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

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

tests

failures

ignored

2.966s

duration

100%

successful

Tests
Standard error

Tests

Test	Duration	Result
testDenoiseReadCounts[0](--I /home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/copynumber/denoise-read-counts-wgs-read-counts-HCC1143_BL-n1-chr20-downsampled-deduplicated.tsv --annotated-intervals /home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/copynumber/denoise-read-counts-wgs-annotated-intervals.tsv --count-panel-of-normals /home/runner/work/gatk/gatk/src/test/resources/large/cnv_somatic_workflows_test_files/wgs-no-gc.pon.hdf5, false)	0.071s	passed
testDenoiseReadCounts[10](--I /home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/copynumber/denoise-read-counts-wgs-read-counts-HCC1143_BL-n1-chr20-downsampled-deduplicated.tsv --annotated-intervals /home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/copynumber/denoise-read-counts-wgs-annotated-intervals.tsv --number-of-eigensamples 1, true)	0.066s	passed
testDenoiseReadCounts[11](--I /home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/copynumber/denoise-read-counts-wgs-read-counts-HCC1143_BL-n1-chr20-downsampled-deduplicated.tsv --annotated-intervals /home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/copynumber/denoise-read-counts-wgs-annotated-intervals.tsv --number-of-eigensamples 10, true)	0.068s	passed
testDenoiseReadCounts[12](--I /home/runner/work/gatk/gatk/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 /home/runner/work/gatk/gatk/src/test/resources/large/cnv_somatic_workflows_test_files/wgs-no-gc.pon.hdf5, false)	0.065s	passed
testDenoiseReadCounts[13](--I /home/runner/work/gatk/gatk/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 /home/runner/work/gatk/gatk/src/test/resources/large/cnv_somatic_workflows_test_files/wgs-no-gc.pon.hdf5 --number-of-eigensamples 0, true)	0.061s	passed
testDenoiseReadCounts[14](--I /home/runner/work/gatk/gatk/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 /home/runner/work/gatk/gatk/src/test/resources/large/cnv_somatic_workflows_test_files/wgs-no-gc.pon.hdf5 --number-of-eigensamples 1, false)	0.061s	passed
testDenoiseReadCounts[15](--I /home/runner/work/gatk/gatk/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 /home/runner/work/gatk/gatk/src/test/resources/large/cnv_somatic_workflows_test_files/wgs-no-gc.pon.hdf5 --number-of-eigensamples 10, false)	0.070s	passed
testDenoiseReadCounts[16](--I /home/runner/work/gatk/gatk/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 /home/runner/work/gatk/gatk/src/test/resources/large/cnv_somatic_workflows_test_files/wgs-do-gc.pon.hdf5, false)	0.058s	passed
testDenoiseReadCounts[17](--I /home/runner/work/gatk/gatk/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 /home/runner/work/gatk/gatk/src/test/resources/large/cnv_somatic_workflows_test_files/wgs-do-gc.pon.hdf5 --number-of-eigensamples 0, true)	0.059s	passed
testDenoiseReadCounts[18](--I /home/runner/work/gatk/gatk/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 /home/runner/work/gatk/gatk/src/test/resources/large/cnv_somatic_workflows_test_files/wgs-do-gc.pon.hdf5 --number-of-eigensamples 1, false)	0.062s	passed
testDenoiseReadCounts[19](--I /home/runner/work/gatk/gatk/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 /home/runner/work/gatk/gatk/src/test/resources/large/cnv_somatic_workflows_test_files/wgs-do-gc.pon.hdf5 --number-of-eigensamples 10, false)	0.065s	passed
testDenoiseReadCounts[1](--I /home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/copynumber/denoise-read-counts-wgs-read-counts-HCC1143_BL-n1-chr20-downsampled-deduplicated.tsv --annotated-intervals /home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/copynumber/denoise-read-counts-wgs-annotated-intervals.tsv --count-panel-of-normals /home/runner/work/gatk/gatk/src/test/resources/large/cnv_somatic_workflows_test_files/wgs-no-gc.pon.hdf5 --number-of-eigensamples 0, true)	0.071s	passed
testDenoiseReadCounts[20](--I /home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/copynumber/denoise-read-counts-wgs-read-counts-HCC1143_BL-n1-chr20-downsampled-deduplicated.tsv, true)	0.059s	passed
testDenoiseReadCounts[21](--I /home/runner/work/gatk/gatk/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)	0.057s	passed
testDenoiseReadCounts[22](--I /home/runner/work/gatk/gatk/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)	0.054s	passed
testDenoiseReadCounts[23](--I /home/runner/work/gatk/gatk/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)	0.059s	passed
testDenoiseReadCounts[24](--I /home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/copynumber/denoise-read-counts-wgs-read-counts-HCC1143_BL-n1-chr20-downsampled-deduplicated.hdf5 --annotated-intervals /home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/copynumber/denoise-read-counts-wgs-annotated-intervals.tsv --count-panel-of-normals /home/runner/work/gatk/gatk/src/test/resources/large/cnv_somatic_workflows_test_files/wgs-no-gc.pon.hdf5, false)	0.057s	passed
testDenoiseReadCounts[25](--I /home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/copynumber/denoise-read-counts-wgs-read-counts-HCC1143_BL-n1-chr20-downsampled-deduplicated.hdf5 --annotated-intervals /home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/copynumber/denoise-read-counts-wgs-annotated-intervals.tsv --count-panel-of-normals /home/runner/work/gatk/gatk/src/test/resources/large/cnv_somatic_workflows_test_files/wgs-no-gc.pon.hdf5 --number-of-eigensamples 0, true)	0.056s	passed
testDenoiseReadCounts[26](--I /home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/copynumber/denoise-read-counts-wgs-read-counts-HCC1143_BL-n1-chr20-downsampled-deduplicated.hdf5 --annotated-intervals /home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/copynumber/denoise-read-counts-wgs-annotated-intervals.tsv --count-panel-of-normals /home/runner/work/gatk/gatk/src/test/resources/large/cnv_somatic_workflows_test_files/wgs-no-gc.pon.hdf5 --number-of-eigensamples 1, false)	0.058s	passed
testDenoiseReadCounts[27](--I /home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/copynumber/denoise-read-counts-wgs-read-counts-HCC1143_BL-n1-chr20-downsampled-deduplicated.hdf5 --annotated-intervals /home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/copynumber/denoise-read-counts-wgs-annotated-intervals.tsv --count-panel-of-normals /home/runner/work/gatk/gatk/src/test/resources/large/cnv_somatic_workflows_test_files/wgs-no-gc.pon.hdf5 --number-of-eigensamples 10, false)	0.058s	passed
testDenoiseReadCounts[28](--I /home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/copynumber/denoise-read-counts-wgs-read-counts-HCC1143_BL-n1-chr20-downsampled-deduplicated.hdf5 --annotated-intervals /home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/copynumber/denoise-read-counts-wgs-annotated-intervals.tsv --count-panel-of-normals /home/runner/work/gatk/gatk/src/test/resources/large/cnv_somatic_workflows_test_files/wgs-do-gc.pon.hdf5, false)	0.061s	passed
testDenoiseReadCounts[29](--I /home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/copynumber/denoise-read-counts-wgs-read-counts-HCC1143_BL-n1-chr20-downsampled-deduplicated.hdf5 --annotated-intervals /home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/copynumber/denoise-read-counts-wgs-annotated-intervals.tsv --count-panel-of-normals /home/runner/work/gatk/gatk/src/test/resources/large/cnv_somatic_workflows_test_files/wgs-do-gc.pon.hdf5 --number-of-eigensamples 0, true)	0.059s	passed
testDenoiseReadCounts[2](--I /home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/copynumber/denoise-read-counts-wgs-read-counts-HCC1143_BL-n1-chr20-downsampled-deduplicated.tsv --annotated-intervals /home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/copynumber/denoise-read-counts-wgs-annotated-intervals.tsv --count-panel-of-normals /home/runner/work/gatk/gatk/src/test/resources/large/cnv_somatic_workflows_test_files/wgs-no-gc.pon.hdf5 --number-of-eigensamples 1, false)	0.070s	passed
testDenoiseReadCounts[30](--I /home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/copynumber/denoise-read-counts-wgs-read-counts-HCC1143_BL-n1-chr20-downsampled-deduplicated.hdf5 --annotated-intervals /home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/copynumber/denoise-read-counts-wgs-annotated-intervals.tsv --count-panel-of-normals /home/runner/work/gatk/gatk/src/test/resources/large/cnv_somatic_workflows_test_files/wgs-do-gc.pon.hdf5 --number-of-eigensamples 1, false)	0.057s	passed
testDenoiseReadCounts[31](--I /home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/copynumber/denoise-read-counts-wgs-read-counts-HCC1143_BL-n1-chr20-downsampled-deduplicated.hdf5 --annotated-intervals /home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/copynumber/denoise-read-counts-wgs-annotated-intervals.tsv --count-panel-of-normals /home/runner/work/gatk/gatk/src/test/resources/large/cnv_somatic_workflows_test_files/wgs-do-gc.pon.hdf5 --number-of-eigensamples 10, false)	0.064s	passed
testDenoiseReadCounts[32](--I /home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/copynumber/denoise-read-counts-wgs-read-counts-HCC1143_BL-n1-chr20-downsampled-deduplicated.hdf5 --annotated-intervals /home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/copynumber/denoise-read-counts-wgs-annotated-intervals.tsv, true)	0.074s	passed
testDenoiseReadCounts[33](--I /home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/copynumber/denoise-read-counts-wgs-read-counts-HCC1143_BL-n1-chr20-downsampled-deduplicated.hdf5 --annotated-intervals /home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/copynumber/denoise-read-counts-wgs-annotated-intervals.tsv --number-of-eigensamples 0, true)	0.060s	passed
testDenoiseReadCounts[34](--I /home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/copynumber/denoise-read-counts-wgs-read-counts-HCC1143_BL-n1-chr20-downsampled-deduplicated.hdf5 --annotated-intervals /home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/copynumber/denoise-read-counts-wgs-annotated-intervals.tsv --number-of-eigensamples 1, true)	0.056s	passed
testDenoiseReadCounts[35](--I /home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/copynumber/denoise-read-counts-wgs-read-counts-HCC1143_BL-n1-chr20-downsampled-deduplicated.hdf5 --annotated-intervals /home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/copynumber/denoise-read-counts-wgs-annotated-intervals.tsv --number-of-eigensamples 10, true)	0.056s	passed
testDenoiseReadCounts[36](--I /home/runner/work/gatk/gatk/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 /home/runner/work/gatk/gatk/src/test/resources/large/cnv_somatic_workflows_test_files/wgs-no-gc.pon.hdf5, false)	0.058s	passed
testDenoiseReadCounts[37](--I /home/runner/work/gatk/gatk/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 /home/runner/work/gatk/gatk/src/test/resources/large/cnv_somatic_workflows_test_files/wgs-no-gc.pon.hdf5 --number-of-eigensamples 0, true)	0.059s	passed
testDenoiseReadCounts[38](--I /home/runner/work/gatk/gatk/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 /home/runner/work/gatk/gatk/src/test/resources/large/cnv_somatic_workflows_test_files/wgs-no-gc.pon.hdf5 --number-of-eigensamples 1, false)	0.056s	passed
testDenoiseReadCounts[39](--I /home/runner/work/gatk/gatk/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 /home/runner/work/gatk/gatk/src/test/resources/large/cnv_somatic_workflows_test_files/wgs-no-gc.pon.hdf5 --number-of-eigensamples 10, false)	0.055s	passed
testDenoiseReadCounts[3](--I /home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/copynumber/denoise-read-counts-wgs-read-counts-HCC1143_BL-n1-chr20-downsampled-deduplicated.tsv --annotated-intervals /home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/copynumber/denoise-read-counts-wgs-annotated-intervals.tsv --count-panel-of-normals /home/runner/work/gatk/gatk/src/test/resources/large/cnv_somatic_workflows_test_files/wgs-no-gc.pon.hdf5 --number-of-eigensamples 10, false)	0.069s	passed
testDenoiseReadCounts[40](--I /home/runner/work/gatk/gatk/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 /home/runner/work/gatk/gatk/src/test/resources/large/cnv_somatic_workflows_test_files/wgs-do-gc.pon.hdf5, false)	0.056s	passed
testDenoiseReadCounts[41](--I /home/runner/work/gatk/gatk/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 /home/runner/work/gatk/gatk/src/test/resources/large/cnv_somatic_workflows_test_files/wgs-do-gc.pon.hdf5 --number-of-eigensamples 0, true)	0.062s	passed
testDenoiseReadCounts[42](--I /home/runner/work/gatk/gatk/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 /home/runner/work/gatk/gatk/src/test/resources/large/cnv_somatic_workflows_test_files/wgs-do-gc.pon.hdf5 --number-of-eigensamples 1, false)	0.061s	passed
testDenoiseReadCounts[43](--I /home/runner/work/gatk/gatk/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 /home/runner/work/gatk/gatk/src/test/resources/large/cnv_somatic_workflows_test_files/wgs-do-gc.pon.hdf5 --number-of-eigensamples 10, false)	0.061s	passed
testDenoiseReadCounts[44](--I /home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/copynumber/denoise-read-counts-wgs-read-counts-HCC1143_BL-n1-chr20-downsampled-deduplicated.hdf5, true)	0.059s	passed
testDenoiseReadCounts[45](--I /home/runner/work/gatk/gatk/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)	0.061s	passed
testDenoiseReadCounts[46](--I /home/runner/work/gatk/gatk/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)	0.059s	passed
testDenoiseReadCounts[47](--I /home/runner/work/gatk/gatk/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)	0.057s	passed
testDenoiseReadCounts[4](--I /home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/copynumber/denoise-read-counts-wgs-read-counts-HCC1143_BL-n1-chr20-downsampled-deduplicated.tsv --annotated-intervals /home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/copynumber/denoise-read-counts-wgs-annotated-intervals.tsv --count-panel-of-normals /home/runner/work/gatk/gatk/src/test/resources/large/cnv_somatic_workflows_test_files/wgs-do-gc.pon.hdf5, false)	0.069s	passed
testDenoiseReadCounts[5](--I /home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/copynumber/denoise-read-counts-wgs-read-counts-HCC1143_BL-n1-chr20-downsampled-deduplicated.tsv --annotated-intervals /home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/copynumber/denoise-read-counts-wgs-annotated-intervals.tsv --count-panel-of-normals /home/runner/work/gatk/gatk/src/test/resources/large/cnv_somatic_workflows_test_files/wgs-do-gc.pon.hdf5 --number-of-eigensamples 0, true)	0.066s	passed
testDenoiseReadCounts[6](--I /home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/copynumber/denoise-read-counts-wgs-read-counts-HCC1143_BL-n1-chr20-downsampled-deduplicated.tsv --annotated-intervals /home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/copynumber/denoise-read-counts-wgs-annotated-intervals.tsv --count-panel-of-normals /home/runner/work/gatk/gatk/src/test/resources/large/cnv_somatic_workflows_test_files/wgs-do-gc.pon.hdf5 --number-of-eigensamples 1, false)	0.066s	passed
testDenoiseReadCounts[7](--I /home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/copynumber/denoise-read-counts-wgs-read-counts-HCC1143_BL-n1-chr20-downsampled-deduplicated.tsv --annotated-intervals /home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/copynumber/denoise-read-counts-wgs-annotated-intervals.tsv --count-panel-of-normals /home/runner/work/gatk/gatk/src/test/resources/large/cnv_somatic_workflows_test_files/wgs-do-gc.pon.hdf5 --number-of-eigensamples 10, false)	0.067s	passed
testDenoiseReadCounts[8](--I /home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/copynumber/denoise-read-counts-wgs-read-counts-HCC1143_BL-n1-chr20-downsampled-deduplicated.tsv --annotated-intervals /home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/copynumber/denoise-read-counts-wgs-annotated-intervals.tsv, true)	0.067s	passed
testDenoiseReadCounts[9](--I /home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/copynumber/denoise-read-counts-wgs-read-counts-HCC1143_BL-n1-chr20-downsampled-deduplicated.tsv --annotated-intervals /home/runner/work/gatk/gatk/src/test/resources/org/broadinstitute/hellbender/tools/copynumber/denoise-read-counts-wgs-annotated-intervals.tsv --number-of-eigensamples 0, true)	0.066s	passed

Standard error

[March 28, 2025 at 10:36:26 PM UTC] org.broadinstitute.hellbender.tools.copynumber.DenoiseReadCounts done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=524288000
[March 28, 2025 at 10:36:26 PM UTC] org.broadinstitute.hellbender.tools.copynumber.DenoiseReadCounts done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=524288000
[March 28, 2025 at 10:36:27 PM UTC] org.broadinstitute.hellbender.tools.copynumber.DenoiseReadCounts done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=524288000
[March 28, 2025 at 10:36:27 PM UTC] org.broadinstitute.hellbender.tools.copynumber.DenoiseReadCounts done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=524288000
[March 28, 2025 at 10:36:27 PM UTC] org.broadinstitute.hellbender.tools.copynumber.DenoiseReadCounts done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=524288000
[March 28, 2025 at 10:36:27 PM UTC] org.broadinstitute.hellbender.tools.copynumber.DenoiseReadCounts done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=524288000
[March 28, 2025 at 10:36:27 PM UTC] org.broadinstitute.hellbender.tools.copynumber.DenoiseReadCounts done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=524288000
[March 28, 2025 at 10:36:27 PM UTC] org.broadinstitute.hellbender.tools.copynumber.DenoiseReadCounts done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=524288000
[March 28, 2025 at 10:36:27 PM UTC] org.broadinstitute.hellbender.tools.copynumber.DenoiseReadCounts done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=524288000
[March 28, 2025 at 10:36:27 PM UTC] org.broadinstitute.hellbender.tools.copynumber.DenoiseReadCounts done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=524288000
[March 28, 2025 at 10:36:27 PM UTC] org.broadinstitute.hellbender.tools.copynumber.DenoiseReadCounts done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=524288000
[March 28, 2025 at 10:36:27 PM UTC] org.broadinstitute.hellbender.tools.copynumber.DenoiseReadCounts done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=524288000
[March 28, 2025 at 10:36:27 PM UTC] org.broadinstitute.hellbender.tools.copynumber.DenoiseReadCounts done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=524288000
[March 28, 2025 at 10:36:27 PM UTC] org.broadinstitute.hellbender.tools.copynumber.DenoiseReadCounts done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=524288000
[March 28, 2025 at 10:36:27 PM UTC] org.broadinstitute.hellbender.tools.copynumber.DenoiseReadCounts done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=524288000
[March 28, 2025 at 10:36:27 PM UTC] org.broadinstitute.hellbender.tools.copynumber.DenoiseReadCounts done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=524288000
[March 28, 2025 at 10:36:27 PM UTC] org.broadinstitute.hellbender.tools.copynumber.DenoiseReadCounts done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=524288000
[March 28, 2025 at 10:36:27 PM UTC] org.broadinstitute.hellbender.tools.copynumber.DenoiseReadCounts done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=524288000
[March 28, 2025 at 10:36:28 PM UTC] org.broadinstitute.hellbender.tools.copynumber.DenoiseReadCounts done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=524288000
[March 28, 2025 at 10:36:28 PM UTC] org.broadinstitute.hellbender.tools.copynumber.DenoiseReadCounts done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=524288000
[March 28, 2025 at 10:36:28 PM UTC] org.broadinstitute.hellbender.tools.copynumber.DenoiseReadCounts done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=524288000
[March 28, 2025 at 10:36:28 PM UTC] org.broadinstitute.hellbender.tools.copynumber.DenoiseReadCounts done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=524288000
[March 28, 2025 at 10:36:28 PM UTC] org.broadinstitute.hellbender.tools.copynumber.DenoiseReadCounts done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=524288000
[March 28, 2025 at 10:36:28 PM UTC] org.broadinstitute.hellbender.tools.copynumber.DenoiseReadCounts done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=524288000
[March 28, 2025 at 10:36:28 PM UTC] org.broadinstitute.hellbender.tools.copynumber.DenoiseReadCounts done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=524288000
[March 28, 2025 at 10:36:28 PM UTC] org.broadinstitute.hellbender.tools.copynumber.DenoiseReadCounts done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=524288000
[March 28, 2025 at 10:36:28 PM UTC] org.broadinstitute.hellbender.tools.copynumber.DenoiseReadCounts done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=524288000
[March 28, 2025 at 10:36:28 PM UTC] org.broadinstitute.hellbender.tools.copynumber.DenoiseReadCounts done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=524288000
[March 28, 2025 at 10:36:28 PM UTC] org.broadinstitute.hellbender.tools.copynumber.DenoiseReadCounts done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=524288000
[March 28, 2025 at 10:36:28 PM UTC] org.broadinstitute.hellbender.tools.copynumber.DenoiseReadCounts done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=524288000
[March 28, 2025 at 10:36:28 PM UTC] org.broadinstitute.hellbender.tools.copynumber.DenoiseReadCounts done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=524288000
[March 28, 2025 at 10:36:28 PM UTC] org.broadinstitute.hellbender.tools.copynumber.DenoiseReadCounts done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=524288000
[March 28, 2025 at 10:36:28 PM UTC] org.broadinstitute.hellbender.tools.copynumber.DenoiseReadCounts done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=524288000
[March 28, 2025 at 10:36:28 PM UTC] org.broadinstitute.hellbender.tools.copynumber.DenoiseReadCounts done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=524288000
[March 28, 2025 at 10:36:29 PM UTC] org.broadinstitute.hellbender.tools.copynumber.DenoiseReadCounts done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=524288000
[March 28, 2025 at 10:36:29 PM UTC] org.broadinstitute.hellbender.tools.copynumber.DenoiseReadCounts done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=524288000
[March 28, 2025 at 10:36:29 PM UTC] org.broadinstitute.hellbender.tools.copynumber.DenoiseReadCounts done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=524288000
[March 28, 2025 at 10:36:29 PM UTC] org.broadinstitute.hellbender.tools.copynumber.DenoiseReadCounts done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=524288000
[March 28, 2025 at 10:36:29 PM UTC] org.broadinstitute.hellbender.tools.copynumber.DenoiseReadCounts done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=524288000
[March 28, 2025 at 10:36:29 PM UTC] org.broadinstitute.hellbender.tools.copynumber.DenoiseReadCounts done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=524288000
[March 28, 2025 at 10:36:29 PM UTC] org.broadinstitute.hellbender.tools.copynumber.DenoiseReadCounts done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=524288000
[March 28, 2025 at 10:36:29 PM UTC] org.broadinstitute.hellbender.tools.copynumber.DenoiseReadCounts done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=524288000
[March 28, 2025 at 10:36:29 PM UTC] org.broadinstitute.hellbender.tools.copynumber.DenoiseReadCounts done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=524288000
[March 28, 2025 at 10:36:29 PM UTC] org.broadinstitute.hellbender.tools.copynumber.DenoiseReadCounts done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=524288000
[March 28, 2025 at 10:36:29 PM UTC] org.broadinstitute.hellbender.tools.copynumber.DenoiseReadCounts done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=524288000
[March 28, 2025 at 10:36:29 PM UTC] org.broadinstitute.hellbender.tools.copynumber.DenoiseReadCounts done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=524288000
[March 28, 2025 at 10:36:29 PM UTC] org.broadinstitute.hellbender.tools.copynumber.DenoiseReadCounts done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=524288000
[March 28, 2025 at 10:36:29 PM UTC] org.broadinstitute.hellbender.tools.copynumber.DenoiseReadCounts done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=524288000