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

all > org.broadinstitute.hellbender.tools.spark.validation > CompareDuplicatesSparkIntegrationTest
6

tests
0

failures
0

ignored
3.449s

duration
100%

successful

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) 0.300s 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) 0.603s 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) 0.529s 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) 0.612s 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) 0.524s passed
testOutputFile 0.881s passed

Standard output

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

Standard error

[May 27, 2025 at 3:13:18 PM GMT] org.broadinstitute.hellbender.tools.spark.validation.CompareDuplicatesSpark done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=754974720
[May 27, 2025 at 3:13:19 PM GMT] org.broadinstitute.hellbender.tools.spark.validation.CompareDuplicatesSpark done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=754974720
[May 27, 2025 at 3:13:19 PM GMT] org.broadinstitute.hellbender.tools.spark.validation.CompareDuplicatesSpark done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=754974720
[May 27, 2025 at 3:13:20 PM GMT] org.broadinstitute.hellbender.tools.spark.validation.CompareDuplicatesSpark done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=566231040
[May 27, 2025 at 3:13:20 PM GMT] org.broadinstitute.hellbender.tools.spark.validation.CompareDuplicatesSpark done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=566231040
[May 27, 2025 at 3:13:21 PM GMT] org.broadinstitute.hellbender.tools.spark.validation.CompareDuplicatesSpark done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=562036736