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

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

tests
0

failures
0

ignored
3.625s

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) 0.344s 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) 0.624s 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) 0.570s 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) 0.617s 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) 0.573s passed
testOutputFile 0.897s passed

Standard output

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

Standard error

[May 19, 2025 at 4:02:59 PM GMT] org.broadinstitute.hellbender.tools.spark.validation.CompareDuplicatesSpark done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=784334848
[May 19, 2025 at 4:02:59 PM GMT] org.broadinstitute.hellbender.tools.spark.validation.CompareDuplicatesSpark done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=637534208
[May 19, 2025 at 4:03:00 PM GMT] org.broadinstitute.hellbender.tools.spark.validation.CompareDuplicatesSpark done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=601882624
[May 19, 2025 at 4:03:00 PM GMT] org.broadinstitute.hellbender.tools.spark.validation.CompareDuplicatesSpark done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=574619648
[May 19, 2025 at 4:03:01 PM GMT] org.broadinstitute.hellbender.tools.spark.validation.CompareDuplicatesSpark done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=545259520
[May 19, 2025 at 4:03:02 PM GMT] org.broadinstitute.hellbender.tools.spark.validation.CompareDuplicatesSpark done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=545259520