Class org.broadinstitute.hellbender.tools.spark.pipelines.metrics.CollectQualityYieldMetricsSparkIntegrationTest

all > org.broadinstitute.hellbender.tools.spark.pipelines.metrics > CollectQualityYieldMetricsSparkIntegrationTest

tests

failures

ignored

1.159s

duration

100%

successful

Tests
Standard error

Tests

Test	Duration	Result
test[0](valid.bam, valid.CollectQualityYieldMetrics.txt, null, true)	0.196s	passed
test[1](valid.cram, valid.CollectQualityYieldMetrics.txt, /gatkCloneMountPoint/src/test/resources/org/broadinstitute/hellbender/metrics/analysis/CollectQualityYieldMetrics/valid.fasta, true)	0.167s	passed
test[2](collect_quality_yield_metrics.sam, collect_quality_yield_metrics.originalquals.txt, null, true)	0.114s	passed
test[3](collect_quality_yield_metrics.sam, collect_quality_yield_metrics.quals.txt, null, false)	0.115s	passed
test[4](collect_quality_yield_metrics.dictFix.sam, collect_quality_yield_metrics.originalquals.txt, null, true)	0.119s	passed
test[5](collect_quality_yield_metrics.dictFix.sam, collect_quality_yield_metrics.quals.txt, null, false)	0.110s	passed
test[6](collect_quality_yield_metrics.dictFix.cram, collect_quality_yield_metrics.originalquals.txt, /gatkCloneMountPoint/src/test/resources/Homo_sapiens_assembly19_chr1_1M.fasta, true)	0.167s	passed
test[7](collect_quality_yield_metrics.dictFix.cram, collect_quality_yield_metrics.quals.txt, /gatkCloneMountPoint/src/test/resources/Homo_sapiens_assembly19_chr1_1M.fasta, false)	0.171s	passed

Standard error

14:05:52.746 INFO  BlockManagerInfo - Removed broadcast_3457_piece0 on localhost:46769 in memory (size: 64.0 KiB, free: 1917.3 MiB)
14:05:52.747 INFO  BlockManagerInfo - Removed broadcast_3450_piece0 on localhost:46769 in memory (size: 8.4 KiB, free: 1917.3 MiB)
14:05:52.747 INFO  BlockManagerInfo - Removed broadcast_3454_piece0 on localhost:46769 in memory (size: 64.1 KiB, free: 1917.4 MiB)
14:05:52.747 INFO  BlockManagerInfo - Removed broadcast_3452_piece0 on localhost:46769 in memory (size: 14.6 KiB, free: 1917.4 MiB)
14:05:52.747 INFO  BlockManagerInfo - Removed broadcast_3451_piece0 on localhost:46769 in memory (size: 64.1 KiB, free: 1917.4 MiB)
14:05:52.748 INFO  BlockManagerInfo - Removed broadcast_3437_piece0 on localhost:46769 in memory (size: 64.1 KiB, free: 1917.5 MiB)
14:05:52.748 INFO  BlockManagerInfo - Removed broadcast_3459_piece0 on localhost:46769 in memory (size: 64.0 KiB, free: 1917.6 MiB)
14:05:52.748 INFO  BlockManagerInfo - Removed broadcast_3448_piece0 on localhost:46769 in memory (size: 8.4 KiB, free: 1917.6 MiB)
14:05:52.748 INFO  BlockManagerInfo - Removed broadcast_3445_piece0 on localhost:46769 in memory (size: 145.1 KiB, free: 1917.7 MiB)
14:05:52.749 INFO  BlockManagerInfo - Removed broadcast_3446_piece0 on localhost:46769 in memory (size: 147.5 KiB, free: 1917.8 MiB)
14:05:52.749 INFO  BlockManagerInfo - Removed broadcast_3444_piece0 on localhost:46769 in memory (size: 64.0 KiB, free: 1917.9 MiB)
14:05:52.749 INFO  BlockManagerInfo - Removed broadcast_3439_piece0 on localhost:46769 in memory (size: 211.9 KiB, free: 1918.1 MiB)
14:05:52.749 INFO  BlockManagerInfo - Removed broadcast_3440_piece0 on localhost:46769 in memory (size: 207.9 KiB, free: 1918.3 MiB)
14:05:52.750 INFO  BlockManager - Removing RDD 10349
14:05:52.750 INFO  BlockManagerInfo - Removed broadcast_3431_piece0 on localhost:46769 in memory (size: 8.4 KiB, free: 1918.4 MiB)
14:05:52.751 INFO  BlockManagerInfo - Removed broadcast_3429_piece0 on localhost:46769 in memory (size: 8.4 KiB, free: 1918.4 MiB)
14:05:52.751 INFO  BlockManagerInfo - Removed broadcast_3456_piece0 on localhost:46769 in memory (size: 209.0 B, free: 1918.4 MiB)
14:05:52.751 INFO  BlockManagerInfo - Removed broadcast_3453_piece0 on localhost:46769 in memory (size: 64.1 KiB, free: 1918.4 MiB)
14:05:52.751 INFO  BlockManagerInfo - Removed broadcast_3430_piece0 on localhost:46769 in memory (size: 64.1 KiB, free: 1918.5 MiB)
14:05:52.752 INFO  BlockManagerInfo - Removed broadcast_3449_piece0 on localhost:46769 in memory (size: 64.1 KiB, free: 1918.5 MiB)
14:05:52.752 INFO  BlockManagerInfo - Removed broadcast_3432_piece0 on localhost:46769 in memory (size: 64.1 KiB, free: 1918.6 MiB)
14:05:52.752 INFO  BlockManagerInfo - Removed broadcast_3460_piece0 on localhost:46769 in memory (size: 143.3 KiB, free: 1918.8 MiB)
14:05:52.752 INFO  BlockManagerInfo - Removed broadcast_3434_piece0 on localhost:46769 in memory (size: 19.0 KiB, free: 1918.8 MiB)
14:05:52.753 INFO  BlockManager - Removing RDD 10362
14:05:52.753 INFO  BlockManagerInfo - Removed broadcast_3433_piece0 on localhost:46769 in memory (size: 16.5 KiB, free: 1918.8 MiB)
14:05:52.753 INFO  BlockManagerInfo - Removed broadcast_3455_piece0 on localhost:46769 in memory (size: 207.4 KiB, free: 1919.0 MiB)
14:05:52.754 INFO  BlockManager - Removing RDD 10334
14:05:52.754 INFO  BlockManagerInfo - Removed broadcast_3443_piece0 on localhost:46769 in memory (size: 209.0 B, free: 1919.1 MiB)
14:05:52.754 INFO  BlockManagerInfo - Removed broadcast_3458_piece0 on localhost:46769 in memory (size: 209.0 B, free: 1919.1 MiB)
14:05:52.755 INFO  BlockManagerInfo - Removed broadcast_3447_piece0 on localhost:46769 in memory (size: 143.8 KiB, free: 1919.2 MiB)
14:05:52.755 INFO  BlockManagerInfo - Removed broadcast_3442_piece0 on localhost:46769 in memory (size: 64.0 KiB, free: 1919.3 MiB)
14:05:52.755 INFO  BlockManagerInfo - Removed broadcast_3435_piece0 on localhost:46769 in memory (size: 15.2 KiB, free: 1919.3 MiB)
14:05:52.755 INFO  BlockManagerInfo - Removed broadcast_3438_piece0 on localhost:46769 in memory (size: 209.3 KiB, free: 1919.5 MiB)
14:05:52.756 INFO  BlockManagerInfo - Removed broadcast_3441_piece0 on localhost:46769 in memory (size: 209.0 B, free: 1919.5 MiB)
14:05:52.756 INFO  BlockManagerInfo - Removed broadcast_3436_piece0 on localhost:46769 in memory (size: 64.1 KiB, free: 1919.6 MiB)
[May 27, 2025 at 2:05:52 PM GMT] org.broadinstitute.hellbender.tools.spark.pipelines.metrics.CollectQualityYieldMetricsSpark done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1528823808
[May 27, 2025 at 2:05:53 PM GMT] org.broadinstitute.hellbender.tools.spark.pipelines.metrics.CollectQualityYieldMetricsSpark done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1528823808
[May 27, 2025 at 2:05:53 PM GMT] org.broadinstitute.hellbender.tools.spark.pipelines.metrics.CollectQualityYieldMetricsSpark done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1528823808
[May 27, 2025 at 2:05:53 PM GMT] org.broadinstitute.hellbender.tools.spark.pipelines.metrics.CollectQualityYieldMetricsSpark done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1528823808
[May 27, 2025 at 2:05:53 PM GMT] org.broadinstitute.hellbender.tools.spark.pipelines.metrics.CollectQualityYieldMetricsSpark done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1528823808
[May 27, 2025 at 2:05:53 PM GMT] org.broadinstitute.hellbender.tools.spark.pipelines.metrics.CollectQualityYieldMetricsSpark done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1528823808
[May 27, 2025 at 2:05:53 PM GMT] org.broadinstitute.hellbender.tools.spark.pipelines.metrics.CollectQualityYieldMetricsSpark done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1528823808
[May 27, 2025 at 2:05:53 PM GMT] org.broadinstitute.hellbender.tools.spark.pipelines.metrics.CollectQualityYieldMetricsSpark done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1528823808