Class org.broadinstitute.hellbender.engine.ReadWalkerGCSSupportIntegrationTest

all > org.broadinstitute.hellbender.engine > ReadWalkerGCSSupportIntegrationTest

tests

failures

ignored

15.493s

duration

100%

successful

Tests
Standard output
Standard error

Tests

Test	Duration	Result
testBAMReferenceAndIntervalsOnGCS	10.943s	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)	1.174s	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)	1.050s	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)	0.783s	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)	0.754s	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)	0.789s	passed

Standard output

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[15:30:11] Executing test ReadWalkerGCSSupportIntegrationTest:testReadBAMOnGCS
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[15:30:12] Executing test ReadWalkerGCSSupportIntegrationTest:testReadBAMOnGCS
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[15:30:13] Executing test ReadWalkerGCSSupportIntegrationTest:testReadBAMOnGCS
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[15:30:14] Executing test ReadWalkerGCSSupportIntegrationTest:testReadBAMOnGCS
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[15:30:15] Executing test ReadWalkerGCSSupportIntegrationTest:testReadBAMOnGCS

Standard error

15:30:01.707 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
15:30:01.738 INFO  ExampleReadWalkerWithReference - ------------------------------------------------------------
15:30:01.741 INFO  ExampleReadWalkerWithReference - org.broadinstitute.hellbender.tools.examples vUnavailable
15:30:01.742 INFO  ExampleReadWalkerWithReference - For support and documentation go to https://software.broadinstitute.org/gatk/
15:30:01.742 INFO  ExampleReadWalkerWithReference - Executing as runner@pkrvmf6wy0o8zjz on Linux v6.11.0-1014-azure amd64
15:30:01.742 INFO  ExampleReadWalkerWithReference - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
15:30:01.742 INFO  ExampleReadWalkerWithReference - Start Date/Time: May 19, 2025 at 3:30:01 PM UTC
15:30:01.742 INFO  ExampleReadWalkerWithReference - ------------------------------------------------------------
15:30:01.743 INFO  ExampleReadWalkerWithReference - ------------------------------------------------------------
15:30:01.743 INFO  ExampleReadWalkerWithReference - HTSJDK Defaults.COMPRESSION_LEVEL : 2
15:30:01.743 INFO  ExampleReadWalkerWithReference - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
15:30:01.743 INFO  ExampleReadWalkerWithReference - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
15:30:01.744 INFO  ExampleReadWalkerWithReference - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
15:30:01.744 INFO  ExampleReadWalkerWithReference - Deflater: IntelDeflater
15:30:01.744 INFO  ExampleReadWalkerWithReference - Inflater: IntelInflater
15:30:01.744 INFO  ExampleReadWalkerWithReference - GCS max retries/reopens: 20
15:30:01.745 INFO  ExampleReadWalkerWithReference - Requester pays: disabled
15:30:01.745 INFO  ExampleReadWalkerWithReference - Initializing engine
15:30:08.158 INFO  IntervalArgumentCollection - Processing 13502 bp from intervals
15:30:08.160 INFO  ExampleReadWalkerWithReference - Done initializing engine
15:30:08.161 INFO  ProgressMeter - Starting traversal
15:30:08.162 INFO  ProgressMeter -        Current Locus  Elapsed Minutes       Reads Processed     Reads/Minute
15:30:11.505 INFO  ExampleReadWalkerWithReference - 0 read(s) filtered by: WellformedReadFilter 

15:30:11.507 INFO  ProgressMeter -          21:10004600              0.1                 16955         304216.5
15:30:11.507 INFO  ProgressMeter - Traversal complete. Processed 16955 total reads in 0.1 minutes.
15:30:11.508 INFO  ExampleReadWalkerWithReference - Shutting down engine
[May 19, 2025 at 3:30:11 PM UTC] org.broadinstitute.hellbender.tools.examples.ExampleReadWalkerWithReference done. Elapsed time: 0.16 minutes.
Runtime.totalMemory()=524288000
[May 19, 2025 at 3:30:12 PM UTC] org.broadinstitute.hellbender.tools.PrintReads done. Elapsed time: 0.02 minutes.
Runtime.totalMemory()=524288000
[May 19, 2025 at 3:30:13 PM UTC] org.broadinstitute.hellbender.tools.PrintReads done. Elapsed time: 0.02 minutes.
Runtime.totalMemory()=524288000
[May 19, 2025 at 3:30:14 PM UTC] org.broadinstitute.hellbender.tools.PrintReads done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=524288000
[May 19, 2025 at 3:30:15 PM UTC] org.broadinstitute.hellbender.tools.PrintReads done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=524288000
[May 19, 2025 at 3:30:16 PM UTC] org.broadinstitute.hellbender.tools.PrintReads done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=524288000