Class org.broadinstitute.hellbender.tools.spark.validation.CompareDuplicatesSparkIntegrationTest

all > org.broadinstitute.hellbender.tools.spark.validation > CompareDuplicatesSparkIntegrationTest

tests

failures

ignored

3.485s

duration

100%

successful

Tests
Standard output
Standard error

Tests

Test	Duration	Result
differentBamTest[0](src/test/resources/org/broadinstitute/hellbender/tools/validation/tmp.gatk4.CEUTrio.HiSeq.WGS.b37.ch20.1m-1m1k.NA12878.bam, src/test/resources/org/broadinstitute/hellbender/tools/validation/single.read.bam)	0.272s	passed
differentBamTest[1](src/test/resources/org/broadinstitute/hellbender/tools/validation/tmp.gatk4.CEUTrio.HiSeq.WGS.b37.ch20.1m-1m1k.NA12878.bam, src/test/resources/org/broadinstitute/hellbender/tools/validation/CEUTrio.HiSeq.WGS.b37.ch20.1m-1m1k.NA12878.bam)	0.594s	passed
differentBamTest[2](src/test/resources/org/broadinstitute/hellbender/tools/validation/tmp.gatk4.CEUTrio.HiSeq.WGS.b37.ch20.1m-1m1k.NA12878.bam, src/test/resources/org/broadinstitute/hellbender/tools/validation/clean.CEUTrio.HiSeq.WGS.b37.ch20.1m-1m1k.NA12878.bam)	0.551s	passed
identicalBamTest[0](src/test/resources/org/broadinstitute/hellbender/tools/validation/tmp.legacy.CEUTrio.HiSeq.WGS.b37.ch20.1m-1m1k.NA12878.bam, src/test/resources/org/broadinstitute/hellbender/tools/validation/tmp.legacy.CEUTrio.HiSeq.WGS.b37.ch20.1m-1m1k.NA12878.bam)	0.563s	passed
identicalBamTest[1](src/test/resources/org/broadinstitute/hellbender/tools/validation/tmp.legacy.CEUTrio.HiSeq.WGS.b37.ch20.1m-1m1k.NA12878.bam, src/test/resources/org/broadinstitute/hellbender/tools/validation/tmp.gatk4.CEUTrio.HiSeq.WGS.b37.ch20.1m-1m1k.NA12878.bam)	0.532s	passed
testOutputFile	0.973s	passed

Standard output

processing bams with 1510 mapped reads
BAMs have different number of total duplicates: 96,128
first and second: 96,128
##############################
DIFFERENT_REPRESENTATIVE_READ: 80
READ_MISMATCH: 0
SIZE_UNEQUAL: 0
DIFF_NUM_DUPES: 34
EQUAL: 1137
processing bams with 1510 mapped reads
BAMs have different number of total duplicates: 96,0
first and second: 96,0
##############################
DIFFERENT_REPRESENTATIVE_READ: 0
READ_MISMATCH: 0
SIZE_UNEQUAL: 0
DIFF_NUM_DUPES: 87
EQUAL: 1164
processing bams with 1510 mapped reads
first and second: 96,96
##############################
DIFFERENT_REPRESENTATIVE_READ: 0
READ_MISMATCH: 0
SIZE_UNEQUAL: 0
DIFF_NUM_DUPES: 0
EQUAL: 1251
processing bams with 1510 mapped reads
first and second: 96,96
##############################
DIFFERENT_REPRESENTATIVE_READ: 0
READ_MISMATCH: 0
SIZE_UNEQUAL: 0
DIFF_NUM_DUPES: 0
EQUAL: 1251
processing bams with 1510 mapped reads
BAMs have different number of total duplicates: 96,0
first and second: 96,0
##############################
DIFFERENT_REPRESENTATIVE_READ: 0
READ_MISMATCH: 0
SIZE_UNEQUAL: 0
DIFF_NUM_DUPES: 87
EQUAL: 1164

Standard error

[October 27, 2025 at 5:48:46 PM UTC] org.broadinstitute.hellbender.tools.spark.validation.CompareDuplicatesSpark done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1048576000
[October 27, 2025 at 5:48:47 PM UTC] org.broadinstitute.hellbender.tools.spark.validation.CompareDuplicatesSpark done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=910163968
[October 27, 2025 at 5:48:47 PM UTC] org.broadinstitute.hellbender.tools.spark.validation.CompareDuplicatesSpark done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=910163968
[October 27, 2025 at 5:48:48 PM UTC] org.broadinstitute.hellbender.tools.spark.validation.CompareDuplicatesSpark done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=784334848
[October 27, 2025 at 5:48:48 PM UTC] org.broadinstitute.hellbender.tools.spark.validation.CompareDuplicatesSpark done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=784334848
[October 27, 2025 at 5:48:49 PM UTC] org.broadinstitute.hellbender.tools.spark.validation.CompareDuplicatesSpark done. Elapsed time: 0.02 minutes.
Runtime.totalMemory()=685768704