Class org.broadinstitute.hellbender.engine.ReadWalkerGCSSupportIntegrationTest

all > org.broadinstitute.hellbender.engine > ReadWalkerGCSSupportIntegrationTest

tests

failures

ignored

1m6.57s

duration

100%

successful

Tests
Standard output
Standard error

Tests

Test	Duration	Result
testBAMReferenceAndIntervalsOnGCS	36.118s	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)	0.843s	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)	0.684s	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)	8.972s	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)	7.555s	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)	12.402s	passed

Standard output

--------------------------------------------------------------------------------
[20:33:00] Executing test ReadWalkerGCSSupportIntegrationTest:testReadBAMOnGCS
--------------------------------------------------------------------------------
[20:33:00] Executing test ReadWalkerGCSSupportIntegrationTest:testReadBAMOnGCS
--------------------------------------------------------------------------------
[20:33:01] Executing test ReadWalkerGCSSupportIntegrationTest:testReadBAMOnGCS
--------------------------------------------------------------------------------
[20:33:10] Executing test ReadWalkerGCSSupportIntegrationTest:testReadBAMOnGCS
--------------------------------------------------------------------------------
[20:33:18] Executing test ReadWalkerGCSSupportIntegrationTest:testReadBAMOnGCS

Standard error

20:32:25.100 INFO  NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/home/runner/.gradle/caches/modules-2/files-2.1/com.intel.gkl/gkl/0.9.0/5ec646c7bf8c4f7681c2a59819384e5da469db31/gkl-0.9.0.jar!/com/intel/gkl/native/libgkl_compression.so
20:32:25.130 INFO  ExampleReadWalkerWithReference - ------------------------------------------------------------
20:32:25.133 INFO  ExampleReadWalkerWithReference - org.broadinstitute.hellbender.tools.examples vUnavailable
20:32:25.133 INFO  ExampleReadWalkerWithReference - For support and documentation go to https://software.broadinstitute.org/gatk/
20:32:25.133 INFO  ExampleReadWalkerWithReference - Executing as runner@pkrvmxyh4eaekms on Linux v6.11.0-1015-azure amd64
20:32:25.133 INFO  ExampleReadWalkerWithReference - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
20:32:25.134 INFO  ExampleReadWalkerWithReference - Start Date/Time: June 12, 2025 at 8:32:25 PM UTC
20:32:25.134 INFO  ExampleReadWalkerWithReference - ------------------------------------------------------------
20:32:25.134 INFO  ExampleReadWalkerWithReference - ------------------------------------------------------------
20:32:25.135 INFO  ExampleReadWalkerWithReference - HTSJDK Defaults.COMPRESSION_LEVEL : 2
20:32:25.135 INFO  ExampleReadWalkerWithReference - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
20:32:25.135 INFO  ExampleReadWalkerWithReference - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
20:32:25.136 INFO  ExampleReadWalkerWithReference - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
20:32:25.136 INFO  ExampleReadWalkerWithReference - Deflater: IntelDeflater
20:32:25.136 INFO  ExampleReadWalkerWithReference - Inflater: IntelInflater
20:32:25.136 INFO  ExampleReadWalkerWithReference - GCS max retries/reopens: 20
20:32:25.136 INFO  ExampleReadWalkerWithReference - Requester pays: disabled
20:32:25.137 INFO  ExampleReadWalkerWithReference - Initializing engine
20:32:50.602 INFO  IntervalArgumentCollection - Processing 13502 bp from intervals
20:32:50.604 INFO  ExampleReadWalkerWithReference - Done initializing engine
20:32:50.605 INFO  ProgressMeter - Starting traversal
20:32:50.605 INFO  ProgressMeter -        Current Locus  Elapsed Minutes       Reads Processed     Reads/Minute
20:32:59.985 INFO  ExampleReadWalkerWithReference - 0 read(s) filtered by: WellformedReadFilter 

20:32:59.986 INFO  ProgressMeter -          21:10004600              0.2                 16955         108454.2
20:32:59.986 INFO  ProgressMeter - Traversal complete. Processed 16955 total reads in 0.2 minutes.
20:32:59.987 INFO  ExampleReadWalkerWithReference - Shutting down engine
[June 12, 2025 at 8:32:59 PM UTC] org.broadinstitute.hellbender.tools.examples.ExampleReadWalkerWithReference done. Elapsed time: 0.58 minutes.
Runtime.totalMemory()=524288000
[June 12, 2025 at 8:33:00 PM UTC] org.broadinstitute.hellbender.tools.PrintReads done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=524288000
[June 12, 2025 at 8:33:01 PM UTC] org.broadinstitute.hellbender.tools.PrintReads done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=524288000
[June 12, 2025 at 8:33:10 PM UTC] org.broadinstitute.hellbender.tools.PrintReads done. Elapsed time: 0.15 minutes.
Runtime.totalMemory()=524288000
[June 12, 2025 at 8:33:18 PM UTC] org.broadinstitute.hellbender.tools.PrintReads done. Elapsed time: 0.12 minutes.
Runtime.totalMemory()=524288000
[June 12, 2025 at 8:33:30 PM UTC] org.broadinstitute.hellbender.tools.PrintReads done. Elapsed time: 0.21 minutes.
Runtime.totalMemory()=524288000