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

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

tests
0

failures
0

ignored
3.664s

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) 0.389s 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) 0.615s 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) 0.559s 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) 0.567s 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) 0.614s passed
testOutputFile 0.920s 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
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
##############################
EQUAL: 1164
READ_MISMATCH: 0
DIFF_NUM_DUPES: 87
DIFFERENT_REPRESENTATIVE_READ: 0
SIZE_UNEQUAL: 0
processing bams with 1510 mapped reads
first and second: 96,96
##############################
EQUAL: 1251
READ_MISMATCH: 0
DIFF_NUM_DUPES: 0
DIFFERENT_REPRESENTATIVE_READ: 0
SIZE_UNEQUAL: 0
processing bams with 1510 mapped reads
first and second: 96,96
##############################
EQUAL: 1251
READ_MISMATCH: 0
DIFF_NUM_DUPES: 0
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
##############################
EQUAL: 1164
READ_MISMATCH: 0
DIFF_NUM_DUPES: 87
DIFFERENT_REPRESENTATIVE_READ: 0
SIZE_UNEQUAL: 0

Standard error

[June 12, 2025 at 9:01:15 PM GMT] org.broadinstitute.hellbender.tools.spark.validation.CompareDuplicatesSpark done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=754974720
[June 12, 2025 at 9:01:16 PM GMT] org.broadinstitute.hellbender.tools.spark.validation.CompareDuplicatesSpark done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=637534208
[June 12, 2025 at 9:01:16 PM GMT] org.broadinstitute.hellbender.tools.spark.validation.CompareDuplicatesSpark done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=580911104
[June 12, 2025 at 9:01:17 PM GMT] org.broadinstitute.hellbender.tools.spark.validation.CompareDuplicatesSpark done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=559939584
[June 12, 2025 at 9:01:17 PM GMT] org.broadinstitute.hellbender.tools.spark.validation.CompareDuplicatesSpark done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=532676608
[June 12, 2025 at 9:01:18 PM GMT] org.broadinstitute.hellbender.tools.spark.validation.CompareDuplicatesSpark done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=532676608