Class org.broadinstitute.hellbender.engine.AssemblyRegionIteratorUnitTest

all > org.broadinstitute.hellbender.engine > AssemblyRegionIteratorUnitTest
4

tests
0

failures
0

ignored
12.199s

duration
100%

successful

Tests

Test Duration Result
testRegionsHaveCorrectReadsAndSize[0](/home/runner/work/gatk/gatk/src/test/resources/large/CEUTrio.HiSeq.WGS.b37.NA12878.20.21.bam, /home/runner/work/gatk/gatk/src/test/resources/large/human_g1k_v37.20.21.fasta, [20:10000000-10100000], 50, 300, 100) 7.558s passed
testRegionsHaveCorrectReadsAndSize[1](/home/runner/work/gatk/gatk/src/test/resources/large/CEUTrio.HiSeq.WGS.b37.NA12878.20.21.bam, /home/runner/work/gatk/gatk/src/test/resources/large/human_g1k_v37.20.21.fasta, [20:10000000-10010000, 20:10040000-10050000, 20:10060000-10070000], 50, 300, 100) 1.872s passed
testRegionsHaveCorrectReadsAndSize[2](/home/runner/work/gatk/gatk/src/test/resources/large/CEUTrio.HiSeq.WGS.b37.NA12878.20.21.bam, /home/runner/work/gatk/gatk/src/test/resources/large/human_g1k_v37.20.21.fasta, [20:10000000-10020000, 20:10020050-10030000], 50, 300, 100) 1.869s passed
testRegionsHaveCorrectReadsAndSize[3](/home/runner/work/gatk/gatk/src/test/resources/large/CEUTrio.HiSeq.WGS.b37.NA12878.20.21.bam, /home/runner/work/gatk/gatk/src/test/resources/large/human_g1k_v37.20.21.fasta, [20:10000000-10010000, 21:10013000-10015000], 50, 300, 100) 0.900s passed

Standard error

20:13:24.329 INFO  NativeLibraryLoader - Loading libgkl_utils.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_utils.so
20:13:24.330 INFO  NativeLibraryLoader - Loading libgkl_smithwaterman.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_smithwaterman.so
20:13:24.331 INFO  SmithWatermanAligner - Using AVX accelerated SmithWaterman implementation
20:13:24.332 INFO  HaplotypeCallerEngine - Disabling physical phasing, which is supported only for reference-model confidence output
20:13:24.338 INFO  NativeLibraryLoader - Loading libgkl_pairhmm_omp.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_pairhmm_omp.so
20:13:24.349 INFO  IntelPairHmm - Flush-to-zero (FTZ) is enabled when running PairHMM
20:13:24.349 INFO  IntelPairHmm - Available threads: 4
20:13:24.349 INFO  IntelPairHmm - Requested threads: 4
20:13:24.349 INFO  PairHMM - Using the OpenMP multi-threaded AVX-accelerated native PairHMM implementation
20:13:31.872 INFO  SmithWatermanAligner - Using AVX accelerated SmithWaterman implementation
20:13:31.872 INFO  HaplotypeCallerEngine - Disabling physical phasing, which is supported only for reference-model confidence output
20:13:31.872 INFO  IntelPairHmm - Flush-to-zero (FTZ) is enabled when running PairHMM
20:13:31.872 INFO  IntelPairHmm - Available threads: 4
20:13:31.873 INFO  IntelPairHmm - Requested threads: 4
20:13:31.873 INFO  PairHMM - Using the OpenMP multi-threaded AVX-accelerated native PairHMM implementation
20:13:33.743 INFO  SmithWatermanAligner - Using AVX accelerated SmithWaterman implementation
20:13:33.743 INFO  HaplotypeCallerEngine - Disabling physical phasing, which is supported only for reference-model confidence output
20:13:33.743 INFO  IntelPairHmm - Flush-to-zero (FTZ) is enabled when running PairHMM
20:13:33.743 INFO  IntelPairHmm - Available threads: 4
20:13:33.743 INFO  IntelPairHmm - Requested threads: 4
20:13:33.743 INFO  PairHMM - Using the OpenMP multi-threaded AVX-accelerated native PairHMM implementation
20:13:35.612 INFO  SmithWatermanAligner - Using AVX accelerated SmithWaterman implementation
20:13:35.612 INFO  HaplotypeCallerEngine - Disabling physical phasing, which is supported only for reference-model confidence output
20:13:35.613 INFO  IntelPairHmm - Flush-to-zero (FTZ) is enabled when running PairHMM
20:13:35.613 INFO  IntelPairHmm - Available threads: 4
20:13:35.613 INFO  IntelPairHmm - Requested threads: 4
20:13:35.613 INFO  PairHMM - Using the OpenMP multi-threaded AVX-accelerated native PairHMM implementation