Class org.broadinstitute.hellbender.engine.ReadWalkerGCSSupportIntegrationTest

all > org.broadinstitute.hellbender.engine > ReadWalkerGCSSupportIntegrationTest

tests

failures

ignored

14.688s

duration

100%

successful

Tests
Standard output
Standard error

Tests

Test	Duration	Result
testBAMReferenceAndIntervalsOnGCS	10.330s	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)	0.927s	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)	0.943s	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)	0.820s	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)	0.853s	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)	0.815s	passed

Standard output

--------------------------------------------------------------------------------
[17:36:55] Executing test ReadWalkerGCSSupportIntegrationTest:testReadBAMOnGCS
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[17:36:55] Executing test ReadWalkerGCSSupportIntegrationTest:testReadBAMOnGCS
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[17:36:56] Executing test ReadWalkerGCSSupportIntegrationTest:testReadBAMOnGCS
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[17:36:57] Executing test ReadWalkerGCSSupportIntegrationTest:testReadBAMOnGCS
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[17:36:58] Executing test ReadWalkerGCSSupportIntegrationTest:testReadBAMOnGCS

Standard error

17:36:45.691 INFO  NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/home/runner/.gradle/caches/modules-2/files-2.1/com.intel.gkl/gkl/0.9.1/e23340ee393a396807581d7af5b835c7fcf10ab3/gkl-0.9.1.jar!/com/intel/gkl/native/libgkl_compression.so
17:36:45.708 WARN  NativeLibraryLoader - Unable to load libgkl_compression.so from native/libgkl_compression.so (/tmp/libgkl_compression4430625336544064209.so: /tmp/libgkl_compression4430625336544064209.so: cannot open shared object file: No such file or directory (Possible cause: can't load AMD 64 .so on a AARCH64 platform))
17:36:45.712 INFO  NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/home/runner/.gradle/caches/modules-2/files-2.1/com.intel.gkl/gkl/0.9.1/e23340ee393a396807581d7af5b835c7fcf10ab3/gkl-0.9.1.jar!/com/intel/gkl/native/libgkl_compression.so
17:36:45.717 WARN  NativeLibraryLoader - Unable to load libgkl_compression.so from native/libgkl_compression.so (/tmp/libgkl_compression7111803473975753413.so: /tmp/libgkl_compression7111803473975753413.so: cannot open shared object file: No such file or directory (Possible cause: can't load AMD 64 .so on a AARCH64 platform))
17:36:45.726 INFO  ExampleReadWalkerWithReference - ------------------------------------------------------------
17:36:45.728 INFO  ExampleReadWalkerWithReference - org.broadinstitute.hellbender.tools.examples vUnavailable
17:36:45.728 INFO  ExampleReadWalkerWithReference - For support and documentation go to https://software.broadinstitute.org/gatk/
17:36:45.728 INFO  ExampleReadWalkerWithReference - Executing as runner@runnervmrcw8b on Linux v6.11.0-1018-azure aarch64
17:36:45.729 INFO  ExampleReadWalkerWithReference - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
17:36:45.729 INFO  ExampleReadWalkerWithReference - Start Date/Time: October 27, 2025 at 5:36:45 PM UTC
17:36:45.729 INFO  ExampleReadWalkerWithReference - ------------------------------------------------------------
17:36:45.729 INFO  ExampleReadWalkerWithReference - ------------------------------------------------------------
17:36:45.729 INFO  ExampleReadWalkerWithReference - HTSJDK Defaults.COMPRESSION_LEVEL : 2
17:36:45.730 INFO  ExampleReadWalkerWithReference - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
17:36:45.730 INFO  ExampleReadWalkerWithReference - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
17:36:45.730 INFO  ExampleReadWalkerWithReference - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
17:36:45.730 INFO  ExampleReadWalkerWithReference - Deflater: JdkDeflater
17:36:45.730 INFO  ExampleReadWalkerWithReference - Inflater: JdkInflater
17:36:45.730 INFO  ExampleReadWalkerWithReference - GCS max retries/reopens: 20
17:36:45.730 INFO  ExampleReadWalkerWithReference - Requester pays: disabled
17:36:45.731 INFO  ExampleReadWalkerWithReference - Initializing engine
17:36:50.335 WARN  IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater
17:36:50.461 WARN  IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater
17:36:51.252 INFO  IntervalArgumentCollection - Processing 13502 bp from intervals
17:36:51.254 INFO  ExampleReadWalkerWithReference - Done initializing engine
17:36:51.255 INFO  ProgressMeter - Starting traversal
17:36:51.255 INFO  ProgressMeter -        Current Locus  Elapsed Minutes       Reads Processed     Reads/Minute
17:36:55.006 INFO  ExampleReadWalkerWithReference - 0 read(s) filtered by: WellformedReadFilter 

17:36:55.008 INFO  ProgressMeter -          21:10004600              0.1                 16955         271207.7
17:36:55.008 INFO  ProgressMeter - Traversal complete. Processed 16955 total reads in 0.1 minutes.
17:36:55.009 INFO  ExampleReadWalkerWithReference - Shutting down engine
[October 27, 2025 at 5:36:55 PM UTC] org.broadinstitute.hellbender.tools.examples.ExampleReadWalkerWithReference done. Elapsed time: 0.16 minutes.
Runtime.totalMemory()=524288000
[October 27, 2025 at 5:36:55 PM UTC] org.broadinstitute.hellbender.tools.PrintReads done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=524288000
[October 27, 2025 at 5:36:56 PM UTC] org.broadinstitute.hellbender.tools.PrintReads done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=524288000
[October 27, 2025 at 5:36:57 PM UTC] org.broadinstitute.hellbender.tools.PrintReads done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=524288000
[October 27, 2025 at 5:36:58 PM UTC] org.broadinstitute.hellbender.tools.PrintReads done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=524288000
[October 27, 2025 at 5:36:59 PM UTC] org.broadinstitute.hellbender.tools.PrintReads done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=524288000