Class org.broadinstitute.hellbender.engine.ReadWalkerGCSSupportIntegrationTest

all > org.broadinstitute.hellbender.engine > ReadWalkerGCSSupportIntegrationTest

tests

failures

ignored

13.485s

duration

100%

successful

Tests
Standard output
Standard error

Tests

Test	Duration	Result
testBAMReferenceAndIntervalsOnGCS	9.537s	passed
testReadBAMOnGCS[0](org/broadinstitute/hellbender/engine/CEUTrio.HiSeq.WGS.b37.NA12878.20.21.10000000-10000020.with.unmapped.bam, null, false, /home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/engine/GCSTests/expected_ReadWalkerGCSSupportIntegrationTest_bam_wholefile.bam)	0.814s	passed
testReadBAMOnGCS[1](org/broadinstitute/hellbender/engine/CEUTrio.HiSeq.WGS.b37.NA12878.20.21.10000000-10000020.with.unmapped.bam, [20:10000010-10000016], false, /home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/engine/GCSTests/expected_ReadWalkerGCSSupportIntegrationTest_bam_single_interval.bam)	0.838s	passed
testReadBAMOnGCS[2](org/broadinstitute/hellbender/engine/CEUTrio.HiSeq.WGS.b37.NA12878.20.21.10000000-10000020.with.unmapped.bam, [20:10000010-10000016, 21:10000005-10000011], false, /home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/engine/GCSTests/expected_ReadWalkerGCSSupportIntegrationTest_bam_multiple_intervals.bam)	0.745s	passed
testReadBAMOnGCS[3](org/broadinstitute/hellbender/engine/CEUTrio.HiSeq.WGS.b37.NA12878.20.21.10000000-10000020.with.unmapped.bam, [20:10000010-10000016, 21:10000005-10000011], true, /home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/engine/GCSTests/expected_ReadWalkerGCSSupportIntegrationTest_bam_multiple_intervals_with_unmapped.bam)	0.781s	passed
testReadBAMOnGCS[4](org/broadinstitute/hellbender/engine/CEUTrio.HiSeq.WGS.b37.NA12878.20.21.10000000-10000020.with.unmapped.bam, null, true, /home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/engine/GCSTests/expected_ReadWalkerGCSSupportIntegrationTest_bam_unmapped_only.bam)	0.770s	passed

Standard output

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[22:31:50] Executing test ReadWalkerGCSSupportIntegrationTest:testReadBAMOnGCS
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[22:31:51] Executing test ReadWalkerGCSSupportIntegrationTest:testReadBAMOnGCS
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[22:31:51] Executing test ReadWalkerGCSSupportIntegrationTest:testReadBAMOnGCS
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[22:31:52] Executing test ReadWalkerGCSSupportIntegrationTest:testReadBAMOnGCS
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[22:31:53] Executing test ReadWalkerGCSSupportIntegrationTest:testReadBAMOnGCS

Standard error

22:31:41.847 INFO  NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/home/runner/.gradle/caches/modules-2/files-2.1/com.intel.gkl/gkl/0.8.11/13f95ee601084b8bf047b2a37f6ea36cd588b96b/gkl-0.8.11.jar!/com/intel/gkl/native/libgkl_compression.so
22:31:41.879 INFO  ExampleReadWalkerWithReference - ------------------------------------------------------------
22:31:41.883 INFO  ExampleReadWalkerWithReference - org.broadinstitute.hellbender.tools.examples vUnavailable
22:31:41.883 INFO  ExampleReadWalkerWithReference - For support and documentation go to https://software.broadinstitute.org/gatk/
22:31:41.883 INFO  ExampleReadWalkerWithReference - Executing as runner@fv-az2219-44 on Linux v6.8.0-1021-azure amd64
22:31:41.883 INFO  ExampleReadWalkerWithReference - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
22:31:41.884 INFO  ExampleReadWalkerWithReference - Start Date/Time: March 28, 2025 at 10:31:41 PM UTC
22:31:41.884 INFO  ExampleReadWalkerWithReference - ------------------------------------------------------------
22:31:41.884 INFO  ExampleReadWalkerWithReference - ------------------------------------------------------------
22:31:41.884 INFO  ExampleReadWalkerWithReference - HTSJDK Defaults.COMPRESSION_LEVEL : 2
22:31:41.885 INFO  ExampleReadWalkerWithReference - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
22:31:41.885 INFO  ExampleReadWalkerWithReference - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
22:31:41.885 INFO  ExampleReadWalkerWithReference - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
22:31:41.886 INFO  ExampleReadWalkerWithReference - Deflater: IntelDeflater
22:31:41.886 INFO  ExampleReadWalkerWithReference - Inflater: IntelInflater
22:31:41.886 INFO  ExampleReadWalkerWithReference - GCS max retries/reopens: 20
22:31:41.886 INFO  ExampleReadWalkerWithReference - Requester pays: disabled
22:31:41.887 INFO  ExampleReadWalkerWithReference - Initializing engine
22:31:47.415 INFO  IntervalArgumentCollection - Processing 13502 bp from intervals
22:31:47.417 INFO  ExampleReadWalkerWithReference - Done initializing engine
22:31:47.418 INFO  ProgressMeter - Starting traversal
22:31:47.419 INFO  ProgressMeter -        Current Locus  Elapsed Minutes       Reads Processed     Reads/Minute
22:31:50.192 INFO  ExampleReadWalkerWithReference - 0 read(s) filtered by: WellformedReadFilter 

22:31:50.193 INFO  ProgressMeter -          21:10004600              0.0                 16955         366859.0
22:31:50.193 INFO  ProgressMeter - Traversal complete. Processed 16955 total reads in 0.0 minutes.
22:31:50.194 INFO  ExampleReadWalkerWithReference - Shutting down engine
[March 28, 2025 at 10:31:50 PM UTC] org.broadinstitute.hellbender.tools.examples.ExampleReadWalkerWithReference done. Elapsed time: 0.14 minutes.
Runtime.totalMemory()=524288000
[March 28, 2025 at 10:31:51 PM UTC] org.broadinstitute.hellbender.tools.PrintReads done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=524288000
[March 28, 2025 at 10:31:51 PM UTC] org.broadinstitute.hellbender.tools.PrintReads done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=524288000
[March 28, 2025 at 10:31:52 PM UTC] org.broadinstitute.hellbender.tools.PrintReads done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=524288000
[March 28, 2025 at 10:31:53 PM UTC] org.broadinstitute.hellbender.tools.PrintReads done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=524288000
[March 28, 2025 at 10:31:54 PM UTC] org.broadinstitute.hellbender.tools.PrintReads done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=524288000