSetsRequest
Sep 09, 2015 8:16:20 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for ListBasesResponse
Sep 09, 2015 8:16:20 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for SearchReferencesResponse
Sep 09, 2015 8:16:20 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for PairedFastqSource
Sep 09, 2015 8:16:20 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for BatchAnnotationsResponse
Sep 09, 2015 8:16:20 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for SearchCallSetsRequest
Sep 09, 2015 8:16:20 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for RangePosition
Sep 09, 2015 8:16:20 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for Transcript
Sep 09, 2015 8:16:20 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for BatchAnnotationsResponseEntryStatus
Sep 09, 2015 8:16:20 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for ExportReadGroupSetsResponse
Sep 09, 2015 8:16:20 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for SearchAnnotationSetsResponse
Sep 09, 2015 8:16:20 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for ListDatasetsResponse
Sep 09, 2015 8:16:20 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for ReadGroupSet
Sep 09, 2015 8:16:20 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for Range
Sep 09, 2015 8:16:20 AM com.google.cloud.dataflow.sdk.Pipeline applyInternal
WARNING: Transform Create.Values2 does not have a stable unique name. This will prevent reloading of pipelines.
Sep 09, 2015 8:16:20 AM com.google.cloud.dataflow.sdk.Pipeline applyInternal
WARNING: Transform Create.Values3 does not have a stable unique name. This will prevent reloading of pipelines.
Sep 09, 2015 8:16:20 AM com.google.cloud.dataflow.sdk.Pipeline applyInternal
WARNING: Transform View.AsSingleton2 does not have a stable unique name. This will prevent reloading of pipelines.
Sep 09, 2015 8:16:20 AM com.google.cloud.dataflow.sdk.Pipeline applyInternal
WARNING: Transform Create.Values4 does not have a stable unique name. This will prevent reloading of pipelines.
Sep 09, 2015 8:16:20 AM com.google.cloud.dataflow.sdk.Pipeline applyInternal
WARNING: Transform AnonymousParDo2 does not have a stable unique name. This will prevent reloading of pipelines.
Sep 09, 2015 8:16:20 AM com.google.cloud.dataflow.sdk.Pipeline applyInternal
WARNING: Transform RemoveDuplicateReadVariantPairs/AnonymousParDo2 does not have a stable unique name. This will prevent reloading of pipelines.
Sep 09, 2015 8:16:20 AM com.google.cloud.dataflow.sdk.Pipeline applyInternal
WARNING: Transform RemoveDuplicateReadVariantPairs/CoGroupByKey2 does not have a stable unique name. This will prevent reloading of pipelines.
Sep 09, 2015 8:16:20 AM com.google.cloud.dataflow.sdk.Pipeline applyInternal
WARNING: Transform RemoveDuplicateReadVariantPairs/AnonymousParDo3 does not have a stable unique name. This will prevent reloading of pipelines.
Sep 09, 2015 8:16:20 AM com.google.cloud.dataflow.sdk.Pipeline applyInternal
WARNING: Transform AnonymousParDo3 does not have a stable unique name. This will prevent reloading of pipelines.
Sep 09, 2015 8:16:20 AM com.google.cloud.dataflow.sdk.Pipeline applyInternal
WARNING: Transform AddContextDataToRead.StripToUUID2 does not have a stable unique name. This will prevent reloading of pipelines.
Sep 09, 2015 8:16:20 AM com.google.cloud.dataflow.sdk.Pipeline applyInternal
WARNING: Transform Keys2 does not have a stable unique name. This will prevent reloading of pipelines.
Sep 09, 2015 8:16:20 AM com.google.cloud.dataflow.sdk.Pipeline applyInternal
WARNING: Transform AddContextDataToRead.StripToUUID3 does not have a stable unique name. This will prevent reloading of pipelines.
Sep 09, 2015 8:16:20 AM com.google.cloud.dataflow.sdk.Pipeline applyInternal
WARNING: Transform View.AsSingleton3 does not have a stable unique name. This will prevent reloading of pipelines.
Sep 09, 2015 8:16:20 AM com.google.cloud.dataflow.sdk.Pipeline applyInternal
WARNING: Transform Count.Globally2 does not have a stable unique name. This will prevent reloading of pipelines.
Sep 09, 2015 8:16:20 AM com.google.cloud.dataflow.sdk.Pipeline applyInternal
WARNING: Transform View.AsSingleton4 does not have a stable unique name. This will prevent reloading of pipelines.
Sep 09, 2015 8:16:20 AM com.google.cloud.dataflow.sdk.Pipeline applyInternal
WARNING: Transform Count.Globally3 does not have a stable unique name. This will prevent reloading of pipelines.
Sep 09, 2015 8:16:20 AM com.google.cloud.dataflow.sdk.Pipeline applyInternal
WARNING: Transform View.AsSingleton5 does not have a stable unique name. This will prevent reloading of pipelines.
Sep 09, 2015 8:16:20 AM com.google.cloud.dataflow.sdk.Pipeline applyInternal
WARNING: Transform Count.Globally4 does not have a stable unique name. This will prevent reloading of pipelines.
Sep 09, 2015 8:16:20 AM com.google.cloud.dataflow.sdk.Pipeline applyInternal
WARNING: Transform CoGroupByKey2 does not have a stable unique name. This will prevent reloading of pipelines.
Sep 09, 2015 8:16:20 AM com.google.cloud.dataflow.sdk.Pipeline applyInternal
WARNING: Transform CoGroupByKey3 does not have a stable unique name. This will prevent reloading of pipelines.
Sep 09, 2015 8:16:20 AM com.google.cloud.dataflow.sdk.Pipeline applyInternal
WARNING: Transform AnonymousParDo4 does not have a stable unique name. This will prevent reloading of pipelines.
Sep 09, 2015 8:16:20 AM com.google.cloud.dataflow.sdk.runners.DirectPipelineRunner run
INFO: Executing pipeline using the DirectPipelineRunner.
Sep 09, 2015 8:16:42 AM com.google.cloud.dataflow.sdk.runners.DirectPipelineRunner run
INFO: Pipeline execution complete.
[September 9, 2015 8:16:51 AM UTC] org.broadinstitute.hellbender.tools.dataflow.pipelines.BaseRecalibratorDataflow done. Elapsed time: 0.53 minutes.
Runtime.totalMemory()=1886388224