Class org.broadinstitute.hellbender.engine.AssemblyRegionIteratorUnitTest
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) |
7.894s |
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) |
1.874s |
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) |
1.866s |
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) |
0.927s |
passed |
Standard error
20:32:53.564 INFO NativeLibraryLoader - Loading libgkl_utils.so from jar:file:/home/runner/.gradle/caches/modules-2/files-2.1/com.intel.gkl/gkl/0.9.0/5ec646c7bf8c4f7681c2a59819384e5da469db31/gkl-0.9.0.jar!/com/intel/gkl/native/libgkl_utils.so
20:32:53.565 INFO NativeLibraryLoader - Loading libgkl_smithwaterman.so from jar:file:/home/runner/.gradle/caches/modules-2/files-2.1/com.intel.gkl/gkl/0.9.0/5ec646c7bf8c4f7681c2a59819384e5da469db31/gkl-0.9.0.jar!/com/intel/gkl/native/libgkl_smithwaterman.so
20:32:53.566 INFO SmithWatermanAligner - Using AVX accelerated SmithWaterman implementation
20:32:53.567 INFO HaplotypeCallerEngine - Disabling physical phasing, which is supported only for reference-model confidence output
20:32:53.574 INFO NativeLibraryLoader - Loading libgkl_pairhmm_omp.so from jar:file:/home/runner/.gradle/caches/modules-2/files-2.1/com.intel.gkl/gkl/0.9.0/5ec646c7bf8c4f7681c2a59819384e5da469db31/gkl-0.9.0.jar!/com/intel/gkl/native/libgkl_pairhmm_omp.so
20:32:53.586 INFO IntelPairHmm - Flush-to-zero (FTZ) is enabled when running PairHMM
20:32:53.586 INFO IntelPairHmm - Available threads: 4
20:32:53.586 INFO IntelPairHmm - Requested threads: 4
20:32:53.586 INFO PairHMM - Using the OpenMP multi-threaded AVX-accelerated native PairHMM implementation
20:33:01.439 INFO SmithWatermanAligner - Using AVX accelerated SmithWaterman implementation
20:33:01.439 INFO HaplotypeCallerEngine - Disabling physical phasing, which is supported only for reference-model confidence output
20:33:01.440 INFO IntelPairHmm - Flush-to-zero (FTZ) is enabled when running PairHMM
20:33:01.440 INFO IntelPairHmm - Available threads: 4
20:33:01.440 INFO IntelPairHmm - Requested threads: 4
20:33:01.440 INFO PairHMM - Using the OpenMP multi-threaded AVX-accelerated native PairHMM implementation
20:33:03.313 INFO SmithWatermanAligner - Using AVX accelerated SmithWaterman implementation
20:33:03.313 INFO HaplotypeCallerEngine - Disabling physical phasing, which is supported only for reference-model confidence output
20:33:03.314 INFO IntelPairHmm - Flush-to-zero (FTZ) is enabled when running PairHMM
20:33:03.314 INFO IntelPairHmm - Available threads: 4
20:33:03.314 INFO IntelPairHmm - Requested threads: 4
20:33:03.314 INFO PairHMM - Using the OpenMP multi-threaded AVX-accelerated native PairHMM implementation
20:33:05.180 INFO SmithWatermanAligner - Using AVX accelerated SmithWaterman implementation
20:33:05.181 INFO HaplotypeCallerEngine - Disabling physical phasing, which is supported only for reference-model confidence output
20:33:05.181 INFO IntelPairHmm - Flush-to-zero (FTZ) is enabled when running PairHMM
20:33:05.181 INFO IntelPairHmm - Available threads: 4
20:33:05.181 INFO IntelPairHmm - Requested threads: 4
20:33:05.181 INFO PairHMM - Using the OpenMP multi-threaded AVX-accelerated native PairHMM implementation