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

all > org.broadinstitute.hellbender.tools.dataflow.pipelines > ApplyBQSRDataflowIntegrationTest

tests

failures

ignored

6m48.74s

duration

100%

successful

Tests
Standard output
Standard error

Tests

Test	Duration	Result
testPR_Cloud[0](ApplyBQSR(args=''))	6m36.28s	passed
testPR_GCS[0](ApplyBQSR(args=''))	12.457s	passed

Standard output

--------------------------------------------------------------------------------
[08:03:25] Executing test ApplyBQSRDataflowIntegrationTest:testPrintReads-
Dataflow SDK version: 0.4.150727
Submitted job: 2015-09-09_01_03_57-11503430311039115193
2015-09-09T08:04:09.283Z: Detail:  (7976fbd970c855f7): Checking required Cloud APIs are enabled.
2015-09-09T08:04:09.503Z: Detail:  (7976fbd970c853af): Expanding GroupByKey operations into optimizable parts.
2015-09-09T08:04:09.506Z: Detail:  (7976fbd970c8571d): Lifting ValueCombiningMappingFns into MergeBucketsMappingFns
2015-09-09T08:04:09.509Z: Detail:  (7976fbd970c85a8b): Annotating graph with Autotuner information.
2015-09-09T08:04:09.521Z: Detail:  (7976fbd970c85843): Fusing adjacent ParDo, Read, Write, and Flatten operations
2015-09-09T08:04:09.526Z: Detail:  (7976fbd970c85f1f): Fusing consumer ApplyBQSRTransform/ApplyBQSR into GoogleGenomicsReadToGATKRead/AnonymousParDo
2015-09-09T08:04:09.533Z: Detail:  (7976fbd970c85969): Fusing consumer GoogleGenomicsReadToGATKRead/AnonymousParDo into ParDo(Read)
2015-09-09T08:04:09.570Z: Detail:  (7976fbd970c85049): Adding StepResource setup and teardown to workflow graph.
2015-09-09T08:04:10.245Z: Basic:  (bfe0905c201ab9f4): Starting 3 workers...
2015-09-09T08:04:10.278Z: Basic:  S01: (2e58376b2274311c): Executing operation View.AsSingleton/View.CreatePCollectionView
2015-09-09T08:04:10.287Z: Basic:  S02: (703625f60a61a671): Executing operation ingest calibration report
2015-09-09T08:05:02.660Z: Detail:  (95646dc0054da812): Workers have started successfully.
2015-09-09T08:05:29.573Z: Basic:  S03: (904c2cecc4de5474): Executing operation View.AsSingleton2/View.CreatePCollectionView
2015-09-09T08:05:29.607Z: Basic:  S04: (9b5758480a207f96): Executing operation ParDo(Read)+GoogleGenomicsReadToGATKRead/AnonymousParDo+ApplyBQSRTransform/ApplyBQSR
2015-09-09T08:05:37.717Z: Basic:  S05: (703625f60a61a16c): Executing operation View.AsIterable/View.CreatePCollectionView
2015-09-09T08:05:37.753Z: Basic:  S06: (84f3900232b29333): Executing operation save to BAM file
2015-09-09T08:05:40.136Z: Basic:  (ba78299476d76a4): Stopping worker pool...
2015-09-09T08:06:27.798Z: Basic:  (ba78299476d7abb): Worker pool stopped.
2015-09-09T08:06:27.854Z: Detail:  (904c2cecc4de5c6a): Cleaning up.
--------------------------------------------------------------------------------
[08:10:01] Executing test ApplyBQSRDataflowIntegrationTest:testPrintReads-

Standard error

[September 9, 2015 8:03:26 AM UTC] org.broadinstitute.hellbender.tools.dataflow.pipelines.ApplyBQSRDataflow  --input gs://hellbender/test/resources/org/broadinstitute/hellbender/tools/BQSR/HiSeq.1mb.1RG.2k_lines.alternate_allaligned.bam --output /tmp/walktest.tmp_param.06040313098481188367.tmp --bqsr_recal_file gs://hellbender/test/resources/org/broadinstitute/hellbender/tools/BQSR/HiSeq.20mb.1RG.table.gz --runner BLOCKING --project broad-dsde-dev --staging gs://hellbender/test/staging/ --apiKey *********** --VERBOSITY ERROR  --interval_set_rule UNION --interval_padding 0 --quantize_quals 0 --disable_indel_quals false --emit_original_quals false --preserve_qscores_less_than 6 --globalQScorePrior -1.0 --numWorkers 0 --help false --version false --QUIET false
[September 9, 2015 8:03:26 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
SLF4J: Class path contains multiple SLF4J bindings.
SLF4J: Found binding in [jar:file:/home/travis/.gradle/caches/modules-2/files-2.1/org.slf4j/slf4j-jdk14/1.7.7/25d160723ea37a6cb84e87cd70773ff02997e857/slf4j-jdk14-1.7.7.jar!/org/slf4j/impl/StaticLoggerBinder.class]
SLF4J: Found binding in [jar:file:/home/travis/.gradle/caches/modules-2/files-2.1/org.slf4j/slf4j-log4j12/1.7.10/b3eeae7d1765f988a1f45ea81517191315c69c9e/slf4j-log4j12-1.7.10.jar!/org/slf4j/impl/StaticLoggerBinder.class]
SLF4J: See http://www.slf4j.org/codes.html#multiple_bindings for an explanation.
SLF4J: Actual binding is of type [org.slf4j.impl.JDK14LoggerFactory]
Sep 09, 2015 8:03:28 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 8:03:29 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coders for genomics classes
Sep 09, 2015 8:03:30 AM org.reflections.Reflections scan
INFO: Reflections took 1157 ms to scan 250 urls, producing 79 keys and 156 values 
Sep 09, 2015 8:03:30 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for SearchVariantsResponse
Sep 09, 2015 8:03:30 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for ImportVariantsRequest
Sep 09, 2015 8:03:30 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for ExperimentalCreateJobResponse
Sep 09, 2015 8:03:30 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for SearchVariantSetsRequest
Sep 09, 2015 8:03:30 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for VariantSet
Sep 09, 2015 8:03:30 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for ExportVariantSetResponse
Sep 09, 2015 8:03:30 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for KeyValue
Sep 09, 2015 8:03:30 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for ListCoverageBucketsResponse
Sep 09, 2015 8:03:30 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for AlignReadGroupSetsResponse
Sep 09, 2015 8:03:30 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for ImportVariantsResponse
Sep 09, 2015 8:03:30 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for SearchReferenceSetsResponse
Sep 09, 2015 8:03:30 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for ReadGroupProgram
Sep 09, 2015 8:03:30 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for SearchCallSetsResponse
Sep 09, 2015 8:03:31 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for Reference
Sep 09, 2015 8:03:31 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for ExternalId
Sep 09, 2015 8:03:31 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for SearchReadsRequest
Sep 09, 2015 8:03:31 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for ExportVariantSetRequest
Sep 09, 2015 8:03:31 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for CallSet
Sep 09, 2015 8:03:31 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for JobRequest
Sep 09, 2015 8:03:31 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for Metadata
Sep 09, 2015 8:03:31 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for ReferenceSet
Sep 09, 2015 8:03:31 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for CallReadGroupSetsResponse
Sep 09, 2015 8:03:31 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for FastqMetadata
Sep 09, 2015 8:03:31 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for SearchVariantsRequest
Sep 09, 2015 8:03:31 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for SearchAnnotationSetsRequest
Sep 09, 2015 8:03:31 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for SearchReadGroupSetsRequest
Sep 09, 2015 8:03:31 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for CoverageBucket
Sep 09, 2015 8:03:31 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for SearchJobsResponse
Sep 09, 2015 8:03:31 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for ImportReadGroupSetsRequest
Sep 09, 2015 8:03:31 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for TranscriptCodingSequence
Sep 09, 2015 8:03:31 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for Variant
Sep 09, 2015 8:03:31 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for SearchReadGroupSetsResponse
Sep 09, 2015 8:03:31 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for SearchAnnotationsRequest
Sep 09, 2015 8:03:31 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for SearchVariantSetsResponse
Sep 09, 2015 8:03:31 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for InterleavedFastqSource
Sep 09, 2015 8:03:31 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for BatchCreateAnnotationsRequest
Sep 09, 2015 8:03:31 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for SearchReferencesRequest
Sep 09, 2015 8:03:31 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for SearchJobsRequest
Sep 09, 2015 8:03:31 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for AlignReadGroupSetsRequest
Sep 09, 2015 8:03:31 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for Job
Sep 09, 2015 8:03:31 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for TranscriptExon
Sep 09, 2015 8:03:31 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for SearchReferenceSetsRequest
Sep 09, 2015 8:03:31 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for QueryRange
Sep 09, 2015 8:03:31 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for LinearAlignment
Sep 09, 2015 8:03:31 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for Position
Sep 09, 2015 8:03:31 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for Annotation
Sep 09, 2015 8:03:31 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for SearchReadsResponse
Sep 09, 2015 8:03:31 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for ExperimentalCreateJobRequest
Sep 09, 2015 8:03:31 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for AnnotationSet
Sep 09, 2015 8:03:31 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for Dataset
Sep 09, 2015 8:03:31 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for Read
Sep 09, 2015 8:03:31 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for Call
Sep 09, 2015 8:03:31 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for ReadGroupExperiment
Sep 09, 2015 8:03:31 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for VariantAnnotationCondition
Sep 09, 2015 8:03:31 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for ReadGroup
Sep 09, 2015 8:03:31 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for VariantAnnotation
Sep 09, 2015 8:03:31 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for Int32Value
Sep 09, 2015 8:03:31 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for ExportReadGroupSetsRequest
Sep 09, 2015 8:03:31 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for ReferenceBound
Sep 09, 2015 8:03:31 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for ImportReadGroupSetsResponse
Sep 09, 2015 8:03:31 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for MergeVariantsRequest
Sep 09, 2015 8:03:31 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for CigarUnit
Sep 09, 2015 8:03:31 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for SearchAnnotationsResponse
Sep 09, 2015 8:03:31 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for BatchAnnotationsResponseEntry
Sep 09, 2015 8:03:31 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for CallReadGroupSetsRequest
Sep 09, 2015 8:03:31 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for ListBasesResponse
Sep 09, 2015 8:03:31 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for SearchReferencesResponse
Sep 09, 2015 8:03:31 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for PairedFastqSource
Sep 09, 2015 8:03:31 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for BatchAnnotationsResponse
Sep 09, 2015 8:03:31 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for SearchCallSetsRequest
Sep 09, 2015 8:03:31 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for RangePosition
Sep 09, 2015 8:03:31 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for Transcript
Sep 09, 2015 8:03:31 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for BatchAnnotationsResponseEntryStatus
Sep 09, 2015 8:03:31 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for ExportReadGroupSetsResponse
Sep 09, 2015 8:03:31 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for SearchAnnotationSetsResponse
Sep 09, 2015 8:03:31 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for ListDatasetsResponse
Sep 09, 2015 8:03:31 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for ReadGroupSet
Sep 09, 2015 8:03:31 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for Range
Sep 09, 2015 8:03:31 AM com.google.cloud.genomics.dataflow.utils.GCSOptions$Methods createStorageClient
INFO: Creating storgae client for DataflowCommandLineProgram
Sep 09, 2015 8:03:31 AM com.google.cloud.genomics.dataflow.readers.bam.SeekableGCSStream <init>
INFO: Creating SeekableGCSStream: gs://hellbender/test/resources/org/broadinstitute/hellbender/tools/BQSR/HiSeq.1mb.1RG.2k_lines.alternate_allaligned.bam.bai
Sep 09, 2015 8:03:31 AM com.google.cloud.genomics.dataflow.readers.bam.SeekableGCSStream uriToStorageObject
INFO: uriToStorageObject hellbender/test/resources/org/broadinstitute/hellbender/tools/BQSR/HiSeq.1mb.1RG.2k_lines.alternate_allaligned.bam.bai=hellbender:test/resources/org/broadinstitute/hellbender/tools/BQSR/HiSeq.1mb.1RG.2k_lines.alternate_allaligned.bam.bai
Sep 09, 2015 8:03:32 AM com.google.cloud.genomics.dataflow.readers.bam.SeekableGCSStream <init>
INFO: Creating SeekableGCSStream: gs://hellbender/test/resources/org/broadinstitute/hellbender/tools/BQSR/HiSeq.1mb.1RG.2k_lines.alternate_allaligned.bam
Sep 09, 2015 8:03:32 AM com.google.cloud.genomics.dataflow.readers.bam.SeekableGCSStream uriToStorageObject
INFO: uriToStorageObject hellbender/test/resources/org/broadinstitute/hellbender/tools/BQSR/HiSeq.1mb.1RG.2k_lines.alternate_allaligned.bam=hellbender:test/resources/org/broadinstitute/hellbender/tools/BQSR/HiSeq.1mb.1RG.2k_lines.alternate_allaligned.bam
Sep 09, 2015 8:03:32 AM com.google.cloud.genomics.dataflow.readers.bam.BAMIO openBAMFile
INFO: getReadsFromBAMFile - got input resources
Sep 09, 2015 8:03:32 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 8:03:32 AM com.google.cloud.genomics.dataflow.readers.bam.Sharder process
INFO: Processing BAM file gs://hellbender/test/resources/org/broadinstitute/hellbender/tools/BQSR/HiSeq.1mb.1RG.2k_lines.alternate_allaligned.bam
Sep 09, 2015 8:03:32 AM com.google.cloud.genomics.dataflow.readers.bam.SeekableGCSStream <init>
INFO: Creating SeekableGCSStream: gs://hellbender/test/resources/org/broadinstitute/hellbender/tools/BQSR/HiSeq.1mb.1RG.2k_lines.alternate_allaligned.bam.bai
Sep 09, 2015 8:03:32 AM com.google.cloud.genomics.dataflow.readers.bam.SeekableGCSStream uriToStorageObject
INFO: uriToStorageObject hellbender/test/resources/org/broadinstitute/hellbender/tools/BQSR/HiSeq.1mb.1RG.2k_lines.alternate_allaligned.bam.bai=hellbender:test/resources/org/broadinstitute/hellbender/tools/BQSR/HiSeq.1mb.1RG.2k_lines.alternate_allaligned.bam.bai
Sep 09, 2015 8:03:33 AM com.google.cloud.genomics.dataflow.readers.bam.SeekableGCSStream <init>
INFO: Creating SeekableGCSStream: gs://hellbender/test/resources/org/broadinstitute/hellbender/tools/BQSR/HiSeq.1mb.1RG.2k_lines.alternate_allaligned.bam
Sep 09, 2015 8:03:33 AM com.google.cloud.genomics.dataflow.readers.bam.SeekableGCSStream uriToStorageObject
INFO: uriToStorageObject hellbender/test/resources/org/broadinstitute/hellbender/tools/BQSR/HiSeq.1mb.1RG.2k_lines.alternate_allaligned.bam=hellbender:test/resources/org/broadinstitute/hellbender/tools/BQSR/HiSeq.1mb.1RG.2k_lines.alternate_allaligned.bam
Sep 09, 2015 8:03:33 AM com.google.cloud.genomics.dataflow.readers.bam.BAMIO openBAMFile
INFO: getReadsFromBAMFile - got input resources
Sep 09, 2015 8:03:33 AM com.google.cloud.genomics.dataflow.readers.bam.Sharder openFile
INFO: Has index = true
Sep 09, 2015 8:03:33 AM com.google.cloud.genomics.dataflow.readers.bam.Sharder processHeader
INFO: All references = false
Sep 09, 2015 8:03:33 AM com.google.cloud.genomics.dataflow.readers.bam.Sharder processHeader
INFO: BAM has index = true
Sep 09, 2015 8:03:33 AM com.google.cloud.genomics.dataflow.readers.bam.Sharder processHeader
INFO: BAM has browseable index = true
Sep 09, 2015 8:03:33 AM com.google.cloud.genomics.dataflow.readers.bam.Sharder processHeader
INFO: Class for index = htsjdk.samtools.CachingBAMFileIndex
Sep 09, 2015 8:03:34 AM com.google.cloud.genomics.dataflow.readers.bam.Sharder createShardsForReference
INFO: Outputting last shard of size 32767, 416346 bytes
Sep 09, 2015 8:03:37 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 8:03:38 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 8:03:38 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 8:03:56 AM com.google.cloud.dataflow.sdk.util.PackageUtil stageClasspathElements
INFO: Uploading PipelineOptions.filesToStage complete: 1 files newly uploaded, 240 files cached
Sep 09, 2015 8:03:57 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_03_57-11503430311039115193
Sep 09, 2015 8:03:57 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_03_57-11503430311039115193
Sep 09, 2015 8:10:00 AM com.google.cloud.dataflow.sdk.runners.BlockingDataflowPipelineRunner run
INFO: Job finished with status DONE
[September 9, 2015 8:10:01 AM UTC] org.broadinstitute.hellbender.tools.dataflow.pipelines.ApplyBQSRDataflow done. Elapsed time: 6.58 minutes.
Runtime.totalMemory()=1360527360
[September 9, 2015 8:10:01 AM UTC] org.broadinstitute.hellbender.tools.dataflow.pipelines.ApplyBQSRDataflow  --input gs://hellbender/test/resources/org/broadinstitute/hellbender/tools/BQSR/HiSeq.1mb.1RG.2k_lines.alternate_allaligned.bam --output /tmp/walktest.tmp_param.04624453026405980675.tmp --bqsr_recal_file src/test/resources/org/broadinstitute/hellbender/tools/BQSR/HiSeq.20mb.1RG.table.gz --project broad-dsde-dev --apiKey *********** --VERBOSITY ERROR  --interval_set_rule UNION --interval_padding 0 --quantize_quals 0 --disable_indel_quals false --emit_original_quals false --preserve_qscores_less_than 6 --globalQScorePrior -1.0 --runner LOCAL --numWorkers 0 --help false --version false --QUIET false
[September 9, 2015 8:10:01 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 8:10:01 AM com.google.cloud.dataflow.sdk.runners.DirectPipelineRunner <init>
INFO: DirectPipelineRunner using random seed 1252588654636513587.
Sep 09, 2015 8:10:01 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coders for genomics classes
Sep 09, 2015 8:10:01 AM org.reflections.Reflections scan
INFO: Reflections took 262 ms to scan 250 urls, producing 79 keys and 156 values 
Sep 09, 2015 8:10:01 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for SearchVariantsResponse
Sep 09, 2015 8:10:01 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for ImportVariantsRequest
Sep 09, 2015 8:10:01 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for ExperimentalCreateJobResponse
Sep 09, 2015 8:10:01 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for SearchVariantSetsRequest
Sep 09, 2015 8:10:01 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for VariantSet
Sep 09, 2015 8:10:01 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for ExportVariantSetResponse
Sep 09, 2015 8:10:01 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for KeyValue
Sep 09, 2015 8:10:01 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for ListCoverageBucketsResponse
Sep 09, 2015 8:10:01 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for AlignReadGroupSetsResponse
Sep 09, 2015 8:10:01 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for ImportVariantsResponse
Sep 09, 2015 8:10:01 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for SearchReferenceSetsResponse
Sep 09, 2015 8:10:01 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for ReadGroupProgram
Sep 09, 2015 8:10:01 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for SearchCallSetsResponse
Sep 09, 2015 8:10:01 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for Reference
Sep 09, 2015 8:10:01 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for ExternalId
Sep 09, 2015 8:10:01 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for SearchReadsRequest
Sep 09, 2015 8:10:01 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for ExportVariantSetRequest
Sep 09, 2015 8:10:01 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for CallSet
Sep 09, 2015 8:10:01 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for JobRequest
Sep 09, 2015 8:10:01 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for Metadata
Sep 09, 2015 8:10:01 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for ReferenceSet
Sep 09, 2015 8:10:01 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for CallReadGroupSetsResponse
Sep 09, 2015 8:10:01 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for FastqMetadata
Sep 09, 2015 8:10:01 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for SearchVariantsRequest
Sep 09, 2015 8:10:01 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for SearchAnnotationSetsRequest
Sep 09, 2015 8:10:01 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for SearchReadGroupSetsRequest
Sep 09, 2015 8:10:01 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for CoverageBucket
Sep 09, 2015 8:10:01 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for SearchJobsResponse
Sep 09, 2015 8:10:01 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for ImportReadGroupSetsRequest
Sep 09, 2015 8:10:01 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for TranscriptCodingSequence
Sep 09, 2015 8:10:01 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for Variant
Sep 09, 2015 8:10:01 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for SearchReadGroupSetsResponse
Sep 09, 2015 8:10:01 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for SearchAnnotationsRequest
Sep 09, 2015 8:10:01 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for SearchVariantSetsResponse
Sep 09, 2015 8:10:01 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for InterleavedFastqSource
Sep 09, 2015 8:10:01 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for BatchCreateAnnotationsRequest
Sep 09, 2015 8:10:01 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for SearchReferencesRequest
Sep 09, 2015 8:10:01 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for SearchJobsRequest
Sep 09, 2015 8:10:01 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for AlignReadGroupSetsRequest
Sep 09, 2015 8:10:01 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for Job
Sep 09, 2015 8:10:01 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for TranscriptExon
Sep 09, 2015 8:10:01 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for SearchReferenceSetsRequest
Sep 09, 2015 8:10:01 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for QueryRange
Sep 09, 2015 8:10:01 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for LinearAlignment
Sep 09, 2015 8:10:01 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for Position
Sep 09, 2015 8:10:01 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for Annotation
Sep 09, 2015 8:10:01 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for SearchReadsResponse
Sep 09, 2015 8:10:01 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for ExperimentalCreateJobRequest
Sep 09, 2015 8:10:01 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for AnnotationSet
Sep 09, 2015 8:10:01 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for Dataset
Sep 09, 2015 8:10:01 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for Read
Sep 09, 2015 8:10:01 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for Call
Sep 09, 2015 8:10:01 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for ReadGroupExperiment
Sep 09, 2015 8:10:01 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for VariantAnnotationCondition
Sep 09, 2015 8:10:01 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for ReadGroup
Sep 09, 2015 8:10:01 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for VariantAnnotation
Sep 09, 2015 8:10:01 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for Int32Value
Sep 09, 2015 8:10:01 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for ExportReadGroupSetsRequest
Sep 09, 2015 8:10:01 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for ReferenceBound
Sep 09, 2015 8:10:01 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for ImportReadGroupSetsResponse
Sep 09, 2015 8:10:01 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for MergeVariantsRequest
Sep 09, 2015 8:10:01 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for CigarUnit
Sep 09, 2015 8:10:01 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for SearchAnnotationsResponse
Sep 09, 2015 8:10:01 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for BatchAnnotationsResponseEntry
Sep 09, 2015 8:10:01 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for CallReadGroupSetsRequest
Sep 09, 2015 8:10:01 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for ListBasesResponse
Sep 09, 2015 8:10:01 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for SearchReferencesResponse
Sep 09, 2015 8:10:01 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for PairedFastqSource
Sep 09, 2015 8:10:01 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for BatchAnnotationsResponse
Sep 09, 2015 8:10:01 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for SearchCallSetsRequest
Sep 09, 2015 8:10:01 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for RangePosition
Sep 09, 2015 8:10:01 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for Transcript
Sep 09, 2015 8:10:01 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for BatchAnnotationsResponseEntryStatus
Sep 09, 2015 8:10:01 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for ExportReadGroupSetsResponse
Sep 09, 2015 8:10:01 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for SearchAnnotationSetsResponse
Sep 09, 2015 8:10:01 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for ListDatasetsResponse
Sep 09, 2015 8:10:01 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for ReadGroupSet
Sep 09, 2015 8:10:01 AM com.google.cloud.genomics.dataflow.utils.DataflowWorkarounds registerGenomicsCoders
INFO: Registering coder for Range
Sep 09, 2015 8:10:01 AM com.google.cloud.genomics.dataflow.utils.GCSOptions$Methods createStorageClient
INFO: Creating storgae client for DataflowCommandLineProgram
Sep 09, 2015 8:10:01 AM com.google.cloud.genomics.dataflow.readers.bam.SeekableGCSStream <init>
INFO: Creating SeekableGCSStream: gs://hellbender/test/resources/org/broadinstitute/hellbender/tools/BQSR/HiSeq.1mb.1RG.2k_lines.alternate_allaligned.bam.bai
Sep 09, 2015 8:10:01 AM com.google.cloud.genomics.dataflow.readers.bam.SeekableGCSStream uriToStorageObject
INFO: uriToStorageObject hellbender/test/resources/org/broadinstitute/hellbender/tools/BQSR/HiSeq.1mb.1RG.2k_lines.alternate_allaligned.bam.bai=hellbender:test/resources/org/broadinstitute/hellbender/tools/BQSR/HiSeq.1mb.1RG.2k_lines.alternate_allaligned.bam.bai
Sep 09, 2015 8:10:02 AM com.google.cloud.genomics.dataflow.readers.bam.SeekableGCSStream <init>
INFO: Creating SeekableGCSStream: gs://hellbender/test/resources/org/broadinstitute/hellbender/tools/BQSR/HiSeq.1mb.1RG.2k_lines.alternate_allaligned.bam
Sep 09, 2015 8:10:02 AM com.google.cloud.genomics.dataflow.readers.bam.SeekableGCSStream uriToStorageObject
INFO: uriToStorageObject hellbender/test/resources/org/broadinstitute/hellbender/tools/BQSR/HiSeq.1mb.1RG.2k_lines.alternate_allaligned.bam=hellbender:test/resources/org/broadinstitute/hellbender/tools/BQSR/HiSeq.1mb.1RG.2k_lines.alternate_allaligned.bam
Sep 09, 2015 8:10:02 AM com.google.cloud.genomics.dataflow.readers.bam.BAMIO openBAMFile
INFO: getReadsFromBAMFile - got input resources
Sep 09, 2015 8:10:03 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 8:10:03 AM com.google.cloud.genomics.dataflow.readers.bam.Sharder process
INFO: Processing BAM file gs://hellbender/test/resources/org/broadinstitute/hellbender/tools/BQSR/HiSeq.1mb.1RG.2k_lines.alternate_allaligned.bam
Sep 09, 2015 8:10:03 AM com.google.cloud.genomics.dataflow.readers.bam.SeekableGCSStream <init>
INFO: Creating SeekableGCSStream: gs://hellbender/test/resources/org/broadinstitute/hellbender/tools/BQSR/HiSeq.1mb.1RG.2k_lines.alternate_allaligned.bam.bai
Sep 09, 2015 8:10:03 AM com.google.cloud.genomics.dataflow.readers.bam.SeekableGCSStream uriToStorageObject
INFO: uriToStorageObject hellbender/test/resources/org/broadinstitute/hellbender/tools/BQSR/HiSeq.1mb.1RG.2k_lines.alternate_allaligned.bam.bai=hellbender:test/resources/org/broadinstitute/hellbender/tools/BQSR/HiSeq.1mb.1RG.2k_lines.alternate_allaligned.bam.bai
Sep 09, 2015 8:10:03 AM com.google.cloud.genomics.dataflow.readers.bam.SeekableGCSStream <init>
INFO: Creating SeekableGCSStream: gs://hellbender/test/resources/org/broadinstitute/hellbender/tools/BQSR/HiSeq.1mb.1RG.2k_lines.alternate_allaligned.bam
Sep 09, 2015 8:10:03 AM com.google.cloud.genomics.dataflow.readers.bam.SeekableGCSStream uriToStorageObject
INFO: uriToStorageObject hellbender/test/resources/org/broadinstitute/hellbender/tools/BQSR/HiSeq.1mb.1RG.2k_lines.alternate_allaligned.bam=hellbender:test/resources/org/broadinstitute/hellbender/tools/BQSR/HiSeq.1mb.1RG.2k_lines.alternate_allaligned.bam
Sep 09, 2015 8:10:03 AM com.google.cloud.genomics.dataflow.readers.bam.BAMIO openBAMFile
INFO: getReadsFromBAMFile - got input resources
Sep 09, 2015 8:10:04 AM com.google.cloud.genomics.dataflow.readers.bam.Sharder openFile
INFO: Has index = true
Sep 09, 2015 8:10:04 AM com.google.cloud.genomics.dataflow.readers.bam.Sharder processHeader
INFO: All references = false
Sep 09, 2015 8:10:04 AM com.google.cloud.genomics.dataflow.readers.bam.Sharder processHeader
INFO: BAM has index = true
Sep 09, 2015 8:10:04 AM com.google.cloud.genomics.dataflow.readers.bam.Sharder processHeader
INFO: BAM has browseable index = true
Sep 09, 2015 8:10:04 AM com.google.cloud.genomics.dataflow.readers.bam.Sharder processHeader
INFO: Class for index = htsjdk.samtools.CachingBAMFileIndex
Sep 09, 2015 8:10:04 AM com.google.cloud.genomics.dataflow.readers.bam.Sharder createShardsForReference
INFO: Outputting last shard of size 32767, 416346 bytes
Sep 09, 2015 8:10:07 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 8:10:07 AM com.google.cloud.dataflow.sdk.runners.DirectPipelineRunner run
INFO: Executing pipeline using the DirectPipelineRunner.
Sep 09, 2015 8:10:08 AM com.google.cloud.genomics.dataflow.readers.bam.Reader openFile
INFO: Processing shard gs://hellbender/test/resources/org/broadinstitute/hellbender/tools/BQSR/HiSeq.1mb.1RG.2k_lines.alternate_allaligned.bam: chr1:10076161:247249720, locus size = 237173559, span size = 418971
Sep 09, 2015 8:10:08 AM com.google.cloud.genomics.dataflow.readers.bam.SeekableGCSStream <init>
INFO: Creating SeekableGCSStream: gs://hellbender/test/resources/org/broadinstitute/hellbender/tools/BQSR/HiSeq.1mb.1RG.2k_lines.alternate_allaligned.bam.bai
Sep 09, 2015 8:10:08 AM com.google.cloud.genomics.dataflow.readers.bam.SeekableGCSStream uriToStorageObject
INFO: uriToStorageObject hellbender/test/resources/org/broadinstitute/hellbender/tools/BQSR/HiSeq.1mb.1RG.2k_lines.alternate_allaligned.bam.bai=hellbender:test/resources/org/broadinstitute/hellbender/tools/BQSR/HiSeq.1mb.1RG.2k_lines.alternate_allaligned.bam.bai
Sep 09, 2015 8:10:08 AM com.google.cloud.genomics.dataflow.readers.bam.SeekableGCSStream <init>
INFO: Creating SeekableGCSStream: gs://hellbender/test/resources/org/broadinstitute/hellbender/tools/BQSR/HiSeq.1mb.1RG.2k_lines.alternate_allaligned.bam
Sep 09, 2015 8:10:08 AM com.google.cloud.genomics.dataflow.readers.bam.SeekableGCSStream uriToStorageObject
INFO: uriToStorageObject hellbender/test/resources/org/broadinstitute/hellbender/tools/BQSR/HiSeq.1mb.1RG.2k_lines.alternate_allaligned.bam=hellbender:test/resources/org/broadinstitute/hellbender/tools/BQSR/HiSeq.1mb.1RG.2k_lines.alternate_allaligned.bam
Sep 09, 2015 8:10:09 AM com.google.cloud.genomics.dataflow.readers.bam.BAMIO openBAMFile
INFO: getReadsFromBAMFile - got input resources
Sep 09, 2015 8:10:09 AM com.google.cloud.genomics.dataflow.readers.bam.Reader openFile
INFO: Processing span
Sep 09, 2015 8:10:09 AM com.google.cloud.genomics.dataflow.readers.bam.Reader dumpStats
INFO: Processed 1311 in 446.5 ms. Speed: 2939 reads/sec, skipped other sequences 0, skippedBefore 0, skipped after 0
Sep 09, 2015 8:10:13 AM com.google.cloud.dataflow.sdk.runners.DirectPipelineRunner run
INFO: Pipeline execution complete.
[September 9, 2015 8:10:13 AM UTC] org.broadinstitute.hellbender.tools.dataflow.pipelines.ApplyBQSRDataflow done. Elapsed time: 0.20 minutes.
Runtime.totalMemory()=1358954496