Class org.broadinstitute.hellbender.tools.copynumber.DenoiseReadCountsIntegrationTest

all > org.broadinstitute.hellbender.tools.copynumber > DenoiseReadCountsIntegrationTest
48

tests
0

failures
0

ignored
3.798s

duration
100%

successful

Tests

Test Duration Result
testDenoiseReadCounts[0](--I /gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/copynumber/denoise-read-counts-wgs-read-counts-HCC1143_BL-n1-chr20-downsampled-deduplicated.tsv --annotated-intervals /gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/copynumber/denoise-read-counts-wgs-annotated-intervals.tsv --count-panel-of-normals /gatkCloneMountPoint/src/test/resources/large/cnv_somatic_workflows_test_files/wgs-no-gc.pon.hdf5, false) 0.081s passed
testDenoiseReadCounts[10](--I /gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/copynumber/denoise-read-counts-wgs-read-counts-HCC1143_BL-n1-chr20-downsampled-deduplicated.tsv --annotated-intervals /gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/copynumber/denoise-read-counts-wgs-annotated-intervals.tsv --number-of-eigensamples 1, true) 0.077s passed
testDenoiseReadCounts[11](--I /gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/copynumber/denoise-read-counts-wgs-read-counts-HCC1143_BL-n1-chr20-downsampled-deduplicated.tsv --annotated-intervals /gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/copynumber/denoise-read-counts-wgs-annotated-intervals.tsv --number-of-eigensamples 10, true) 0.079s passed
testDenoiseReadCounts[12](--I /gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/copynumber/denoise-read-counts-wgs-read-counts-HCC1143_BL-n1-chr20-downsampled-deduplicated.tsv --count-panel-of-normals /gatkCloneMountPoint/src/test/resources/large/cnv_somatic_workflows_test_files/wgs-no-gc.pon.hdf5, false) 0.081s passed
testDenoiseReadCounts[13](--I /gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/copynumber/denoise-read-counts-wgs-read-counts-HCC1143_BL-n1-chr20-downsampled-deduplicated.tsv --count-panel-of-normals /gatkCloneMountPoint/src/test/resources/large/cnv_somatic_workflows_test_files/wgs-no-gc.pon.hdf5 --number-of-eigensamples 0, true) 0.077s passed
testDenoiseReadCounts[14](--I /gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/copynumber/denoise-read-counts-wgs-read-counts-HCC1143_BL-n1-chr20-downsampled-deduplicated.tsv --count-panel-of-normals /gatkCloneMountPoint/src/test/resources/large/cnv_somatic_workflows_test_files/wgs-no-gc.pon.hdf5 --number-of-eigensamples 1, false) 0.075s passed
testDenoiseReadCounts[15](--I /gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/copynumber/denoise-read-counts-wgs-read-counts-HCC1143_BL-n1-chr20-downsampled-deduplicated.tsv --count-panel-of-normals /gatkCloneMountPoint/src/test/resources/large/cnv_somatic_workflows_test_files/wgs-no-gc.pon.hdf5 --number-of-eigensamples 10, false) 0.077s passed
testDenoiseReadCounts[16](--I /gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/copynumber/denoise-read-counts-wgs-read-counts-HCC1143_BL-n1-chr20-downsampled-deduplicated.tsv --count-panel-of-normals /gatkCloneMountPoint/src/test/resources/large/cnv_somatic_workflows_test_files/wgs-do-gc.pon.hdf5, false) 0.074s passed
testDenoiseReadCounts[17](--I /gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/copynumber/denoise-read-counts-wgs-read-counts-HCC1143_BL-n1-chr20-downsampled-deduplicated.tsv --count-panel-of-normals /gatkCloneMountPoint/src/test/resources/large/cnv_somatic_workflows_test_files/wgs-do-gc.pon.hdf5 --number-of-eigensamples 0, true) 0.083s passed
testDenoiseReadCounts[18](--I /gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/copynumber/denoise-read-counts-wgs-read-counts-HCC1143_BL-n1-chr20-downsampled-deduplicated.tsv --count-panel-of-normals /gatkCloneMountPoint/src/test/resources/large/cnv_somatic_workflows_test_files/wgs-do-gc.pon.hdf5 --number-of-eigensamples 1, false) 0.089s passed
testDenoiseReadCounts[19](--I /gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/copynumber/denoise-read-counts-wgs-read-counts-HCC1143_BL-n1-chr20-downsampled-deduplicated.tsv --count-panel-of-normals /gatkCloneMountPoint/src/test/resources/large/cnv_somatic_workflows_test_files/wgs-do-gc.pon.hdf5 --number-of-eigensamples 10, false) 0.088s passed
testDenoiseReadCounts[1](--I /gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/copynumber/denoise-read-counts-wgs-read-counts-HCC1143_BL-n1-chr20-downsampled-deduplicated.tsv --annotated-intervals /gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/copynumber/denoise-read-counts-wgs-annotated-intervals.tsv --count-panel-of-normals /gatkCloneMountPoint/src/test/resources/large/cnv_somatic_workflows_test_files/wgs-no-gc.pon.hdf5 --number-of-eigensamples 0, true) 0.077s passed
testDenoiseReadCounts[20](--I /gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/copynumber/denoise-read-counts-wgs-read-counts-HCC1143_BL-n1-chr20-downsampled-deduplicated.tsv, true) 0.087s passed
testDenoiseReadCounts[21](--I /gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/copynumber/denoise-read-counts-wgs-read-counts-HCC1143_BL-n1-chr20-downsampled-deduplicated.tsv --number-of-eigensamples 0, true) 0.081s passed
testDenoiseReadCounts[22](--I /gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/copynumber/denoise-read-counts-wgs-read-counts-HCC1143_BL-n1-chr20-downsampled-deduplicated.tsv --number-of-eigensamples 1, true) 0.082s passed
testDenoiseReadCounts[23](--I /gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/copynumber/denoise-read-counts-wgs-read-counts-HCC1143_BL-n1-chr20-downsampled-deduplicated.tsv --number-of-eigensamples 10, true) 0.079s passed
testDenoiseReadCounts[24](--I /gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/copynumber/denoise-read-counts-wgs-read-counts-HCC1143_BL-n1-chr20-downsampled-deduplicated.hdf5 --annotated-intervals /gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/copynumber/denoise-read-counts-wgs-annotated-intervals.tsv --count-panel-of-normals /gatkCloneMountPoint/src/test/resources/large/cnv_somatic_workflows_test_files/wgs-no-gc.pon.hdf5, false) 0.082s passed
testDenoiseReadCounts[25](--I /gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/copynumber/denoise-read-counts-wgs-read-counts-HCC1143_BL-n1-chr20-downsampled-deduplicated.hdf5 --annotated-intervals /gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/copynumber/denoise-read-counts-wgs-annotated-intervals.tsv --count-panel-of-normals /gatkCloneMountPoint/src/test/resources/large/cnv_somatic_workflows_test_files/wgs-no-gc.pon.hdf5 --number-of-eigensamples 0, true) 0.078s passed
testDenoiseReadCounts[26](--I /gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/copynumber/denoise-read-counts-wgs-read-counts-HCC1143_BL-n1-chr20-downsampled-deduplicated.hdf5 --annotated-intervals /gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/copynumber/denoise-read-counts-wgs-annotated-intervals.tsv --count-panel-of-normals /gatkCloneMountPoint/src/test/resources/large/cnv_somatic_workflows_test_files/wgs-no-gc.pon.hdf5 --number-of-eigensamples 1, false) 0.083s passed
testDenoiseReadCounts[27](--I /gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/copynumber/denoise-read-counts-wgs-read-counts-HCC1143_BL-n1-chr20-downsampled-deduplicated.hdf5 --annotated-intervals /gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/copynumber/denoise-read-counts-wgs-annotated-intervals.tsv --count-panel-of-normals /gatkCloneMountPoint/src/test/resources/large/cnv_somatic_workflows_test_files/wgs-no-gc.pon.hdf5 --number-of-eigensamples 10, false) 0.075s passed
testDenoiseReadCounts[28](--I /gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/copynumber/denoise-read-counts-wgs-read-counts-HCC1143_BL-n1-chr20-downsampled-deduplicated.hdf5 --annotated-intervals /gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/copynumber/denoise-read-counts-wgs-annotated-intervals.tsv --count-panel-of-normals /gatkCloneMountPoint/src/test/resources/large/cnv_somatic_workflows_test_files/wgs-do-gc.pon.hdf5, false) 0.076s passed
testDenoiseReadCounts[29](--I /gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/copynumber/denoise-read-counts-wgs-read-counts-HCC1143_BL-n1-chr20-downsampled-deduplicated.hdf5 --annotated-intervals /gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/copynumber/denoise-read-counts-wgs-annotated-intervals.tsv --count-panel-of-normals /gatkCloneMountPoint/src/test/resources/large/cnv_somatic_workflows_test_files/wgs-do-gc.pon.hdf5 --number-of-eigensamples 0, true) 0.082s passed
testDenoiseReadCounts[2](--I /gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/copynumber/denoise-read-counts-wgs-read-counts-HCC1143_BL-n1-chr20-downsampled-deduplicated.tsv --annotated-intervals /gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/copynumber/denoise-read-counts-wgs-annotated-intervals.tsv --count-panel-of-normals /gatkCloneMountPoint/src/test/resources/large/cnv_somatic_workflows_test_files/wgs-no-gc.pon.hdf5 --number-of-eigensamples 1, false) 0.081s passed
testDenoiseReadCounts[30](--I /gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/copynumber/denoise-read-counts-wgs-read-counts-HCC1143_BL-n1-chr20-downsampled-deduplicated.hdf5 --annotated-intervals /gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/copynumber/denoise-read-counts-wgs-annotated-intervals.tsv --count-panel-of-normals /gatkCloneMountPoint/src/test/resources/large/cnv_somatic_workflows_test_files/wgs-do-gc.pon.hdf5 --number-of-eigensamples 1, false) 0.080s passed
testDenoiseReadCounts[31](--I /gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/copynumber/denoise-read-counts-wgs-read-counts-HCC1143_BL-n1-chr20-downsampled-deduplicated.hdf5 --annotated-intervals /gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/copynumber/denoise-read-counts-wgs-annotated-intervals.tsv --count-panel-of-normals /gatkCloneMountPoint/src/test/resources/large/cnv_somatic_workflows_test_files/wgs-do-gc.pon.hdf5 --number-of-eigensamples 10, false) 0.088s passed
testDenoiseReadCounts[32](--I /gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/copynumber/denoise-read-counts-wgs-read-counts-HCC1143_BL-n1-chr20-downsampled-deduplicated.hdf5 --annotated-intervals /gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/copynumber/denoise-read-counts-wgs-annotated-intervals.tsv, true) 0.074s passed
testDenoiseReadCounts[33](--I /gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/copynumber/denoise-read-counts-wgs-read-counts-HCC1143_BL-n1-chr20-downsampled-deduplicated.hdf5 --annotated-intervals /gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/copynumber/denoise-read-counts-wgs-annotated-intervals.tsv --number-of-eigensamples 0, true) 0.076s passed
testDenoiseReadCounts[34](--I /gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/copynumber/denoise-read-counts-wgs-read-counts-HCC1143_BL-n1-chr20-downsampled-deduplicated.hdf5 --annotated-intervals /gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/copynumber/denoise-read-counts-wgs-annotated-intervals.tsv --number-of-eigensamples 1, true) 0.080s passed
testDenoiseReadCounts[35](--I /gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/copynumber/denoise-read-counts-wgs-read-counts-HCC1143_BL-n1-chr20-downsampled-deduplicated.hdf5 --annotated-intervals /gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/copynumber/denoise-read-counts-wgs-annotated-intervals.tsv --number-of-eigensamples 10, true) 0.077s passed
testDenoiseReadCounts[36](--I /gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/copynumber/denoise-read-counts-wgs-read-counts-HCC1143_BL-n1-chr20-downsampled-deduplicated.hdf5 --count-panel-of-normals /gatkCloneMountPoint/src/test/resources/large/cnv_somatic_workflows_test_files/wgs-no-gc.pon.hdf5, false) 0.077s passed
testDenoiseReadCounts[37](--I /gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/copynumber/denoise-read-counts-wgs-read-counts-HCC1143_BL-n1-chr20-downsampled-deduplicated.hdf5 --count-panel-of-normals /gatkCloneMountPoint/src/test/resources/large/cnv_somatic_workflows_test_files/wgs-no-gc.pon.hdf5 --number-of-eigensamples 0, true) 0.075s passed
testDenoiseReadCounts[38](--I /gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/copynumber/denoise-read-counts-wgs-read-counts-HCC1143_BL-n1-chr20-downsampled-deduplicated.hdf5 --count-panel-of-normals /gatkCloneMountPoint/src/test/resources/large/cnv_somatic_workflows_test_files/wgs-no-gc.pon.hdf5 --number-of-eigensamples 1, false) 0.078s passed
testDenoiseReadCounts[39](--I /gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/copynumber/denoise-read-counts-wgs-read-counts-HCC1143_BL-n1-chr20-downsampled-deduplicated.hdf5 --count-panel-of-normals /gatkCloneMountPoint/src/test/resources/large/cnv_somatic_workflows_test_files/wgs-no-gc.pon.hdf5 --number-of-eigensamples 10, false) 0.080s passed
testDenoiseReadCounts[3](--I /gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/copynumber/denoise-read-counts-wgs-read-counts-HCC1143_BL-n1-chr20-downsampled-deduplicated.tsv --annotated-intervals /gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/copynumber/denoise-read-counts-wgs-annotated-intervals.tsv --count-panel-of-normals /gatkCloneMountPoint/src/test/resources/large/cnv_somatic_workflows_test_files/wgs-no-gc.pon.hdf5 --number-of-eigensamples 10, false) 0.079s passed
testDenoiseReadCounts[40](--I /gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/copynumber/denoise-read-counts-wgs-read-counts-HCC1143_BL-n1-chr20-downsampled-deduplicated.hdf5 --count-panel-of-normals /gatkCloneMountPoint/src/test/resources/large/cnv_somatic_workflows_test_files/wgs-do-gc.pon.hdf5, false) 0.075s passed
testDenoiseReadCounts[41](--I /gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/copynumber/denoise-read-counts-wgs-read-counts-HCC1143_BL-n1-chr20-downsampled-deduplicated.hdf5 --count-panel-of-normals /gatkCloneMountPoint/src/test/resources/large/cnv_somatic_workflows_test_files/wgs-do-gc.pon.hdf5 --number-of-eigensamples 0, true) 0.076s passed
testDenoiseReadCounts[42](--I /gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/copynumber/denoise-read-counts-wgs-read-counts-HCC1143_BL-n1-chr20-downsampled-deduplicated.hdf5 --count-panel-of-normals /gatkCloneMountPoint/src/test/resources/large/cnv_somatic_workflows_test_files/wgs-do-gc.pon.hdf5 --number-of-eigensamples 1, false) 0.075s passed
testDenoiseReadCounts[43](--I /gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/copynumber/denoise-read-counts-wgs-read-counts-HCC1143_BL-n1-chr20-downsampled-deduplicated.hdf5 --count-panel-of-normals /gatkCloneMountPoint/src/test/resources/large/cnv_somatic_workflows_test_files/wgs-do-gc.pon.hdf5 --number-of-eigensamples 10, false) 0.075s passed
testDenoiseReadCounts[44](--I /gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/copynumber/denoise-read-counts-wgs-read-counts-HCC1143_BL-n1-chr20-downsampled-deduplicated.hdf5, true) 0.076s passed
testDenoiseReadCounts[45](--I /gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/copynumber/denoise-read-counts-wgs-read-counts-HCC1143_BL-n1-chr20-downsampled-deduplicated.hdf5 --number-of-eigensamples 0, true) 0.077s passed
testDenoiseReadCounts[46](--I /gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/copynumber/denoise-read-counts-wgs-read-counts-HCC1143_BL-n1-chr20-downsampled-deduplicated.hdf5 --number-of-eigensamples 1, true) 0.077s passed
testDenoiseReadCounts[47](--I /gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/copynumber/denoise-read-counts-wgs-read-counts-HCC1143_BL-n1-chr20-downsampled-deduplicated.hdf5 --number-of-eigensamples 10, true) 0.081s passed
testDenoiseReadCounts[4](--I /gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/copynumber/denoise-read-counts-wgs-read-counts-HCC1143_BL-n1-chr20-downsampled-deduplicated.tsv --annotated-intervals /gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/copynumber/denoise-read-counts-wgs-annotated-intervals.tsv --count-panel-of-normals /gatkCloneMountPoint/src/test/resources/large/cnv_somatic_workflows_test_files/wgs-do-gc.pon.hdf5, false) 0.083s passed
testDenoiseReadCounts[5](--I /gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/copynumber/denoise-read-counts-wgs-read-counts-HCC1143_BL-n1-chr20-downsampled-deduplicated.tsv --annotated-intervals /gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/copynumber/denoise-read-counts-wgs-annotated-intervals.tsv --count-panel-of-normals /gatkCloneMountPoint/src/test/resources/large/cnv_somatic_workflows_test_files/wgs-do-gc.pon.hdf5 --number-of-eigensamples 0, true) 0.075s passed
testDenoiseReadCounts[6](--I /gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/copynumber/denoise-read-counts-wgs-read-counts-HCC1143_BL-n1-chr20-downsampled-deduplicated.tsv --annotated-intervals /gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/copynumber/denoise-read-counts-wgs-annotated-intervals.tsv --count-panel-of-normals /gatkCloneMountPoint/src/test/resources/large/cnv_somatic_workflows_test_files/wgs-do-gc.pon.hdf5 --number-of-eigensamples 1, false) 0.081s passed
testDenoiseReadCounts[7](--I /gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/copynumber/denoise-read-counts-wgs-read-counts-HCC1143_BL-n1-chr20-downsampled-deduplicated.tsv --annotated-intervals /gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/copynumber/denoise-read-counts-wgs-annotated-intervals.tsv --count-panel-of-normals /gatkCloneMountPoint/src/test/resources/large/cnv_somatic_workflows_test_files/wgs-do-gc.pon.hdf5 --number-of-eigensamples 10, false) 0.082s passed
testDenoiseReadCounts[8](--I /gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/copynumber/denoise-read-counts-wgs-read-counts-HCC1143_BL-n1-chr20-downsampled-deduplicated.tsv --annotated-intervals /gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/copynumber/denoise-read-counts-wgs-annotated-intervals.tsv, true) 0.077s passed
testDenoiseReadCounts[9](--I /gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/copynumber/denoise-read-counts-wgs-read-counts-HCC1143_BL-n1-chr20-downsampled-deduplicated.tsv --annotated-intervals /gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/tools/copynumber/denoise-read-counts-wgs-annotated-intervals.tsv --number-of-eigensamples 0, true) 0.080s passed

Standard error

[June 12, 2025 at 8:51:31 PM GMT] org.broadinstitute.hellbender.tools.copynumber.DenoiseReadCounts done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=524288000
[June 12, 2025 at 8:51:31 PM GMT] org.broadinstitute.hellbender.tools.copynumber.DenoiseReadCounts done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=524288000
[June 12, 2025 at 8:51:31 PM GMT] org.broadinstitute.hellbender.tools.copynumber.DenoiseReadCounts done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=524288000
[June 12, 2025 at 8:51:31 PM GMT] org.broadinstitute.hellbender.tools.copynumber.DenoiseReadCounts done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=524288000
[June 12, 2025 at 8:51:31 PM GMT] org.broadinstitute.hellbender.tools.copynumber.DenoiseReadCounts done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=524288000
[June 12, 2025 at 8:51:31 PM GMT] org.broadinstitute.hellbender.tools.copynumber.DenoiseReadCounts done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=524288000
[June 12, 2025 at 8:51:31 PM GMT] org.broadinstitute.hellbender.tools.copynumber.DenoiseReadCounts done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=524288000
[June 12, 2025 at 8:51:31 PM GMT] org.broadinstitute.hellbender.tools.copynumber.DenoiseReadCounts done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=524288000
[June 12, 2025 at 8:51:32 PM GMT] org.broadinstitute.hellbender.tools.copynumber.DenoiseReadCounts done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=524288000
[June 12, 2025 at 8:51:32 PM GMT] org.broadinstitute.hellbender.tools.copynumber.DenoiseReadCounts done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=524288000
[June 12, 2025 at 8:51:32 PM GMT] org.broadinstitute.hellbender.tools.copynumber.DenoiseReadCounts done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=524288000
[June 12, 2025 at 8:51:32 PM GMT] org.broadinstitute.hellbender.tools.copynumber.DenoiseReadCounts done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=524288000
[June 12, 2025 at 8:51:32 PM GMT] org.broadinstitute.hellbender.tools.copynumber.DenoiseReadCounts done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=524288000
[June 12, 2025 at 8:51:32 PM GMT] org.broadinstitute.hellbender.tools.copynumber.DenoiseReadCounts done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=524288000
[June 12, 2025 at 8:51:32 PM GMT] org.broadinstitute.hellbender.tools.copynumber.DenoiseReadCounts done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=524288000
[June 12, 2025 at 8:51:32 PM GMT] org.broadinstitute.hellbender.tools.copynumber.DenoiseReadCounts done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=524288000
[June 12, 2025 at 8:51:32 PM GMT] org.broadinstitute.hellbender.tools.copynumber.DenoiseReadCounts done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=524288000
[June 12, 2025 at 8:51:32 PM GMT] org.broadinstitute.hellbender.tools.copynumber.DenoiseReadCounts done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1048576000
[June 12, 2025 at 8:51:32 PM GMT] org.broadinstitute.hellbender.tools.copynumber.DenoiseReadCounts done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1048576000
[June 12, 2025 at 8:51:32 PM GMT] org.broadinstitute.hellbender.tools.copynumber.DenoiseReadCounts done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1048576000
[June 12, 2025 at 8:51:33 PM GMT] org.broadinstitute.hellbender.tools.copynumber.DenoiseReadCounts done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1048576000
[June 12, 2025 at 8:51:33 PM GMT] org.broadinstitute.hellbender.tools.copynumber.DenoiseReadCounts done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1048576000
[June 12, 2025 at 8:51:33 PM GMT] org.broadinstitute.hellbender.tools.copynumber.DenoiseReadCounts done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1048576000
[June 12, 2025 at 8:51:33 PM GMT] org.broadinstitute.hellbender.tools.copynumber.DenoiseReadCounts done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1048576000
[June 12, 2025 at 8:51:33 PM GMT] org.broadinstitute.hellbender.tools.copynumber.DenoiseReadCounts done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1048576000
[June 12, 2025 at 8:51:33 PM GMT] org.broadinstitute.hellbender.tools.copynumber.DenoiseReadCounts done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1048576000
[June 12, 2025 at 8:51:33 PM GMT] org.broadinstitute.hellbender.tools.copynumber.DenoiseReadCounts done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1048576000
[June 12, 2025 at 8:51:33 PM GMT] org.broadinstitute.hellbender.tools.copynumber.DenoiseReadCounts done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1048576000
[June 12, 2025 at 8:51:33 PM GMT] org.broadinstitute.hellbender.tools.copynumber.DenoiseReadCounts done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1048576000
[June 12, 2025 at 8:51:33 PM GMT] org.broadinstitute.hellbender.tools.copynumber.DenoiseReadCounts done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1048576000
[June 12, 2025 at 8:51:33 PM GMT] org.broadinstitute.hellbender.tools.copynumber.DenoiseReadCounts done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1048576000
[June 12, 2025 at 8:51:33 PM GMT] org.broadinstitute.hellbender.tools.copynumber.DenoiseReadCounts done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1048576000
[June 12, 2025 at 8:51:33 PM GMT] org.broadinstitute.hellbender.tools.copynumber.DenoiseReadCounts done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1048576000
[June 12, 2025 at 8:51:34 PM GMT] org.broadinstitute.hellbender.tools.copynumber.DenoiseReadCounts done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1048576000
[June 12, 2025 at 8:51:34 PM GMT] org.broadinstitute.hellbender.tools.copynumber.DenoiseReadCounts done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1048576000
[June 12, 2025 at 8:51:34 PM GMT] org.broadinstitute.hellbender.tools.copynumber.DenoiseReadCounts done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1048576000
[June 12, 2025 at 8:51:34 PM GMT] org.broadinstitute.hellbender.tools.copynumber.DenoiseReadCounts done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1048576000
[June 12, 2025 at 8:51:34 PM GMT] org.broadinstitute.hellbender.tools.copynumber.DenoiseReadCounts done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1048576000
[June 12, 2025 at 8:51:34 PM GMT] org.broadinstitute.hellbender.tools.copynumber.DenoiseReadCounts done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1048576000
[June 12, 2025 at 8:51:34 PM GMT] org.broadinstitute.hellbender.tools.copynumber.DenoiseReadCounts done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1048576000
[June 12, 2025 at 8:51:34 PM GMT] org.broadinstitute.hellbender.tools.copynumber.DenoiseReadCounts done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1048576000
[June 12, 2025 at 8:51:34 PM GMT] org.broadinstitute.hellbender.tools.copynumber.DenoiseReadCounts done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1048576000
[June 12, 2025 at 8:51:34 PM GMT] org.broadinstitute.hellbender.tools.copynumber.DenoiseReadCounts done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1048576000
[June 12, 2025 at 8:51:34 PM GMT] org.broadinstitute.hellbender.tools.copynumber.DenoiseReadCounts done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1048576000
[June 12, 2025 at 8:51:34 PM GMT] org.broadinstitute.hellbender.tools.copynumber.DenoiseReadCounts done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1048576000
[June 12, 2025 at 8:51:34 PM GMT] org.broadinstitute.hellbender.tools.copynumber.DenoiseReadCounts done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1048576000
[June 12, 2025 at 8:51:35 PM GMT] org.broadinstitute.hellbender.tools.copynumber.DenoiseReadCounts done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1048576000
[June 12, 2025 at 8:51:35 PM GMT] org.broadinstitute.hellbender.tools.copynumber.DenoiseReadCounts done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1048576000