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

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

tests
0

failures
0

ignored
3.629s

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) 0.369s 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) 0.604s 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) 0.569s 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) 0.576s 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) 0.599s passed
testOutputFile 0.912s 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
DIFF_NUM_DUPES: 34
SIZE_UNEQUAL: 0
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
DIFF_NUM_DUPES: 87
SIZE_UNEQUAL: 0
DIFFERENT_REPRESENTATIVE_READ: 0
processing bams with 1510 mapped reads
first and second: 96,96
##############################
EQUAL: 1251
READ_MISMATCH: 0
DIFF_NUM_DUPES: 0
SIZE_UNEQUAL: 0
DIFFERENT_REPRESENTATIVE_READ: 0
processing bams with 1510 mapped reads
first and second: 96,96
##############################
EQUAL: 1251
READ_MISMATCH: 0
DIFF_NUM_DUPES: 0
SIZE_UNEQUAL: 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
DIFF_NUM_DUPES: 87
SIZE_UNEQUAL: 0
DIFFERENT_REPRESENTATIVE_READ: 0

Standard error

[May 27, 2025 at 4:51:05 PM GMT] org.broadinstitute.hellbender.tools.spark.validation.CompareDuplicatesSpark done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=784334848
[May 27, 2025 at 4:51:05 PM GMT] org.broadinstitute.hellbender.tools.spark.validation.CompareDuplicatesSpark done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=629145600
[May 27, 2025 at 4:51:06 PM GMT] org.broadinstitute.hellbender.tools.spark.validation.CompareDuplicatesSpark done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=608174080
[May 27, 2025 at 4:51:06 PM GMT] org.broadinstitute.hellbender.tools.spark.validation.CompareDuplicatesSpark done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=580911104
[May 27, 2025 at 4:51:07 PM GMT] org.broadinstitute.hellbender.tools.spark.validation.CompareDuplicatesSpark done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=545259520
[May 27, 2025 at 4:51:08 PM GMT] org.broadinstitute.hellbender.tools.spark.validation.CompareDuplicatesSpark done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=528482304