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

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

tests
0

failures
0

ignored
3.464s

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) 0.328s 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) 0.545s 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) 0.585s 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) 0.538s 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) 0.550s passed
testOutputFile 0.918s 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 27, 2025 at 1:51:22 PM UTC] org.broadinstitute.hellbender.tools.spark.validation.CompareDuplicatesSpark done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=853540864
[May 27, 2025 at 1:51:22 PM UTC] org.broadinstitute.hellbender.tools.spark.validation.CompareDuplicatesSpark done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=853540864
[May 27, 2025 at 1:51:23 PM UTC] org.broadinstitute.hellbender.tools.spark.validation.CompareDuplicatesSpark done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=664797184
[May 27, 2025 at 1:51:23 PM UTC] org.broadinstitute.hellbender.tools.spark.validation.CompareDuplicatesSpark done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=664797184
[May 27, 2025 at 1:51:24 PM UTC] org.broadinstitute.hellbender.tools.spark.validation.CompareDuplicatesSpark done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=664797184
[May 27, 2025 at 1:51:25 PM UTC] org.broadinstitute.hellbender.tools.spark.validation.CompareDuplicatesSpark done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=912261120