Class org.broadinstitute.hellbender.engine.AssemblyRegionIteratorUnitTest

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

tests
0

failures
0

ignored
12.883s

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) 8.066s 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) 1.935s 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) 1.937s 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) 0.945s passed

Standard error

14:50:50.243 INFO  NativeLibraryLoader - Loading libgkl_utils.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_utils.so
14:50:50.244 INFO  NativeLibraryLoader - Loading libgkl_smithwaterman.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_smithwaterman.so
14:50:50.245 INFO  SmithWatermanAligner - Using AVX accelerated SmithWaterman implementation
14:50:50.246 INFO  HaplotypeCallerEngine - Disabling physical phasing, which is supported only for reference-model confidence output
14:50:50.254 INFO  NativeLibraryLoader - Loading libgkl_pairhmm_omp.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_pairhmm_omp.so
14:50:50.269 INFO  IntelPairHmm - Flush-to-zero (FTZ) is enabled when running PairHMM
14:50:50.270 INFO  IntelPairHmm - Available threads: 4
14:50:50.270 INFO  IntelPairHmm - Requested threads: 4
14:50:50.270 INFO  PairHMM - Using the OpenMP multi-threaded AVX-accelerated native PairHMM implementation
14:50:58.285 INFO  SmithWatermanAligner - Using AVX accelerated SmithWaterman implementation
14:50:58.285 INFO  HaplotypeCallerEngine - Disabling physical phasing, which is supported only for reference-model confidence output
14:50:58.285 INFO  IntelPairHmm - Flush-to-zero (FTZ) is enabled when running PairHMM
14:50:58.285 INFO  IntelPairHmm - Available threads: 4
14:50:58.286 INFO  IntelPairHmm - Requested threads: 4
14:50:58.286 INFO  PairHMM - Using the OpenMP multi-threaded AVX-accelerated native PairHMM implementation
14:51:00.221 INFO  SmithWatermanAligner - Using AVX accelerated SmithWaterman implementation
14:51:00.221 INFO  HaplotypeCallerEngine - Disabling physical phasing, which is supported only for reference-model confidence output
14:51:00.221 INFO  IntelPairHmm - Flush-to-zero (FTZ) is enabled when running PairHMM
14:51:00.221 INFO  IntelPairHmm - Available threads: 4
14:51:00.222 INFO  IntelPairHmm - Requested threads: 4
14:51:00.222 INFO  PairHMM - Using the OpenMP multi-threaded AVX-accelerated native PairHMM implementation
14:51:02.158 INFO  SmithWatermanAligner - Using AVX accelerated SmithWaterman implementation
14:51:02.159 INFO  HaplotypeCallerEngine - Disabling physical phasing, which is supported only for reference-model confidence output
14:51:02.159 INFO  IntelPairHmm - Flush-to-zero (FTZ) is enabled when running PairHMM
14:51:02.159 INFO  IntelPairHmm - Available threads: 4
14:51:02.159 INFO  IntelPairHmm - Requested threads: 4
14:51:02.159 INFO  PairHMM - Using the OpenMP multi-threaded AVX-accelerated native PairHMM implementation