Class org.broadinstitute.hellbender.engine.AssemblyRegionIteratorUnitTest

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

tests
0

failures
0

ignored
12.725s

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) 7.925s 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) 1.894s 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) 1.949s 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) 0.957s passed

Standard error

22:31:48.058 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
22:31:48.059 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
22:31:48.060 INFO  SmithWatermanAligner - Using AVX accelerated SmithWaterman implementation
22:31:48.061 INFO  HaplotypeCallerEngine - Disabling physical phasing, which is supported only for reference-model confidence output
22:31:48.070 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
22:31:48.085 INFO  IntelPairHmm - Flush-to-zero (FTZ) is enabled when running PairHMM
22:31:48.085 INFO  IntelPairHmm - Available threads: 4
22:31:48.086 INFO  IntelPairHmm - Requested threads: 4
22:31:48.086 INFO  PairHMM - Using the OpenMP multi-threaded AVX-accelerated native PairHMM implementation
22:31:55.960 INFO  SmithWatermanAligner - Using AVX accelerated SmithWaterman implementation
22:31:55.961 INFO  HaplotypeCallerEngine - Disabling physical phasing, which is supported only for reference-model confidence output
22:31:55.961 INFO  IntelPairHmm - Flush-to-zero (FTZ) is enabled when running PairHMM
22:31:55.961 INFO  IntelPairHmm - Available threads: 4
22:31:55.961 INFO  IntelPairHmm - Requested threads: 4
22:31:55.961 INFO  PairHMM - Using the OpenMP multi-threaded AVX-accelerated native PairHMM implementation
22:31:57.854 INFO  SmithWatermanAligner - Using AVX accelerated SmithWaterman implementation
22:31:57.854 INFO  HaplotypeCallerEngine - Disabling physical phasing, which is supported only for reference-model confidence output
22:31:57.855 INFO  IntelPairHmm - Flush-to-zero (FTZ) is enabled when running PairHMM
22:31:57.855 INFO  IntelPairHmm - Available threads: 4
22:31:57.855 INFO  IntelPairHmm - Requested threads: 4
22:31:57.855 INFO  PairHMM - Using the OpenMP multi-threaded AVX-accelerated native PairHMM implementation
22:31:59.803 INFO  SmithWatermanAligner - Using AVX accelerated SmithWaterman implementation
22:31:59.803 INFO  HaplotypeCallerEngine - Disabling physical phasing, which is supported only for reference-model confidence output
22:31:59.803 INFO  IntelPairHmm - Flush-to-zero (FTZ) is enabled when running PairHMM
22:31:59.803 INFO  IntelPairHmm - Available threads: 4
22:31:59.803 INFO  IntelPairHmm - Requested threads: 4
22:31:59.803 INFO  PairHMM - Using the OpenMP multi-threaded AVX-accelerated native PairHMM implementation