Class org.broadinstitute.hellbender.tools.walkers.bqsr.BaseRecalibratorIntegrationTest

all > org.broadinstitute.hellbender.tools.walkers.bqsr > BaseRecalibratorIntegrationTest
21

tests
0

failures
0

ignored
38.233s

duration
100%

successful

Tests

Test Duration Result
testBQSRFailWithIncompatibleReference 0.072s passed
testBQSRFailWithIncompatibleSequenceDictionaries 0.071s passed
testBQSRFailWithoutDBSNP 0.060s passed
testBQSR[0](BQSR(bam='src/test/resources/org/broadinstitute/hellbender/tools/BQSR/CEUTrio.HiSeq.WGS.b37.ch20.1m-1m1k.NA12878.bam', args='')) 4.015s passed
testBQSR[10](BQSR(bam='src/test/resources/org/broadinstitute/hellbender/tools/BQSR/CEUTrio.HiSeq.WGS.b37.ch20.4379150-4379157.bam', args='-indels --enable-baq ')) 1.627s passed
testBQSR[11](BQSR(bam='src/test/resources/org/broadinstitute/hellbender/tools/BQSR/NA12878.chr17_69k_70k.dictFix.bam', args='-indels --enable-baq --known-sites src/test/resources/org/broadinstitute/hellbender/tools/BQSR/bqsr.fakeSitesForTesting.b37.chr17.vcf')) 0.466s passed
testBQSR[12](BQSR(bam='src/test/resources/org/broadinstitute/hellbender/tools/BQSR/NA12878.chr17_69k_70k.dictFix.bam', args='-indels --enable-baq --indels-context-size 4')) 0.505s passed
testBQSR[13](BQSR(bam='src/test/resources/org/broadinstitute/hellbender/tools/BQSR/NA12878.chr17_69k_70k.dictFix.bam', args='-indels --enable-baq --low-quality-tail 5')) 0.448s passed
testBQSR[14](BQSR(bam='src/test/resources/org/broadinstitute/hellbender/tools/BQSR/NA12878.chr17_69k_70k.dictFix.bam', args='-indels --enable-baq --quantizing-levels 6')) 0.445s passed
testBQSR[15](BQSR(bam='src/test/resources/org/broadinstitute/hellbender/tools/BQSR/NA12878.chr17_69k_70k.dictFix.bam', args='-indels --enable-baq --mismatches-context-size 4')) 0.693s passed
testBQSR[16](BQSR(bam='src/test/resources/org/broadinstitute/hellbender/tools/BQSR/originalQuals.1kg.chr1.1-1K.1RG.dictFix.bam', args='-indels --enable-baq -OQ')) 0.125s passed
testBQSR[1](BQSR(bam='src/test/resources/org/broadinstitute/hellbender/tools/BQSR/CEUTrio.HiSeq.WGS.b37.ch20.1m-1m1k.NA12878.bam', args='-indels --enable-baq')) 5.072s passed
testBQSR[2](BQSR(bam='src/test/resources/org/broadinstitute/hellbender/tools/BQSR/overlappingRead.bam', args='-indels --enable-baq')) 0.126s passed
testBQSR[3](BQSR(bam='src/test/resources/org/broadinstitute/hellbender/tools/BQSR/NA12878.oq.read_consumes_zero_ref_bases.chr20.bam', args='-indels --enable-baq')) 0.175s passed
testBQSR[4](BQSR(bam='src/test/resources/org/broadinstitute/hellbender/tools/BQSR/CEUTrio.HiSeq.WGS.b37.ch20.1m-1m1k.NA12878.bam', args='-indels --enable-baq --indels-context-size 4')) 5.447s passed
testBQSR[5](BQSR(bam='src/test/resources/org/broadinstitute/hellbender/tools/BQSR/CEUTrio.HiSeq.WGS.b37.ch20.1m-1m1k.NA12878.bam', args='-indels --enable-baq --low-quality-tail 5')) 4.887s passed
testBQSR[6](BQSR(bam='src/test/resources/org/broadinstitute/hellbender/tools/BQSR/CEUTrio.HiSeq.WGS.b37.ch20.1m-1m1k.NA12878.bam', args='-indels --enable-baq --quantizing-levels 6')) 4.856s passed
testBQSR[7](BQSR(bam='src/test/resources/org/broadinstitute/hellbender/tools/BQSR/CEUTrio.HiSeq.WGS.b37.ch20.1m-1m1k.NA12878.bam', args='-indels --enable-baq --mismatches-context-size 4')) 7.618s passed
testBQSR[8](BQSR(bam='src/test/resources/org/broadinstitute/hellbender/tools/BQSR/NA12878.chr17_69k_70k.dictFix.cram', args='-indels --enable-baq ')) 0.451s passed
testBQSR[9](BQSR(bam='src/test/resources/org/broadinstitute/hellbender/tools/BQSR/NA12878.chr17_69k_70k.dictFix.bam', args='-indels --enable-baq ')) 0.455s passed
testPlottingWorkflow 0.619s passed

Standard output

--------------------------------------------------------------------------------
[17:50:27] Executing test BaseRecalibratorIntegrationTest:testBQSR-
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[17:50:31] Executing test BaseRecalibratorIntegrationTest:testBQSR--indels --enable-baq
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[17:50:36] Executing test BaseRecalibratorIntegrationTest:testBQSR--indels --enable-baq
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[17:50:36] Executing test BaseRecalibratorIntegrationTest:testBQSR--indels --enable-baq
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[17:50:36] Executing test BaseRecalibratorIntegrationTest:testBQSR--indels --enable-baq --indels-context-size 4
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[17:50:42] Executing test BaseRecalibratorIntegrationTest:testBQSR--indels --enable-baq --low-quality-tail 5
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[17:50:46] Executing test BaseRecalibratorIntegrationTest:testBQSR--indels --enable-baq --quantizing-levels 6
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[17:50:51] Executing test BaseRecalibratorIntegrationTest:testBQSR--indels --enable-baq --mismatches-context-size 4
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[17:50:59] Executing test BaseRecalibratorIntegrationTest:testBQSR--indels --enable-baq 
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[17:50:59] Executing test BaseRecalibratorIntegrationTest:testBQSR--indels --enable-baq 
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[17:51:00] Executing test BaseRecalibratorIntegrationTest:testBQSR--indels --enable-baq 
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[17:51:02] Executing test BaseRecalibratorIntegrationTest:testBQSR--indels --enable-baq --known-sites src/test/resources/org/broadinstitute/hellbender/tools/BQSR/bqsr.fakeSitesForTesting.b37.chr17.vcf
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[17:51:02] Executing test BaseRecalibratorIntegrationTest:testBQSR--indels --enable-baq --indels-context-size 4
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[17:51:02] Executing test BaseRecalibratorIntegrationTest:testBQSR--indels --enable-baq --low-quality-tail 5
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[17:51:03] Executing test BaseRecalibratorIntegrationTest:testBQSR--indels --enable-baq --quantizing-levels 6
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[17:51:03] Executing test BaseRecalibratorIntegrationTest:testBQSR--indels --enable-baq --mismatches-context-size 4
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[17:51:04] Executing test BaseRecalibratorIntegrationTest:testBQSR--indels --enable-baq -OQ
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[17:51:04] Executing test BaseRecalibratorIntegrationTest:testBQSRFailWithIncompatibleReference
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[17:51:04] Executing test BaseRecalibratorIntegrationTest:testBQSRFailWithIncompatibleSequenceDictionaries
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[17:51:04] Executing test BaseRecalibratorIntegrationTest:testBQSRFailWithoutDBSNP

Standard error

[October 27, 2025 at 5:50:31 PM UTC] org.broadinstitute.hellbender.tools.walkers.bqsr.BaseRecalibrator done. Elapsed time: 0.07 minutes.
Runtime.totalMemory()=1304428544
[October 27, 2025 at 5:50:36 PM UTC] org.broadinstitute.hellbender.tools.walkers.bqsr.BaseRecalibrator done. Elapsed time: 0.08 minutes.
Runtime.totalMemory()=1304428544
[October 27, 2025 at 5:50:36 PM UTC] org.broadinstitute.hellbender.tools.walkers.bqsr.BaseRecalibrator done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1304428544
[October 27, 2025 at 5:50:36 PM UTC] org.broadinstitute.hellbender.tools.walkers.bqsr.BaseRecalibrator done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1304428544
[October 27, 2025 at 5:50:42 PM UTC] org.broadinstitute.hellbender.tools.walkers.bqsr.BaseRecalibrator done. Elapsed time: 0.09 minutes.
Runtime.totalMemory()=1304428544
[October 27, 2025 at 5:50:46 PM UTC] org.broadinstitute.hellbender.tools.walkers.bqsr.BaseRecalibrator done. Elapsed time: 0.08 minutes.
Runtime.totalMemory()=1304428544
[October 27, 2025 at 5:50:51 PM UTC] org.broadinstitute.hellbender.tools.walkers.bqsr.BaseRecalibrator done. Elapsed time: 0.08 minutes.
Runtime.totalMemory()=1304428544
[October 27, 2025 at 5:50:59 PM UTC] org.broadinstitute.hellbender.tools.walkers.bqsr.BaseRecalibrator done. Elapsed time: 0.13 minutes.
Runtime.totalMemory()=1304428544
[October 27, 2025 at 5:50:59 PM UTC] org.broadinstitute.hellbender.tools.walkers.bqsr.BaseRecalibrator done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=1304428544
[October 27, 2025 at 5:51:00 PM UTC] org.broadinstitute.hellbender.tools.walkers.bqsr.BaseRecalibrator done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=1304428544
[October 27, 2025 at 5:51:01 PM UTC] org.broadinstitute.hellbender.tools.walkers.bqsr.BaseRecalibrator done. Elapsed time: 0.03 minutes.
Runtime.totalMemory()=1304428544
[October 27, 2025 at 5:51:02 PM UTC] org.broadinstitute.hellbender.tools.walkers.bqsr.BaseRecalibrator done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=1304428544
[October 27, 2025 at 5:51:02 PM UTC] org.broadinstitute.hellbender.tools.walkers.bqsr.BaseRecalibrator done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=1304428544
[October 27, 2025 at 5:51:03 PM UTC] org.broadinstitute.hellbender.tools.walkers.bqsr.BaseRecalibrator done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=1304428544
[October 27, 2025 at 5:51:03 PM UTC] org.broadinstitute.hellbender.tools.walkers.bqsr.BaseRecalibrator done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=1304428544
[October 27, 2025 at 5:51:04 PM UTC] org.broadinstitute.hellbender.tools.walkers.bqsr.BaseRecalibrator done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=1304428544
[October 27, 2025 at 5:51:04 PM UTC] org.broadinstitute.hellbender.tools.walkers.bqsr.BaseRecalibrator done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1304428544
[October 27, 2025 at 5:51:04 PM UTC] org.broadinstitute.hellbender.tools.walkers.bqsr.BaseRecalibrator done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1304428544
[October 27, 2025 at 5:51:04 PM UTC] org.broadinstitute.hellbender.tools.walkers.bqsr.BaseRecalibrator done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1304428544
17:51:04.894 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
17:51:04.897 WARN  NativeLibraryLoader - Unable to load libgkl_compression.so from native/libgkl_compression.so (/tmp/local16469784102307886954/libgkl_compression8348650999800368280.so: /tmp/local16469784102307886954/libgkl_compression8348650999800368280.so: cannot open shared object file: No such file or directory (Possible cause: can't load AMD 64 .so on a AARCH64 platform))
17:51:04.897 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
17:51:04.900 WARN  NativeLibraryLoader - Unable to load libgkl_compression.so from native/libgkl_compression.so (/tmp/local16469784102307886954/libgkl_compression3046694843264208369.so: /tmp/local16469784102307886954/libgkl_compression3046694843264208369.so: cannot open shared object file: No such file or directory (Possible cause: can't load AMD 64 .so on a AARCH64 platform))
17:51:04.901 INFO  BaseRecalibrator - ------------------------------------------------------------
17:51:04.901 INFO  BaseRecalibrator - org.broadinstitute.hellbender.tools.walkers.bqsr vUnavailable
17:51:04.901 INFO  BaseRecalibrator - For support and documentation go to https://software.broadinstitute.org/gatk/
17:51:04.901 INFO  BaseRecalibrator - Executing as runner@runnervmrcw8b on Linux v6.11.0-1018-azure aarch64
17:51:04.901 INFO  BaseRecalibrator - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
17:51:04.901 INFO  BaseRecalibrator - Start Date/Time: October 27, 2025 at 5:51:04 PM UTC
17:51:04.901 INFO  BaseRecalibrator - ------------------------------------------------------------
17:51:04.901 INFO  BaseRecalibrator - ------------------------------------------------------------
17:51:04.901 INFO  BaseRecalibrator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
17:51:04.901 INFO  BaseRecalibrator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
17:51:04.901 INFO  BaseRecalibrator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
17:51:04.901 INFO  BaseRecalibrator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
17:51:04.901 INFO  BaseRecalibrator - Deflater: JdkDeflater
17:51:04.901 INFO  BaseRecalibrator - Inflater: JdkInflater
17:51:04.901 INFO  BaseRecalibrator - GCS max retries/reopens: 20
17:51:04.901 INFO  BaseRecalibrator - Requester pays: disabled
17:51:04.902 INFO  BaseRecalibrator - Initializing engine
17:51:04.902 WARN  IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater
17:51:04.902 WARN  IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater
17:51:04.904 INFO  FeatureManager - Using codec VCFCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/BQSR/dbsnp_132.b37.excluding_sites_after_129.chr17_69k_70k.vcf
17:51:04.904 WARN  IndexUtils - Feature file "file:///home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/BQSR/dbsnp_132.b37.excluding_sites_after_129.chr17_69k_70k.vcf" appears to contain no sequence dictionary. Attempting to retrieve a sequence dictionary from the associated index file
17:51:04.904 INFO  BaseRecalibrator - Done initializing engine
17:51:04.913 INFO  BaseRecalibrationEngine - The covariates being used here: 
17:51:04.913 INFO  BaseRecalibrationEngine - 	ReadGroupCovariate
17:51:04.913 INFO  BaseRecalibrationEngine - 	QualityScoreCovariate
17:51:04.913 INFO  BaseRecalibrationEngine - 	ContextCovariate
17:51:04.913 INFO  BaseRecalibrationEngine - 	CycleCovariate
17:51:04.913 INFO  ProgressMeter - Starting traversal
17:51:04.913 INFO  ProgressMeter -        Current Locus  Elapsed Minutes       Reads Processed     Reads/Minute
17:51:04.927 INFO  BaseRecalibrator - 14 read(s) filtered by: MappingQualityNotZeroReadFilter 
0 read(s) filtered by: MappingQualityAvailableReadFilter 
0 read(s) filtered by: MappedReadFilter 
0 read(s) filtered by: NotSecondaryAlignmentReadFilter 
59 read(s) filtered by: NotDuplicateReadFilter 
47 read(s) filtered by: PassesVendorQualityCheckReadFilter 
0 read(s) filtered by: WellformedReadFilter 
120 total reads filtered out of 493 reads processed
17:51:04.927 INFO  ProgressMeter -             unmapped              0.0                   373        1598571.4
17:51:04.927 INFO  ProgressMeter - Traversal complete. Processed 373 total reads in 0.0 minutes.
17:51:04.928 INFO  BaseRecalibrator - Calculating quantized quality scores...
17:51:04.930 INFO  BaseRecalibrator - Writing recalibration report...
17:51:05.282 INFO  BaseRecalibrator - ...done!
17:51:05.282 INFO  BaseRecalibrator - BaseRecalibrator was able to recalibrate 373 reads
17:51:05.282 INFO  BaseRecalibrator - Shutting down engine
[October 27, 2025 at 5:51:05 PM UTC] org.broadinstitute.hellbender.tools.walkers.bqsr.BaseRecalibrator done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=1304428544
17:51:05.286 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
17:51:05.289 WARN  NativeLibraryLoader - Unable to load libgkl_compression.so from native/libgkl_compression.so (/tmp/local16469784102307886954/libgkl_compression6374846504755787977.so: /tmp/local16469784102307886954/libgkl_compression6374846504755787977.so: cannot open shared object file: No such file or directory (Possible cause: can't load AMD 64 .so on a AARCH64 platform))
17:51:05.290 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
17:51:05.292 WARN  NativeLibraryLoader - Unable to load libgkl_compression.so from native/libgkl_compression.so (/tmp/local16469784102307886954/libgkl_compression1577864229005521999.so: /tmp/local16469784102307886954/libgkl_compression1577864229005521999.so: cannot open shared object file: No such file or directory (Possible cause: can't load AMD 64 .so on a AARCH64 platform))
17:51:05.293 INFO  ApplyBQSR - ------------------------------------------------------------
17:51:05.293 INFO  ApplyBQSR - org.broadinstitute.hellbender.tools.walkers.bqsr vUnavailable
17:51:05.293 INFO  ApplyBQSR - For support and documentation go to https://software.broadinstitute.org/gatk/
17:51:05.293 INFO  ApplyBQSR - Executing as runner@runnervmrcw8b on Linux v6.11.0-1018-azure aarch64
17:51:05.293 INFO  ApplyBQSR - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
17:51:05.294 INFO  ApplyBQSR - Start Date/Time: October 27, 2025 at 5:51:05 PM UTC
17:51:05.294 INFO  ApplyBQSR - ------------------------------------------------------------
17:51:05.294 INFO  ApplyBQSR - ------------------------------------------------------------
17:51:05.294 INFO  ApplyBQSR - HTSJDK Defaults.COMPRESSION_LEVEL : 2
17:51:05.294 INFO  ApplyBQSR - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
17:51:05.294 INFO  ApplyBQSR - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
17:51:05.294 INFO  ApplyBQSR - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
17:51:05.294 INFO  ApplyBQSR - Deflater: JdkDeflater
17:51:05.294 INFO  ApplyBQSR - Inflater: JdkInflater
17:51:05.294 INFO  ApplyBQSR - GCS max retries/reopens: 20
17:51:05.294 INFO  ApplyBQSR - Requester pays: disabled
17:51:05.294 INFO  ApplyBQSR - Initializing engine
17:51:05.294 WARN  IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater
17:51:05.294 WARN  IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater
17:51:05.295 INFO  ApplyBQSR - Done initializing engine
17:51:05.295 WARN  IntelDeflaterFactory - Intel Deflater not supported, using Java.util.zip.Deflater
17:51:05.295 INFO  ProgressMeter - Starting traversal
17:51:05.295 INFO  ProgressMeter -        Current Locus  Elapsed Minutes       Reads Processed     Reads/Minute
17:51:05.353 INFO  ApplyBQSR - 0 read(s) filtered by: WellformedReadFilter 

17:51:05.353 INFO  ProgressMeter -             unmapped              0.0                   493         510000.0
17:51:05.353 INFO  ProgressMeter - Traversal complete. Processed 493 total reads in 0.0 minutes.
17:51:05.403 INFO  ApplyBQSR - Shutting down engine
[October 27, 2025 at 5:51:05 PM UTC] org.broadinstitute.hellbender.tools.walkers.bqsr.ApplyBQSR done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1304428544
17:51:05.408 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
17:51:05.411 WARN  NativeLibraryLoader - Unable to load libgkl_compression.so from native/libgkl_compression.so (/tmp/local16469784102307886954/libgkl_compression1995221548976995951.so: /tmp/local16469784102307886954/libgkl_compression1995221548976995951.so: cannot open shared object file: No such file or directory (Possible cause: can't load AMD 64 .so on a AARCH64 platform))
17:51:05.411 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
17:51:05.414 WARN  NativeLibraryLoader - Unable to load libgkl_compression.so from native/libgkl_compression.so (/tmp/local16469784102307886954/libgkl_compression17817127111397844857.so: /tmp/local16469784102307886954/libgkl_compression17817127111397844857.so: cannot open shared object file: No such file or directory (Possible cause: can't load AMD 64 .so on a AARCH64 platform))
17:51:05.415 INFO  BaseRecalibrator - ------------------------------------------------------------
17:51:05.415 INFO  BaseRecalibrator - org.broadinstitute.hellbender.tools.walkers.bqsr vUnavailable
17:51:05.415 INFO  BaseRecalibrator - For support and documentation go to https://software.broadinstitute.org/gatk/
17:51:05.415 INFO  BaseRecalibrator - Executing as runner@runnervmrcw8b on Linux v6.11.0-1018-azure aarch64
17:51:05.415 INFO  BaseRecalibrator - Java runtime: OpenJDK 64-Bit Server VM v17.0.6+10
17:51:05.415 INFO  BaseRecalibrator - Start Date/Time: October 27, 2025 at 5:51:05 PM UTC
17:51:05.415 INFO  BaseRecalibrator - ------------------------------------------------------------
17:51:05.415 INFO  BaseRecalibrator - ------------------------------------------------------------
17:51:05.415 INFO  BaseRecalibrator - HTSJDK Defaults.COMPRESSION_LEVEL : 2
17:51:05.415 INFO  BaseRecalibrator - HTSJDK Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS : false
17:51:05.415 INFO  BaseRecalibrator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS : true
17:51:05.415 INFO  BaseRecalibrator - HTSJDK Defaults.USE_ASYNC_IO_WRITE_FOR_TRIBBLE : false
17:51:05.415 INFO  BaseRecalibrator - Deflater: JdkDeflater
17:51:05.415 INFO  BaseRecalibrator - Inflater: JdkInflater
17:51:05.415 INFO  BaseRecalibrator - GCS max retries/reopens: 20
17:51:05.415 INFO  BaseRecalibrator - Requester pays: disabled
17:51:05.415 INFO  BaseRecalibrator - Initializing engine
17:51:05.416 WARN  IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater
17:51:05.416 WARN  IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater
17:51:05.417 INFO  FeatureManager - Using codec VCFCodec to read file file:///home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/BQSR/dbsnp_132.b37.excluding_sites_after_129.chr17_69k_70k.vcf
17:51:05.418 WARN  IndexUtils - Feature file "file:///home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/BQSR/dbsnp_132.b37.excluding_sites_after_129.chr17_69k_70k.vcf" appears to contain no sequence dictionary. Attempting to retrieve a sequence dictionary from the associated index file
17:51:05.418 INFO  BaseRecalibrator - Done initializing engine
17:51:05.426 INFO  BaseRecalibrationEngine - The covariates being used here: 
17:51:05.426 INFO  BaseRecalibrationEngine - 	ReadGroupCovariate
17:51:05.426 INFO  BaseRecalibrationEngine - 	QualityScoreCovariate
17:51:05.426 INFO  BaseRecalibrationEngine - 	ContextCovariate
17:51:05.426 INFO  BaseRecalibrationEngine - 	CycleCovariate
17:51:05.426 INFO  ProgressMeter - Starting traversal
17:51:05.427 INFO  ProgressMeter -        Current Locus  Elapsed Minutes       Reads Processed     Reads/Minute
17:51:05.439 INFO  BaseRecalibrator - 14 read(s) filtered by: MappingQualityNotZeroReadFilter 
0 read(s) filtered by: MappingQualityAvailableReadFilter 
0 read(s) filtered by: MappedReadFilter 
0 read(s) filtered by: NotSecondaryAlignmentReadFilter 
59 read(s) filtered by: NotDuplicateReadFilter 
47 read(s) filtered by: PassesVendorQualityCheckReadFilter 
0 read(s) filtered by: WellformedReadFilter 
120 total reads filtered out of 493 reads processed
17:51:05.439 INFO  ProgressMeter -             unmapped              0.0                   373        1865000.0
17:51:05.439 INFO  ProgressMeter - Traversal complete. Processed 373 total reads in 0.0 minutes.
17:51:05.439 INFO  BaseRecalibrator - Calculating quantized quality scores...
17:51:05.441 INFO  BaseRecalibrator - Writing recalibration report...
17:51:05.499 INFO  BaseRecalibrator - ...done!
17:51:05.499 INFO  BaseRecalibrator - BaseRecalibrator was able to recalibrate 373 reads
17:51:05.499 INFO  BaseRecalibrator - Shutting down engine
[October 27, 2025 at 5:51:05 PM UTC] org.broadinstitute.hellbender.tools.walkers.bqsr.BaseRecalibrator done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1304428544
17:51:05.500 WARN  IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater
17:51:05.500 WARN  IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater
17:51:05.501 WARN  IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater
17:51:05.501 WARN  IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater
17:51:05.501 WARN  IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater
17:51:05.501 WARN  IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater
17:51:05.502 WARN  IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater
17:51:05.502 WARN  IntelInflaterFactory - IntelInflater is not supported, using Java.util.zip.Inflater
Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 130, 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 130, Read name 809R9ABXX101220:5:6:17918:145992, Mapped mate should have mate reference name
Ignoring SAM validation error: ERROR::INVALID_UNALIGNED_MATE_START:Record 130, 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 130, 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 130, Read name 809R9ABXX101220:5:6:17918:145992, Mapped mate should have mate reference name
Ignoring SAM validation error: ERROR::INVALID_UNALIGNED_MATE_START:Record 130, 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 275, 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 275, Read name 809R9ABXX101220:5:8:7119:101555, Mapped mate should have mate reference name
Ignoring SAM validation error: ERROR::INVALID_UNALIGNED_MATE_START:Record 275, 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 275, 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 275, Read name 809R9ABXX101220:5:8:7119:101555, Mapped mate should have mate reference name
Ignoring SAM validation error: ERROR::INVALID_UNALIGNED_MATE_START:Record 275, 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 419, 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 419, Read name 809R9ABXX101220:5:48:20204:50350, Mapped mate should have mate reference name
Ignoring SAM validation error: ERROR::INVALID_UNALIGNED_MATE_START:Record 419, 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 419, 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 419, Read name 809R9ABXX101220:5:48:20204:50350, Mapped mate should have mate reference name
Ignoring SAM validation error: ERROR::INVALID_UNALIGNED_MATE_START:Record 419, 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 440, 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 440, Read name 809R9ABXX101220:5:44:13776:49360, Mapped mate should have mate reference name
Ignoring SAM validation error: ERROR::INVALID_UNALIGNED_MATE_START:Record 440, Read name 809R9ABXX101220:5:44:13776:49360, The unaligned mate start position is 69592, should be 0
Ignoring SAM validation error: ERROR::INVALID_ALIGNMENT_START:Record 440, 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 440, Read name 809R9ABXX101220:5:44:13776:49360, Mapped mate should have mate reference name
Ignoring SAM validation error: ERROR::INVALID_UNALIGNED_MATE_START:Record 440, Read name 809R9ABXX101220:5:44:13776:49360, The unaligned mate start position is 69592, should be 0