17:37:40.367 WARN IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater
17:37:40.368 WARN IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater
17:37:40.409 WARN IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater
17:37:40.409 WARN IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater
17:37:40.438 INFO FeatureManager - Using codec VCFCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/engine/lexicographically_sorted_dict.vcf
17:37:40.444 WARN IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater
17:37:40.444 WARN IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater
17:37:40.447 WARN IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater
17:37:40.447 WARN IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater
17:37:40.449 WARN IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater
17:37:40.449 WARN IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater
17:37:40.457 INFO FeatureManager - Using codec VCFCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/engine/feature_data_source_test_withSequenceDict.vcf
17:37:40.503 WARN IntelDeflaterFactory - Intel Deflater not supported, using Java.util.zip.Deflater
17:37:40.504 WARN IntelDeflaterFactory - Intel Deflater not supported, using Java.util.zip.Deflater
17:37:40.509 WARN IntelDeflaterFactory - Intel Deflater not supported, using Java.util.zip.Deflater
17:37:40.509 WARN IntelDeflaterFactory - Intel Deflater not supported, using Java.util.zip.Deflater
17:37:40.513 WARN IntelDeflaterFactory - Intel Deflater not supported, using Java.util.zip.Deflater
17:37:40.514 WARN IntelDeflaterFactory - Intel Deflater not supported, using Java.util.zip.Deflater
17:37:40.529 WARN TestGATKVariantToolWithNoSequenceDictionary - A variant index will not be created - a sequence dictionary is required to create an output index
17:37:40.532 WARN TestGATKVariantToolWithNoSequenceDictionary - A variant index will not be created - a sequence dictionary is required to create an output index
17:37:40.534 WARN TestGATKVariantToolWithNoSequenceDictionary - A variant index will not be created - a sequence dictionary is required to create an output index
17:37:40.536 WARN TestGATKVariantToolWithNoSequenceDictionary - A variant index will not be created - a sequence dictionary is required to create an output index
17:37:40.538 WARN TestGATKVariantToolWithNoSequenceDictionary - A variant index will not be created - a sequence dictionary is required to create an output index
17:37:40.538 WARN IntelDeflaterFactory - Intel Deflater not supported, using Java.util.zip.Deflater
17:37:40.539 WARN IntelDeflaterFactory - Intel Deflater not supported, using Java.util.zip.Deflater
17:37:40.541 WARN TestGATKVariantToolWithNoSequenceDictionary - A variant index will not be created - a sequence dictionary is required to create an output index
17:37:40.541 WARN IntelDeflaterFactory - Intel Deflater not supported, using Java.util.zip.Deflater
17:37:40.551 WARN IntelDeflaterFactory - Intel Deflater not supported, using Java.util.zip.Deflater
17:37:40.552 WARN IntelDeflaterFactory - Intel Deflater not supported, using Java.util.zip.Deflater
17:37:40.553 WARN IntelDeflaterFactory - Intel Deflater not supported, using Java.util.zip.Deflater
17:37:40.555 WARN IntelDeflaterFactory - Intel Deflater not supported, using Java.util.zip.Deflater
17:37:40.555 WARN IntelDeflaterFactory - Intel Deflater not supported, using Java.util.zip.Deflater
17:37:40.560 INFO FeatureManager - Using codec VCFCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/engine/lexicographically_sorted_dict.vcf
17:37:40.565 WARN GATKAnnotationPluginDescriptor - Disabled annotation (Coverage) is not enabled by this tool
17:37:40.569 INFO FeatureManager - Using codec VCFCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/engine/feature_data_source_test_with_bigHeader.vcf
17:37:40.572 INFO ProgressMeter - Starting traversal
17:37:40.572 INFO ProgressMeter - Current Locus Elapsed Minutes Records Processed Records/Minute
17:37:40.573 INFO ProgressMeter - unmapped 0.0 0 NaN
17:37:40.573 INFO ProgressMeter - Traversal complete. Processed 0 total records in 0.0 minutes.
17:37:40.584 WARN IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater
17:37:40.584 WARN IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater
17:37:40.603 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
17:37:40.606 WARN NativeLibraryLoader - Unable to load libgkl_compression.so from native/libgkl_compression.so (/tmp/libgkl_compression412741791059577651.so: /tmp/libgkl_compression412741791059577651.so: cannot open shared object file: No such file or directory (Possible cause: can't load AMD 64 .so on a AARCH64 platform))
17:37:40.606 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
17:37:40.609 WARN NativeLibraryLoader - Unable to load libgkl_compression.so from native/libgkl_compression.so (/tmp/libgkl_compression13697222585946880975.so: /tmp/libgkl_compression13697222585946880975.so: cannot open shared object file: No such file or directory (Possible cause: can't load AMD 64 .so on a AARCH64 platform))
17:37:40.610 INFO TestGATKToolWithFeatures - ------------------------------------------------------------
17:37:40.610 INFO TestGATKToolWithFeatures - org.broadinstitute.hellbender.engine vUnavailable
17:37:40.610 INFO TestGATKToolWithFeatures - For support and documentation go to https://software.broadinstitute.org/gatk/
17:37:40.610 INFO TestGATKToolWithFeatures - Executing as runner@runnervmrcw8b on Linux v6.11.0-1018-azure aarch64
17:37:40.611 INFO TestGATKToolWithFeatures - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
17:37:40.611 INFO TestGATKToolWithFeatures - Start Date/Time: October 27, 2025 at 5:37:40 PM UTC
17:37:40.611 INFO TestGATKToolWithFeatures - ------------------------------------------------------------
17:37:40.611 INFO TestGATKToolWithFeatures - ------------------------------------------------------------
17:37:40.613 INFO TestGATKToolWithFeatures - HTSJDK Defaults.COMPRESSION_LEVEL : 2
17:37:40.613 INFO TestGATKToolWithFeatures - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
17:37:40.613 INFO TestGATKToolWithFeatures - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
17:37:40.613 INFO TestGATKToolWithFeatures - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
17:37:40.613 INFO TestGATKToolWithFeatures - Deflater: JdkDeflater
17:37:40.613 INFO TestGATKToolWithFeatures - Inflater: JdkInflater
17:37:40.614 INFO TestGATKToolWithFeatures - GCS max retries/reopens: 20
17:37:40.614 INFO TestGATKToolWithFeatures - Requester pays: disabled
17:37:40.614 INFO TestGATKToolWithFeatures - Initializing engine
17:37:40.614 INFO FeatureManager - Using codec VCFCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/engine/feature_data_source_test_with_bigHeader.vcf
17:37:40.615 INFO TestGATKToolWithFeatures - Done initializing engine
17:37:40.615 INFO ProgressMeter - Starting traversal
17:37:40.615 INFO ProgressMeter - Current Locus Elapsed Minutes Records Processed Records/Minute
17:37:40.615 INFO ProgressMeter - unmapped 0.0 0 NaN
17:37:40.615 INFO ProgressMeter - Traversal complete. Processed 0 total records in 0.0 minutes.
17:37:40.615 INFO TestGATKToolWithFeatures - Shutting down engine
[October 27, 2025 at 5:37:40 PM UTC] org.broadinstitute.hellbender.engine.GATKToolUnitTest$TestGATKToolWithFeatures done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=524288000
17:37:40.618 WARN IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater
17:37:40.619 WARN IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater
17:37:40.622 WARN IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater
17:37:40.623 WARN IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater
17:37:40.636 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
17:37:40.639 WARN NativeLibraryLoader - Unable to load libgkl_compression.so from native/libgkl_compression.so (/tmp/libgkl_compression4021706819380444767.so: /tmp/libgkl_compression4021706819380444767.so: cannot open shared object file: No such file or directory (Possible cause: can't load AMD 64 .so on a AARCH64 platform))
17:37:40.639 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
17:37:40.642 WARN NativeLibraryLoader - Unable to load libgkl_compression.so from native/libgkl_compression.so (/tmp/libgkl_compression1547805760179158078.so: /tmp/libgkl_compression1547805760179158078.so: cannot open shared object file: No such file or directory (Possible cause: can't load AMD 64 .so on a AARCH64 platform))
17:37:40.643 INFO TestIntervalTransformingWalker - ------------------------------------------------------------
17:37:40.643 INFO TestIntervalTransformingWalker - org.broadinstitute.hellbender.engine vUnavailable
17:37:40.643 INFO TestIntervalTransformingWalker - For support and documentation go to https://software.broadinstitute.org/gatk/
17:37:40.643 INFO TestIntervalTransformingWalker - Executing as runner@runnervmrcw8b on Linux v6.11.0-1018-azure aarch64
17:37:40.643 INFO TestIntervalTransformingWalker - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
17:37:40.643 INFO TestIntervalTransformingWalker - Start Date/Time: October 27, 2025 at 5:37:40 PM UTC
17:37:40.643 INFO TestIntervalTransformingWalker - ------------------------------------------------------------
17:37:40.643 INFO TestIntervalTransformingWalker - ------------------------------------------------------------
17:37:40.644 INFO TestIntervalTransformingWalker - HTSJDK Defaults.COMPRESSION_LEVEL : 2
17:37:40.644 INFO TestIntervalTransformingWalker - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
17:37:40.644 INFO TestIntervalTransformingWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
17:37:40.644 INFO TestIntervalTransformingWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
17:37:40.644 INFO TestIntervalTransformingWalker - Deflater: JdkDeflater
17:37:40.644 INFO TestIntervalTransformingWalker - Inflater: JdkInflater
17:37:40.644 INFO TestIntervalTransformingWalker - GCS max retries/reopens: 20
17:37:40.644 INFO TestIntervalTransformingWalker - Requester pays: disabled
17:37:40.644 INFO TestIntervalTransformingWalker - Initializing engine
17:37:40.645 INFO IntervalArgumentCollection - Processing 1 bp from intervals
17:37:40.646 INFO TestIntervalTransformingWalker - Done initializing engine
17:37:40.646 INFO ProgressMeter - Starting traversal
17:37:40.646 INFO ProgressMeter - Current Locus Elapsed Minutes Records Processed Records/Minute
17:37:40.646 INFO ProgressMeter - unmapped 0.0 0 NaN
17:37:40.646 INFO ProgressMeter - Traversal complete. Processed 0 total records in 0.0 minutes.
17:37:40.646 INFO TestIntervalTransformingWalker - Shutting down engine
[October 27, 2025 at 5:37:40 PM UTC] org.broadinstitute.hellbender.engine.GATKToolUnitTest$TestIntervalTransformingWalker done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=524288000
17:37:40.650 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
17:37:40.653 WARN NativeLibraryLoader - Unable to load libgkl_compression.so from native/libgkl_compression.so (/tmp/libgkl_compression14286273573168546589.so: /tmp/libgkl_compression14286273573168546589.so: cannot open shared object file: No such file or directory (Possible cause: can't load AMD 64 .so on a AARCH64 platform))
17:37:40.653 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
17:37:40.656 WARN NativeLibraryLoader - Unable to load libgkl_compression.so from native/libgkl_compression.so (/tmp/libgkl_compression1502440887711900359.so: /tmp/libgkl_compression1502440887711900359.so: cannot open shared object file: No such file or directory (Possible cause: can't load AMD 64 .so on a AARCH64 platform))
17:37:40.657 INFO TestIntervalTransformingWalker - ------------------------------------------------------------
17:37:40.657 INFO TestIntervalTransformingWalker - org.broadinstitute.hellbender.engine vUnavailable
17:37:40.657 INFO TestIntervalTransformingWalker - For support and documentation go to https://software.broadinstitute.org/gatk/
17:37:40.657 INFO TestIntervalTransformingWalker - Executing as runner@runnervmrcw8b on Linux v6.11.0-1018-azure aarch64
17:37:40.657 INFO TestIntervalTransformingWalker - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
17:37:40.657 INFO TestIntervalTransformingWalker - Start Date/Time: October 27, 2025 at 5:37:40 PM UTC
17:37:40.657 INFO TestIntervalTransformingWalker - ------------------------------------------------------------
17:37:40.657 INFO TestIntervalTransformingWalker - ------------------------------------------------------------
17:37:40.657 INFO TestIntervalTransformingWalker - HTSJDK Defaults.COMPRESSION_LEVEL : 2
17:37:40.657 INFO TestIntervalTransformingWalker - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
17:37:40.657 INFO TestIntervalTransformingWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
17:37:40.657 INFO TestIntervalTransformingWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
17:37:40.658 INFO TestIntervalTransformingWalker - Deflater: JdkDeflater
17:37:40.658 INFO TestIntervalTransformingWalker - Inflater: JdkInflater
17:37:40.658 INFO TestIntervalTransformingWalker - GCS max retries/reopens: 20
17:37:40.658 INFO TestIntervalTransformingWalker - Requester pays: disabled
17:37:40.658 INFO TestIntervalTransformingWalker - Initializing engine
17:37:40.658 INFO IntervalArgumentCollection - Processing 6104 bp from intervals
17:37:40.658 INFO TestIntervalTransformingWalker - Done initializing engine
17:37:40.658 INFO ProgressMeter - Starting traversal
17:37:40.658 INFO ProgressMeter - Current Locus Elapsed Minutes Records Processed Records/Minute
17:37:40.658 INFO ProgressMeter - unmapped 0.0 0 NaN
17:37:40.658 INFO ProgressMeter - Traversal complete. Processed 0 total records in 0.0 minutes.
17:37:40.658 INFO TestIntervalTransformingWalker - Shutting down engine
[October 27, 2025 at 5:37:40 PM UTC] org.broadinstitute.hellbender.engine.GATKToolUnitTest$TestIntervalTransformingWalker done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=524288000
17:37:40.662 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
17:37:40.665 WARN NativeLibraryLoader - Unable to load libgkl_compression.so from native/libgkl_compression.so (/tmp/libgkl_compression17099439966535167558.so: /tmp/libgkl_compression17099439966535167558.so: cannot open shared object file: No such file or directory (Possible cause: can't load AMD 64 .so on a AARCH64 platform))
17:37:40.666 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
17:37:40.669 WARN NativeLibraryLoader - Unable to load libgkl_compression.so from native/libgkl_compression.so (/tmp/libgkl_compression14787527140452456076.so: /tmp/libgkl_compression14787527140452456076.so: cannot open shared object file: No such file or directory (Possible cause: can't load AMD 64 .so on a AARCH64 platform))
17:37:40.670 INFO TestIntervalTransformingWalker - ------------------------------------------------------------
17:37:40.670 INFO TestIntervalTransformingWalker - org.broadinstitute.hellbender.engine vUnavailable
17:37:40.670 INFO TestIntervalTransformingWalker - For support and documentation go to https://software.broadinstitute.org/gatk/
17:37:40.670 INFO TestIntervalTransformingWalker - Executing as runner@runnervmrcw8b on Linux v6.11.0-1018-azure aarch64
17:37:40.670 INFO TestIntervalTransformingWalker - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
17:37:40.670 INFO TestIntervalTransformingWalker - Start Date/Time: October 27, 2025 at 5:37:40 PM UTC
17:37:40.670 INFO TestIntervalTransformingWalker - ------------------------------------------------------------
17:37:40.670 INFO TestIntervalTransformingWalker - ------------------------------------------------------------
17:37:40.670 INFO TestIntervalTransformingWalker - HTSJDK Defaults.COMPRESSION_LEVEL : 2
17:37:40.670 INFO TestIntervalTransformingWalker - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
17:37:40.670 INFO TestIntervalTransformingWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
17:37:40.670 INFO TestIntervalTransformingWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
17:37:40.671 INFO TestIntervalTransformingWalker - Deflater: JdkDeflater
17:37:40.671 INFO TestIntervalTransformingWalker - Inflater: JdkInflater
17:37:40.671 INFO TestIntervalTransformingWalker - GCS max retries/reopens: 20
17:37:40.671 INFO TestIntervalTransformingWalker - Requester pays: disabled
17:37:40.671 INFO TestIntervalTransformingWalker - Initializing engine
17:37:40.671 INFO IntervalArgumentCollection - Processing 2652 bp from intervals
17:37:40.672 INFO TestIntervalTransformingWalker - Done initializing engine
17:37:40.672 INFO ProgressMeter - Starting traversal
17:37:40.672 INFO ProgressMeter - Current Locus Elapsed Minutes Records Processed Records/Minute
17:37:40.672 INFO ProgressMeter - unmapped 0.0 0 NaN
17:37:40.672 INFO ProgressMeter - Traversal complete. Processed 0 total records in 0.0 minutes.
17:37:40.672 INFO TestIntervalTransformingWalker - Shutting down engine
[October 27, 2025 at 5:37:40 PM UTC] org.broadinstitute.hellbender.engine.GATKToolUnitTest$TestIntervalTransformingWalker done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=524288000
17:37:40.675 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
17:37:40.678 WARN NativeLibraryLoader - Unable to load libgkl_compression.so from native/libgkl_compression.so (/tmp/libgkl_compression8193010036584039110.so: /tmp/libgkl_compression8193010036584039110.so: cannot open shared object file: No such file or directory (Possible cause: can't load AMD 64 .so on a AARCH64 platform))
17:37:40.678 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
17:37:40.681 WARN NativeLibraryLoader - Unable to load libgkl_compression.so from native/libgkl_compression.so (/tmp/libgkl_compression16380760819565510447.so: /tmp/libgkl_compression16380760819565510447.so: cannot open shared object file: No such file or directory (Possible cause: can't load AMD 64 .so on a AARCH64 platform))
17:37:40.682 INFO TestIntervalTransformingWalker - ------------------------------------------------------------
17:37:40.682 INFO TestIntervalTransformingWalker - org.broadinstitute.hellbender.engine vUnavailable
17:37:40.682 INFO TestIntervalTransformingWalker - For support and documentation go to https://software.broadinstitute.org/gatk/
17:37:40.682 INFO TestIntervalTransformingWalker - Executing as runner@runnervmrcw8b on Linux v6.11.0-1018-azure aarch64
17:37:40.682 INFO TestIntervalTransformingWalker - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
17:37:40.682 INFO TestIntervalTransformingWalker - Start Date/Time: October 27, 2025 at 5:37:40 PM UTC
17:37:40.682 INFO TestIntervalTransformingWalker - ------------------------------------------------------------
17:37:40.682 INFO TestIntervalTransformingWalker - ------------------------------------------------------------
17:37:40.682 INFO TestIntervalTransformingWalker - HTSJDK Defaults.COMPRESSION_LEVEL : 2
17:37:40.682 INFO TestIntervalTransformingWalker - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
17:37:40.682 INFO TestIntervalTransformingWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
17:37:40.682 INFO TestIntervalTransformingWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
17:37:40.682 INFO TestIntervalTransformingWalker - Deflater: JdkDeflater
17:37:40.682 INFO TestIntervalTransformingWalker - Inflater: JdkInflater
17:37:40.682 INFO TestIntervalTransformingWalker - GCS max retries/reopens: 20
17:37:40.683 INFO TestIntervalTransformingWalker - Requester pays: disabled
17:37:40.683 INFO TestIntervalTransformingWalker - Initializing engine
17:37:40.683 INFO TestIntervalTransformingWalker - Done initializing engine
17:37:40.683 INFO ProgressMeter - Starting traversal
17:37:40.683 INFO ProgressMeter - Current Locus Elapsed Minutes Records Processed Records/Minute
17:37:40.683 INFO ProgressMeter - unmapped 0.0 0 NaN
17:37:40.683 INFO ProgressMeter - Traversal complete. Processed 0 total records in 0.0 minutes.
17:37:40.683 INFO TestIntervalTransformingWalker - Shutting down engine
[October 27, 2025 at 5:37:40 PM UTC] org.broadinstitute.hellbender.engine.GATKToolUnitTest$TestIntervalTransformingWalker done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=524288000
17:37:40.687 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
17:37:40.690 WARN NativeLibraryLoader - Unable to load libgkl_compression.so from native/libgkl_compression.so (/tmp/libgkl_compression569203081810871583.so: /tmp/libgkl_compression569203081810871583.so: cannot open shared object file: No such file or directory (Possible cause: can't load AMD 64 .so on a AARCH64 platform))
17:37:40.690 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
17:37:40.693 WARN NativeLibraryLoader - Unable to load libgkl_compression.so from native/libgkl_compression.so (/tmp/libgkl_compression17019208688835242673.so: /tmp/libgkl_compression17019208688835242673.so: cannot open shared object file: No such file or directory (Possible cause: can't load AMD 64 .so on a AARCH64 platform))
17:37:40.694 INFO TestIntervalTransformingWalker - ------------------------------------------------------------
17:37:40.694 INFO TestIntervalTransformingWalker - org.broadinstitute.hellbender.engine vUnavailable
17:37:40.694 INFO TestIntervalTransformingWalker - For support and documentation go to https://software.broadinstitute.org/gatk/
17:37:40.694 INFO TestIntervalTransformingWalker - Executing as runner@runnervmrcw8b on Linux v6.11.0-1018-azure aarch64
17:37:40.694 INFO TestIntervalTransformingWalker - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
17:37:40.694 INFO TestIntervalTransformingWalker - Start Date/Time: October 27, 2025 at 5:37:40 PM UTC
17:37:40.694 INFO TestIntervalTransformingWalker - ------------------------------------------------------------
17:37:40.694 INFO TestIntervalTransformingWalker - ------------------------------------------------------------
17:37:40.694 INFO TestIntervalTransformingWalker - HTSJDK Defaults.COMPRESSION_LEVEL : 2
17:37:40.694 INFO TestIntervalTransformingWalker - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
17:37:40.694 INFO TestIntervalTransformingWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
17:37:40.694 INFO TestIntervalTransformingWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
17:37:40.694 INFO TestIntervalTransformingWalker - Deflater: JdkDeflater
17:37:40.694 INFO TestIntervalTransformingWalker - Inflater: JdkInflater
17:37:40.694 INFO TestIntervalTransformingWalker - GCS max retries/reopens: 20
17:37:40.694 INFO TestIntervalTransformingWalker - Requester pays: disabled
17:37:40.694 INFO TestIntervalTransformingWalker - Initializing engine
17:37:40.694 INFO TestIntervalTransformingWalker - Done initializing engine
17:37:40.694 INFO ProgressMeter - Starting traversal
17:37:40.694 INFO ProgressMeter - Current Locus Elapsed Minutes Records Processed Records/Minute
17:37:40.694 INFO ProgressMeter - unmapped 0.0 0 NaN
17:37:40.695 INFO ProgressMeter - Traversal complete. Processed 0 total records in 0.0 minutes.
17:37:40.695 INFO TestIntervalTransformingWalker - Shutting down engine
[October 27, 2025 at 5:37:40 PM UTC] org.broadinstitute.hellbender.engine.GATKToolUnitTest$TestIntervalTransformingWalker done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=524288000
17:37:40.698 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
17:37:40.701 WARN NativeLibraryLoader - Unable to load libgkl_compression.so from native/libgkl_compression.so (/tmp/libgkl_compression6617951853658893554.so: /tmp/libgkl_compression6617951853658893554.so: cannot open shared object file: No such file or directory (Possible cause: can't load AMD 64 .so on a AARCH64 platform))
17:37:40.702 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
17:37:40.705 WARN NativeLibraryLoader - Unable to load libgkl_compression.so from native/libgkl_compression.so (/tmp/libgkl_compression167874550629276700.so: /tmp/libgkl_compression167874550629276700.so: cannot open shared object file: No such file or directory (Possible cause: can't load AMD 64 .so on a AARCH64 platform))
17:37:40.706 INFO TestIntervalWalker - ------------------------------------------------------------
17:37:40.706 INFO TestIntervalWalker - org.broadinstitute.hellbender.engine vUnavailable
17:37:40.706 INFO TestIntervalWalker - For support and documentation go to https://software.broadinstitute.org/gatk/
17:37:40.706 INFO TestIntervalWalker - Executing as runner@runnervmrcw8b on Linux v6.11.0-1018-azure aarch64
17:37:40.706 INFO TestIntervalWalker - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
17:37:40.706 INFO TestIntervalWalker - Start Date/Time: October 27, 2025 at 5:37:40 PM UTC
17:37:40.706 INFO TestIntervalWalker - ------------------------------------------------------------
17:37:40.706 INFO TestIntervalWalker - ------------------------------------------------------------
17:37:40.706 INFO TestIntervalWalker - HTSJDK Defaults.COMPRESSION_LEVEL : 2
17:37:40.706 INFO TestIntervalWalker - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
17:37:40.706 INFO TestIntervalWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
17:37:40.706 INFO TestIntervalWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
17:37:40.706 INFO TestIntervalWalker - Deflater: JdkDeflater
17:37:40.706 INFO TestIntervalWalker - Inflater: JdkInflater
17:37:40.706 INFO TestIntervalWalker - GCS max retries/reopens: 20
17:37:40.706 INFO TestIntervalWalker - Requester pays: disabled
17:37:40.706 INFO TestIntervalWalker - Initializing engine
17:37:40.707 INFO IntervalArgumentCollection - Processing 1 bp from intervals
17:37:40.707 INFO TestIntervalWalker - Done initializing engine
17:37:40.707 INFO ProgressMeter - Starting traversal
17:37:40.707 INFO ProgressMeter - Current Locus Elapsed Minutes Records Processed Records/Minute
17:37:40.707 INFO ProgressMeter - unmapped 0.0 0 NaN
17:37:40.707 INFO ProgressMeter - Traversal complete. Processed 0 total records in 0.0 minutes.
17:37:40.707 INFO TestIntervalWalker - Shutting down engine
[October 27, 2025 at 5:37:40 PM UTC] org.broadinstitute.hellbender.engine.GATKToolUnitTest$TestIntervalWalker done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=524288000
17:37:40.710 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
17:37:40.713 WARN NativeLibraryLoader - Unable to load libgkl_compression.so from native/libgkl_compression.so (/tmp/libgkl_compression15270196067923974448.so: /tmp/libgkl_compression15270196067923974448.so: cannot open shared object file: No such file or directory (Possible cause: can't load AMD 64 .so on a AARCH64 platform))
17:37:40.713 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
17:37:40.716 WARN NativeLibraryLoader - Unable to load libgkl_compression.so from native/libgkl_compression.so (/tmp/libgkl_compression1917086049967551245.so: /tmp/libgkl_compression1917086049967551245.so: cannot open shared object file: No such file or directory (Possible cause: can't load AMD 64 .so on a AARCH64 platform))
17:37:40.717 INFO TestIntervalWalker - ------------------------------------------------------------
17:37:40.717 INFO TestIntervalWalker - org.broadinstitute.hellbender.engine vUnavailable
17:37:40.717 INFO TestIntervalWalker - For support and documentation go to https://software.broadinstitute.org/gatk/
17:37:40.717 INFO TestIntervalWalker - Executing as runner@runnervmrcw8b on Linux v6.11.0-1018-azure aarch64
17:37:40.717 INFO TestIntervalWalker - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
17:37:40.717 INFO TestIntervalWalker - Start Date/Time: October 27, 2025 at 5:37:40 PM UTC
17:37:40.717 INFO TestIntervalWalker - ------------------------------------------------------------
17:37:40.717 INFO TestIntervalWalker - ------------------------------------------------------------
17:37:40.718 INFO TestIntervalWalker - HTSJDK Defaults.COMPRESSION_LEVEL : 2
17:37:40.718 INFO TestIntervalWalker - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
17:37:40.718 INFO TestIntervalWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
17:37:40.718 INFO TestIntervalWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
17:37:40.718 INFO TestIntervalWalker - Deflater: JdkDeflater
17:37:40.718 INFO TestIntervalWalker - Inflater: JdkInflater
17:37:40.718 INFO TestIntervalWalker - GCS max retries/reopens: 20
17:37:40.718 INFO TestIntervalWalker - Requester pays: disabled
17:37:40.718 INFO TestIntervalWalker - Initializing engine
17:37:40.718 INFO TestIntervalWalker - Done initializing engine
17:37:40.718 INFO ProgressMeter - Starting traversal
17:37:40.718 INFO ProgressMeter - Current Locus Elapsed Minutes Records Processed Records/Minute
17:37:40.718 INFO ProgressMeter - unmapped 0.0 0 NaN
17:37:40.718 INFO ProgressMeter - Traversal complete. Processed 0 total records in 0.0 minutes.
17:37:40.718 INFO TestIntervalWalker - Shutting down engine
[October 27, 2025 at 5:37:40 PM UTC] org.broadinstitute.hellbender.engine.GATKToolUnitTest$TestIntervalWalker done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=524288000
17:37:40.724 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
17:37:40.727 WARN NativeLibraryLoader - Unable to load libgkl_compression.so from native/libgkl_compression.so (/tmp/libgkl_compression9234910804556545445.so: /tmp/libgkl_compression9234910804556545445.so: cannot open shared object file: No such file or directory (Possible cause: can't load AMD 64 .so on a AARCH64 platform))
17:37:40.727 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
17:37:40.730 WARN NativeLibraryLoader - Unable to load libgkl_compression.so from native/libgkl_compression.so (/tmp/libgkl_compression6738976772815470957.so: /tmp/libgkl_compression6738976772815470957.so: cannot open shared object file: No such file or directory (Possible cause: can't load AMD 64 .so on a AARCH64 platform))
17:37:40.731 INFO TestIntervalWalker - ------------------------------------------------------------
17:37:40.731 INFO TestIntervalWalker - org.broadinstitute.hellbender.engine vUnavailable
17:37:40.731 INFO TestIntervalWalker - For support and documentation go to https://software.broadinstitute.org/gatk/
17:37:40.731 INFO TestIntervalWalker - Executing as runner@runnervmrcw8b on Linux v6.11.0-1018-azure aarch64
17:37:40.731 INFO TestIntervalWalker - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
17:37:40.731 INFO TestIntervalWalker - Start Date/Time: October 27, 2025 at 5:37:40 PM UTC
17:37:40.731 INFO TestIntervalWalker - ------------------------------------------------------------
17:37:40.731 INFO TestIntervalWalker - ------------------------------------------------------------
17:37:40.731 INFO TestIntervalWalker - HTSJDK Defaults.COMPRESSION_LEVEL : 2
17:37:40.732 INFO TestIntervalWalker - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
17:37:40.732 INFO TestIntervalWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
17:37:40.732 INFO TestIntervalWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
17:37:40.732 INFO TestIntervalWalker - Deflater: JdkDeflater
17:37:40.732 INFO TestIntervalWalker - Inflater: JdkInflater
17:37:40.732 INFO TestIntervalWalker - GCS max retries/reopens: 20
17:37:40.732 INFO TestIntervalWalker - Requester pays: disabled
17:37:40.732 INFO TestIntervalWalker - Initializing engine
17:37:40.732 INFO TestIntervalWalker - Done initializing engine
17:37:40.732 INFO ProgressMeter - Starting traversal
17:37:40.732 INFO ProgressMeter - Current Locus Elapsed Minutes Records Processed Records/Minute
17:37:40.732 INFO ProgressMeter - unmapped 0.0 0 NaN
17:37:40.732 INFO ProgressMeter - Traversal complete. Processed 0 total records in 0.0 minutes.
17:37:40.732 INFO TestIntervalWalker - Shutting down engine
[October 27, 2025 at 5:37:40 PM UTC] org.broadinstitute.hellbender.engine.GATKToolUnitTest$TestIntervalWalker done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=524288000
USAGE: TestGATKToolWithVariants [arguments]
TestGATKToolWithVariants
Version:null
Optional Arguments:
--add-output-sam-program-record <Boolean>
If true, adds a PG tag to created SAM/BAM/CRAM files. Default value: true. Possible
values: {true, false}
--add-output-vcf-command-line <Boolean>
If true, adds a command line header line to created VCF files. Default value: true.
Possible values: {true, false}
--annotation,-A <String> One or more specific annotations to add to variant calls This argument may be specified 0
or more times. Default value: null. Possible values: {AlleleFraction, AllelePseudoDepth,
AS_BaseQualityRankSumTest, AS_FisherStrand, AS_InbreedingCoeff,
AS_MappingQualityRankSumTest, AS_QualByDepth, AS_ReadPosRankSumTest, AS_RMSMappingQuality,
AS_StrandBiasMutectAnnotation, AS_StrandOddsRatio, AssemblyComplexity, BaseQuality,
BaseQualityHistogram, BaseQualityRankSumTest, ChromosomeCounts, ClippingRankSumTest,
CountNs, Coverage, CycleSkipStatus, DepthPerAlleleBySample, DepthPerSampleHC, ExcessHet,
FisherStrand, FragmentDepthPerAlleleBySample, FragmentLength, GcContent,
GenotypeSummaries, HaplotypeFilteringAnnotation, HmerIndelLength, HmerIndelNuc,
HmerMotifs, InbreedingCoeff, IndelClassify, IndelLength, LikelihoodRankSumTest,
MappingQuality, MappingQualityRankSumTest, MappingQualityZero, OrientationBiasReadCounts,
OriginalAlignment, PossibleDeNovo, QualByDepth, RawGtCount, ReadPosition,
ReadPosRankSumTest, ReferenceBases, RMSMappingQuality, SampleList, StrandBiasBySample,
StrandOddsRatio, TandemRepeat, TransmittedSingleton, UniqueAltReadCount, VariantType}
--annotation-group,-G <String>One or more groups of annotations to apply to variant calls This argument may be
specified 0 or more times. Default value: null. Possible values:
{AlleleSpecificAnnotation, AS_StandardAnnotation, GenotypeAnnotation, InfoFieldAnnotation,
JumboGenotypeAnnotation, JumboInfoAnnotation, ReducibleAnnotation, StandardAnnotation,
StandardFlowBasedAnnotation, StandardHCAnnotation, StandardMutectAnnotation,
VariantAnnotation}
--annotations-to-exclude,-AX <String>
One or more specific annotations to exclude from variant calls This argument may be
specified 0 or more times. Default value: null. Any value allowed
--arguments_file <File> read one or more arguments files and add them to the command line This argument may be
specified 0 or more times. Default value: null.
--cloud-index-prefetch-buffer,-CIPB <Integer>
Size of the cloud-only prefetch buffer (in MB; 0 to disable). Defaults to
cloudPrefetchBuffer if unset. Default value: -1.
--cloud-prefetch-buffer,-CPB <Integer>
Size of the cloud-only prefetch buffer (in MB; 0 to disable). Default value: 40.
--create-output-bam-index,-OBI <Boolean>
If true, create a BAM/CRAM index when writing a coordinate-sorted BAM/CRAM file. Default
value: true. Possible values: {true, false}
--create-output-bam-md5,-OBM <Boolean>
If true, create a MD5 digest for any BAM/SAM/CRAM file created Default value: false.
Possible values: {true, false}
--create-output-variant-index,-OVI <Boolean>
If true, create a VCF index when writing a coordinate-sorted VCF file. Default value:
true. Possible values: {true, false}
--create-output-variant-md5,-OVM <Boolean>
If true, create a a MD5 digest any VCF file created. Default value: false. Possible
values: {true, false}
--disable-bam-index-caching,-DBIC <Boolean>
If true, don't cache bam indexes, this will reduce memory requirements but may harm
performance if many intervals are specified. Caching is automatically disabled if there
are no intervals specified. Default value: false. Possible values: {true, false}
--disable-read-filter,-DF <String>
Read filters to be disabled before analysis This argument may be specified 0 or more
times. Default value: null. Possible values: {WellformedReadFilter}
--disable-sequence-dictionary-validation <Boolean>
If specified, do not check the sequence dictionaries from our inputs for compatibility.
Use at your own risk! Default value: false. Possible values: {true, false}
--exclude-intervals,-XL <String>
One or more genomic intervals to exclude from processing This argument may be specified 0
or more times. Default value: null.
--flow-order-for-annotations <String>
flow order used for this annotations. [readGroup:]flowOrder This argument may be
specified 0 or more times. Default value: null.
--founder-id <String> Samples representing the population "founders" This argument may be specified 0 or more
times. Default value: null.
--gatk-config-file <String> A configuration file to use with the GATK. Default value: null.
--gcs-max-retries,-gcs-retries <Integer>
If the GCS bucket channel errors out, how many times it will attempt to re-initiate the
connection Default value: 20.
--gcs-project-for-requester-pays <String>
Project to bill when accessing "requester pays" buckets. If unset, these buckets cannot be
accessed. User must have storage.buckets.get permission on the bucket being accessed.
Default value: .
--help,-h <Boolean> display the help message Default value: false. Possible values: {true, false}
--input,-I <GATKPath> BAM/SAM/CRAM file containing reads This argument may be specified 0 or more times.
Default value: null.
--interval-exclusion-padding,-ixp <Integer>
Amount of padding (in bp) to add to each interval you are excluding. Default value: 0.
--interval-merging-rule,-imr <IntervalMergingRule>
Interval merging rule for abutting intervals Default value: ALL. Possible values: {ALL,
OVERLAPPING_ONLY}
--interval-padding,-ip <Integer>
Amount of padding (in bp) to add to each interval you are including. Default value: 0.
--interval-set-rule,-isr <IntervalSetRule>
Set merging approach to use for combining interval inputs Default value: UNION. Possible
values: {UNION, INTERSECTION}
--intervals,-L <String> One or more genomic intervals over which to operate This argument may be specified 0 or
more times. Default value: null.
--inverted-read-filter,-XRF <String>
Inverted (with flipped acceptance/failure conditions) read filters applied before analysis
(after regular read filters). This argument may be specified 0 or more times. Default
value: null.
--lenient,-LE <Boolean> Lenient processing of VCF files Default value: false. Possible values: {true, false}
--max-variants-per-shard <Integer>
If non-zero, partitions VCF output into shards, each containing up to the given number of
records. Default value: 0.
--output,-out <File> Input variants Default value: null.
--pedigree,-ped <GATKPath> Pedigree file for determining the population "founders" Default value: null.
--QUIET <Boolean> Whether to suppress job-summary info on System.err. Default value: false. Possible
values: {true, false}
--read-filter,-RF <String> Read filters to be applied before analysis This argument may be specified 0 or more
times. Default value: null. Possible values: {AlignmentAgreesWithHeaderReadFilter,
AllowAllReadsReadFilter, AmbiguousBaseReadFilter, CigarContainsNoNOperator,
ExcessiveEndClippedReadFilter, FirstOfPairReadFilter,
FlowBasedTPAttributeSymetricReadFilter, FlowBasedTPAttributeValidReadFilter,
FragmentLengthReadFilter, GoodCigarReadFilter, HasReadGroupReadFilter,
HmerQualitySymetricReadFilter, IntervalOverlapReadFilter,
JexlExpressionReadTagValueFilter, LibraryReadFilter, MappedReadFilter,
MappingQualityAvailableReadFilter, MappingQualityNotZeroReadFilter,
MappingQualityReadFilter, MatchingBasesAndQualsReadFilter, MateDifferentStrandReadFilter,
MateDistantReadFilter, MateOnSameContigOrNoMappedMateReadFilter,
MateUnmappedAndUnmappedReadFilter, MetricsReadFilter,
NonChimericOriginalAlignmentReadFilter, NonZeroFragmentLengthReadFilter,
NonZeroReferenceLengthAlignmentReadFilter, NotDuplicateReadFilter,
NotOpticalDuplicateReadFilter, NotProperlyPairedReadFilter,
NotSecondaryAlignmentReadFilter, NotSupplementaryAlignmentReadFilter,
OverclippedReadFilter, PairedReadFilter, PassesVendorQualityCheckReadFilter,
PlatformReadFilter, PlatformUnitReadFilter, PrimaryLineReadFilter,
ProperlyPairedReadFilter, ReadGroupBlackListReadFilter, ReadGroupHasFlowOrderReadFilter,
ReadGroupReadFilter, ReadLengthEqualsCigarLengthReadFilter, ReadLengthReadFilter,
ReadNameReadFilter, ReadStrandFilter, ReadTagValueFilter, SampleReadFilter,
SecondOfPairReadFilter, SeqIsStoredReadFilter, SoftClippedReadFilter,
ValidAlignmentEndReadFilter, ValidAlignmentStartReadFilter, WellformedFlowBasedReadFilter,
WellformedReadFilter}
--read-index <GATKPath> Indices to use for the read inputs. If specified, an index must be provided for every read
input and in the same order as the read inputs. If this argument is not specified, the
path to the index for each input will be inferred automatically. This argument may be
specified 0 or more times. Default value: null.
--read-validation-stringency,-VS <ValidationStringency>
Validation stringency for all SAM/BAM/CRAM/SRA files read by this program. The default
stringency value SILENT can improve performance when processing a BAM file in which
variable-length data (read, qualities, tags) do not otherwise need to be decoded. Default
value: SILENT. Possible values: {STRICT, LENIENT, SILENT}
--reference,-R <GATKPath> Reference sequence Default value: null.
--seconds-between-progress-updates <Double>
Output traversal statistics every time this many seconds elapse Default value: 10.0.
--sequence-dictionary <GATKPath>
Use the given sequence dictionary as the master/canonical sequence dictionary. Must be a
.dict file. Default value: null.
--sites-only-vcf-output <Boolean>
If true, don't emit genotype fields when writing vcf file output. Default value: false.
Possible values: {true, false}
--tmp-dir <GATKPath> Temp directory to use. Default value: null.
--use-jdk-deflater,-jdk-deflater <Boolean>
Whether to use the JdkDeflater (as opposed to IntelDeflater) Default value: false.
Possible values: {true, false}
--use-jdk-inflater,-jdk-inflater <Boolean>
Whether to use the JdkInflater (as opposed to IntelInflater) Default value: false.
Possible values: {true, false}
--verbosity <LogLevel> Control verbosity of logging. Default value: INFO. Possible values: {ERROR, WARNING,
INFO, DEBUG}
--version <Boolean> display the version number for this tool Default value: false. Possible values: {true,
false}
Advanced Arguments:
--disable-tool-default-annotations <Boolean>
Disable all tool default annotations Default value: false. Possible values: {true, false}
--disable-tool-default-read-filters <Boolean>
Disable all tool default read filters (WARNING: many tools will not function correctly
without their default read filters on) Default value: false. Possible values: {true,
false}
--enable-all-annotations <Boolean>
Use all possible annotations (not for the faint of heart) Default value: false. Possible
values: {true, false}
--showHidden <Boolean> display hidden arguments Default value: false. Possible values: {true, false}
Conditional Arguments for annotation:
Valid only if "AllelePseudoDepth" is specified:
--dirichlet-keep-prior-in-count <Boolean>
By default we don't keep the prior use in the output counts ase it makes it easier to
interpretthis quantity as the number of supporting reads specially in low depth sites. We
this toggled the prior is included Default value: false. Possible values: {true, false}
--dirichlet-prior-pseudo-count <Double>
Pseudo-count used as prior for all alleles. The default is 1.0 resulting in a flat prior
Default value: 1.0.
--pseudo-count-weight-decay-rate <Double>
A what rate the weight of a read decreases base on its informativeness; e.g. 1.0 is linear
decay (default), 2.0 is for quadratic decay Default value: 1.0.
Valid only if "AssemblyComplexity" is specified:
--assembly-complexity-reference-mode <Boolean>
If enabled will treat the reference as the basis for assembly complexity as opposed to
estimated germline haplotypes Default value: false. Possible values: {true, false}
Valid only if "PossibleDeNovo" is specified:
--denovo-depth-threshold <Integer>
Minimum depth (DP) for all trio members to be considered for de novo calculation. Default
value: 0.
--denovo-parent-gq-threshold <Integer>
Minimum genotype quality for parents to be considered for de novo calculation (separate
from GQ thershold for full trio). Default value: 20.
Valid only if "RMSMappingQuality" is specified:
--allow-old-rms-mapping-quality-annotation-data <Boolean>
Override to allow old RMSMappingQuality annotated VCFs to function Default value: false.
Possible values: {true, false}
Conditional Arguments for readFilter:
Valid only if "AmbiguousBaseReadFilter" is specified:
--ambig-filter-bases <Integer>Threshold number of ambiguous bases. If null, uses threshold fraction; otherwise,
overrides threshold fraction. Default value: null. Cannot be used in conjunction with
argument(s) maxAmbiguousBaseFraction
--ambig-filter-frac <Double> Threshold fraction of ambiguous bases Default value: 0.05. Cannot be used in conjunction
with argument(s) maxAmbiguousBases
Valid only if "ExcessiveEndClippedReadFilter" is specified:
--max-clipped-bases <Integer> Maximum number of clipped bases on either end of a given read Default value: 1000.
Valid only if "FlowBasedTPAttributeValidReadFilter" is specified:
--read-filter-max-hmer <Integer>
maxHmer to use for testing in the filter Default value: 12.
Valid only if "FragmentLengthReadFilter" is specified:
--max-fragment-length <Integer>
Maximum length of fragment (insert size) Default value: 1000000.
--min-fragment-length <Integer>
Minimum length of fragment (insert size) Default value: 0.
Valid only if "IntervalOverlapReadFilter" is specified:
--keep-intervals <String> One or more genomic intervals to keep This argument must be specified at least once.
Required.
Valid only if "JexlExpressionReadTagValueFilter" is specified:
--read-filter-expression <String>
One or more JEXL expressions used to filter This argument must be specified at least
once. Required.
Valid only if "LibraryReadFilter" is specified:
--library <String> Name of the library to keep This argument must be specified at least once. Required.
Valid only if "MappingQualityReadFilter" is specified:
--maximum-mapping-quality <Integer>
Maximum mapping quality to keep (inclusive) Default value: null.
--minimum-mapping-quality <Integer>
Minimum mapping quality to keep (inclusive) Default value: 10.
Valid only if "MateDistantReadFilter" is specified:
--mate-too-distant-length <Integer>
Minimum start location difference at which mapped mates are considered distant Default
value: 1000.
Valid only if "OverclippedReadFilter" is specified:
--dont-require-soft-clips-both-ends <Boolean>
Allow a read to be filtered out based on having only 1 soft-clipped block. By default,
both ends must have a soft-clipped block, setting this flag requires only 1 soft-clipped
block Default value: false. Possible values: {true, false}
--filter-too-short <Integer> Minimum number of aligned bases Default value: 30.
Valid only if "PlatformReadFilter" is specified:
--platform-filter-name <String>
Platform attribute (PL) to match This argument must be specified at least once. Required.
Valid only if "PlatformUnitReadFilter" is specified:
--black-listed-lanes <String> Platform unit (PU) to filter out This argument must be specified at least once. Required.
Valid only if "ReadGroupBlackListReadFilter" is specified:
--read-group-black-list <String>
A read group filter expression in the form "attribute:value", where "attribute" is a two
character read group attribute such as "RG" or "PU". This argument must be specified at
least once. Required.
Valid only if "ReadGroupReadFilter" is specified:
--keep-read-group <String> The name of the read group to keep Required.
Valid only if "ReadLengthReadFilter" is specified:
--max-read-length <Integer> Keep only reads with length at most equal to the specified value Required.
--min-read-length <Integer> Keep only reads with length at least equal to the specified value Default value: 1.
Valid only if "ReadNameReadFilter" is specified:
--read-name <String> Keep only reads with this read name This argument must be specified at least once.
Required.
Valid only if "ReadStrandFilter" is specified:
--keep-reverse-strand-only <Boolean>
Keep only reads on the reverse strand Required. Possible values: {true, false}
Valid only if "ReadTagValueFilter" is specified:
--read-filter-tag <String> Look for this tag in read Required.
--read-filter-tag-comp <Float>Compare value in tag to this value Default value: 0.0.
--read-filter-tag-op <Operator>
Compare value in tag to value with this operator. If T is the value in the tag, OP is the
operation provided, and V is the value in read-filter-tag, then the read will pass the
filter iff T OP V is true. Default value: EQUAL. Possible values: {LESS, LESS_OR_EQUAL,
GREATER, GREATER_OR_EQUAL, EQUAL, NOT_EQUAL}
Valid only if "SampleReadFilter" is specified:
--sample <String> The name of the sample(s) to keep, filtering out all others This argument must be
specified at least once. Required.
Valid only if "SoftClippedReadFilter" is specified:
--max-soft-clipped-leading-trailing-ratio <Double>
Threshold ratio of soft clipped bases (leading / trailing the cigar string) to total bases
in read for read to be filtered. Default value: null. Cannot be used in conjunction with
argument(s) maximumSoftClippedRatio
--max-soft-clipped-ratio <Double>
Threshold ratio of soft clipped bases (anywhere in the cigar string) to total bases in
read for read to be filtered. Default value: null. Cannot be used in conjunction with
argument(s) maximumLeadingTrailingSoftClippedRatio
17:37:40.767 WARN IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater
17:37:40.767 WARN IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater
17:37:40.771 INFO FeatureManager - Using codec IntervalListCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/picard_intervals.interval_list
17:37:40.773 INFO IntervalArgumentCollection - Processing 20 bp from intervals
17:37:40.773 WARN IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater
17:37:40.774 WARN IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater
17:37:40.774 INFO ProgressMeter - Starting traversal
17:37:40.774 INFO ProgressMeter - Current Locus Elapsed Minutes Records Processed Records/Minute
17:37:40.774 INFO ProgressMeter - unmapped 0.0 0 NaN
17:37:40.774 INFO ProgressMeter - Traversal complete. Processed 0 total records in 0.0 minutes.
17:37:40.775 WARN IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater
17:37:40.775 WARN IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater
17:37:40.778 WARN IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater
17:37:40.778 WARN IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater
17:37:40.779 INFO ProgressMeter - Starting traversal
17:37:40.779 INFO ProgressMeter - Current Locus Elapsed Minutes Records Processed Records/Minute
17:37:40.779 INFO ProgressMeter - unmapped 0.0 0 NaN
17:37:40.779 INFO ProgressMeter - Traversal complete. Processed 0 total records in 0.0 minutes.
17:37:40.789 INFO ProgressMeter - Starting traversal
17:37:40.789 INFO ProgressMeter - Current Locus Elapsed Minutes Records Processed Records/Minute
Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 129, Read name 809R9ABXX101220:5:6:17918:145992, Mate Alignment start should be 0 because reference name = *.
Ignoring SAM validation error: ERROR::INVALID_FLAG_MATE_UNMAPPED:Record 129, Read name 809R9ABXX101220:5:6:17918:145992, Mapped mate should have mate reference name
Ignoring SAM validation error: ERROR::INVALID_UNALIGNED_MATE_START:Record 129, Read name 809R9ABXX101220:5:6:17918:145992, The unaligned mate start position is 69400, should be 0
Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 274, Read name 809R9ABXX101220:5:8:7119:101555, Mate Alignment start should be 0 because reference name = *.
Ignoring SAM validation error: ERROR::INVALID_FLAG_MATE_UNMAPPED:Record 274, Read name 809R9ABXX101220:5:8:7119:101555, Mapped mate should have mate reference name
Ignoring SAM validation error: ERROR::INVALID_UNALIGNED_MATE_START:Record 274, Read name 809R9ABXX101220:5:8:7119:101555, The unaligned mate start position is 69471, should be 0
Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 418, Read name 809R9ABXX101220:5:48:20204:50350, Mate Alignment start should be 0 because reference name = *.
Ignoring SAM validation error: ERROR::INVALID_FLAG_MATE_UNMAPPED:Record 418, Read name 809R9ABXX101220:5:48:20204:50350, Mapped mate should have mate reference name
Ignoring SAM validation error: ERROR::INVALID_UNALIGNED_MATE_START:Record 418, Read name 809R9ABXX101220:5:48:20204:50350, The unaligned mate start position is 69569, should be 0
Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 439, Read name 809R9ABXX101220:5:44:13776:49360, Mate Alignment start should be 0 because reference name = *.
Ignoring SAM validation error: ERROR::INVALID_FLAG_MATE_UNMAPPED:Record 439, Read name 809R9ABXX101220:5:44:13776:49360, Mapped mate should have mate reference name
Ignoring SAM validation error: ERROR::INVALID_UNALIGNED_MATE_START:Record 439, Read name 809R9ABXX101220:5:44:13776:49360, The unaligned mate start position is 69592, should be 0
17:37:40.840 INFO ProgressMeter - unmapped 0.0 0 0.0
17:37:40.840 INFO ProgressMeter - Traversal complete. Processed 0 total records in 0.0 minutes.
17:37:40.846 INFO ProgressMeter - Starting traversal
17:37:40.846 INFO ProgressMeter - Current Locus Elapsed Minutes Records Processed Records/Minute
17:37:40.857 INFO ProgressMeter - unmapped 0.0 0 0.0
17:37:40.857 INFO ProgressMeter - Traversal complete. Processed 0 total records in 0.0 minutes.
17:37:40.863 INFO ProgressMeter - Starting traversal
17:37:40.863 INFO ProgressMeter - Current Locus Elapsed Minutes Records Processed Records/Minute
17:37:40.874 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
17:37:40.877 WARN NativeLibraryLoader - Unable to load libgkl_compression.so from native/libgkl_compression.so (/tmp/libgkl_compression15648400857356126322.so: /tmp/libgkl_compression15648400857356126322.so: cannot open shared object file: No such file or directory (Possible cause: can't load AMD 64 .so on a AARCH64 platform))
17:37:40.877 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
17:37:40.880 WARN NativeLibraryLoader - Unable to load libgkl_compression.so from native/libgkl_compression.so (/tmp/libgkl_compression8603038652197688413.so: /tmp/libgkl_compression8603038652197688413.so: cannot open shared object file: No such file or directory (Possible cause: can't load AMD 64 .so on a AARCH64 platform))
17:37:40.881 INFO TestIntervalWalker - ------------------------------------------------------------
17:37:40.882 INFO TestIntervalWalker - org.broadinstitute.hellbender.engine vUnavailable
17:37:40.882 INFO TestIntervalWalker - For support and documentation go to https://software.broadinstitute.org/gatk/
17:37:40.882 INFO TestIntervalWalker - Executing as runner@runnervmrcw8b on Linux v6.11.0-1018-azure aarch64
17:37:40.882 INFO TestIntervalWalker - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
17:37:40.882 INFO TestIntervalWalker - Start Date/Time: October 27, 2025 at 5:37:40 PM UTC
17:37:40.882 INFO TestIntervalWalker - ------------------------------------------------------------
17:37:40.882 INFO TestIntervalWalker - ------------------------------------------------------------
17:37:40.882 INFO TestIntervalWalker - HTSJDK Defaults.COMPRESSION_LEVEL : 2
17:37:40.882 INFO TestIntervalWalker - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
17:37:40.882 INFO TestIntervalWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
17:37:40.882 INFO TestIntervalWalker - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
17:37:40.882 INFO TestIntervalWalker - Deflater: JdkDeflater
17:37:40.882 INFO TestIntervalWalker - Inflater: JdkInflater
17:37:40.882 INFO TestIntervalWalker - GCS max retries/reopens: 20
17:37:40.882 INFO TestIntervalWalker - Requester pays: disabled
17:37:40.882 INFO TestIntervalWalker - Initializing engine
17:37:40.882 INFO TestIntervalWalker - Shutting down engine
[October 27, 2025 at 5:37:40 PM UTC] org.broadinstitute.hellbender.engine.GATKToolUnitTest$TestIntervalWalker done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=524288000