Class picard.analysis.directed.CollectHsMetricsTest

all > picard.analysis.directed > CollectHsMetricsTest
4

tests
0

failures
0

ignored
3.586s

duration
100%

successful

Tests

Test Duration Result
runCollectTargetedMetricsTest[0](testdata/picard/analysis/directed/CollectHsMetrics/lowbaseq.sam, testdata/picard/analysis/directed/CollectHsMetrics/chrM.fasta, testdata/picard/analysis/directed/CollectHsMetrics/chrM.interval_list, NONE, 1, 1, true, 2, 202, 0.5, 0.0, 0.505, 0.0, 1000) 1.488s passed
runCollectTargetedMetricsTest[1](testdata/picard/analysis/directed/CollectHsMetrics/lowmapq.sam, testdata/picard/analysis/directed/CollectHsMetrics/chrM.fasta, testdata/picard/analysis/directed/CollectHsMetrics/chrM.interval_list, NONE, 2, 0, true, 2, 202, 0, 0.0, 0.505, 0.0, 1000) 0.678s passed
runCollectTargetedMetricsTest[2](testdata/picard/analysis/directed/CollectHsMetrics/overlapping.sam, testdata/picard/analysis/directed/CollectHsMetrics/chrM.fasta, testdata/picard/analysis/directed/CollectHsMetrics/chrM.interval_list, NONE, 0, 0, true, 2, 202, 0, 0.5, 0.505, 0.505, 1000) 0.662s passed
runCollectTargetedMetricsTest[3](testdata/picard/analysis/directed/CollectHsMetrics/overlapping.sam, testdata/picard/analysis/directed/CollectHsMetrics/chrM.fasta, testdata/picard/analysis/directed/CollectHsMetrics/chrM.interval_list, NONE, 0, 0, false, 2, 202, 0, 0.0, 0.505, 0.505, 1000) 0.758s passed

Standard error

[Tue Aug 16 04:11:19 CDT 2016] picard.analysis.directed.CollectHsMetrics BAIT_INTERVALS=[testdata/picard/analysis/directed/CollectHsMetrics/chrM.interval_list] MINIMUM_MAPPING_QUALITY=1 MINIMUM_BASE_QUALITY=1 CLIP_OVERLAPPING_READS=true TARGET_INTERVALS=[testdata/picard/analysis/directed/CollectHsMetrics/chrM.interval_list] INPUT=testdata/picard/analysis/directed/CollectHsMetrics/lowbaseq.sam OUTPUT=testdata/picard/analysis/directed/CollectHsMetrics/CollectHsMetrics7618781476060346606.hs_metrics SAMPLE_SIZE=1000    METRIC_ACCUMULATION_LEVEL=[ALL_READS] NEAR_DISTANCE=250 COVERAGE_CAP=200 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
[Tue Aug 16 04:11:19 CDT 2016] Executing as jli@corona on Linux 3.19.0-61-generic amd64; Java HotSpot(TM) 64-Bit Server VM 1.8.0_91-b14; Picard version: null
INFO	2016-08-16 04:11:19	TheoreticalSensitivity	Creating Roulette Wheel
INFO	2016-08-16 04:11:19	TheoreticalSensitivity	Calculating quality sums from quality sampler
INFO	2016-08-16 04:11:19	TheoreticalSensitivity	0 sampling iterations completed
INFO	2016-08-16 04:11:21	TheoreticalSensitivity	Calculating theoretical het sensitivity
[Tue Aug 16 04:11:21 CDT 2016] picard.analysis.directed.CollectHsMetrics done. Elapsed time: 0.02 minutes.
Runtime.totalMemory()=1829765120
[Tue Aug 16 04:11:21 CDT 2016] picard.analysis.directed.CollectHsMetrics BAIT_INTERVALS=[testdata/picard/analysis/directed/CollectHsMetrics/chrM.interval_list] MINIMUM_MAPPING_QUALITY=2 MINIMUM_BASE_QUALITY=0 CLIP_OVERLAPPING_READS=true TARGET_INTERVALS=[testdata/picard/analysis/directed/CollectHsMetrics/chrM.interval_list] INPUT=testdata/picard/analysis/directed/CollectHsMetrics/lowmapq.sam OUTPUT=testdata/picard/analysis/directed/CollectHsMetrics/CollectHsMetrics3018161107158916726.hs_metrics SAMPLE_SIZE=1000    METRIC_ACCUMULATION_LEVEL=[ALL_READS] NEAR_DISTANCE=250 COVERAGE_CAP=200 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
[Tue Aug 16 04:11:21 CDT 2016] Executing as jli@corona on Linux 3.19.0-61-generic amd64; Java HotSpot(TM) 64-Bit Server VM 1.8.0_91-b14; Picard version: null
INFO	2016-08-16 04:11:21	TheoreticalSensitivity	Creating Roulette Wheel
INFO	2016-08-16 04:11:21	TheoreticalSensitivity	Calculating quality sums from quality sampler
INFO	2016-08-16 04:11:21	TheoreticalSensitivity	0 sampling iterations completed
INFO	2016-08-16 04:11:21	TheoreticalSensitivity	Calculating theoretical het sensitivity
[Tue Aug 16 04:11:22 CDT 2016] picard.analysis.directed.CollectHsMetrics done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=1829765120
[Tue Aug 16 04:11:22 CDT 2016] picard.analysis.directed.CollectHsMetrics BAIT_INTERVALS=[testdata/picard/analysis/directed/CollectHsMetrics/chrM.interval_list] MINIMUM_MAPPING_QUALITY=0 MINIMUM_BASE_QUALITY=0 CLIP_OVERLAPPING_READS=true TARGET_INTERVALS=[testdata/picard/analysis/directed/CollectHsMetrics/chrM.interval_list] INPUT=testdata/picard/analysis/directed/CollectHsMetrics/overlapping.sam OUTPUT=testdata/picard/analysis/directed/CollectHsMetrics/CollectHsMetrics7894852720585414691.hs_metrics SAMPLE_SIZE=1000    METRIC_ACCUMULATION_LEVEL=[ALL_READS] NEAR_DISTANCE=250 COVERAGE_CAP=200 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
[Tue Aug 16 04:11:22 CDT 2016] Executing as jli@corona on Linux 3.19.0-61-generic amd64; Java HotSpot(TM) 64-Bit Server VM 1.8.0_91-b14; Picard version: null
INFO	2016-08-16 04:11:22	TheoreticalSensitivity	Creating Roulette Wheel
INFO	2016-08-16 04:11:22	TheoreticalSensitivity	Calculating quality sums from quality sampler
INFO	2016-08-16 04:11:22	TheoreticalSensitivity	0 sampling iterations completed
INFO	2016-08-16 04:11:22	TheoreticalSensitivity	Calculating theoretical het sensitivity
[Tue Aug 16 04:11:22 CDT 2016] picard.analysis.directed.CollectHsMetrics done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=1829765120
[Tue Aug 16 04:11:22 CDT 2016] picard.analysis.directed.CollectHsMetrics BAIT_INTERVALS=[testdata/picard/analysis/directed/CollectHsMetrics/chrM.interval_list] MINIMUM_MAPPING_QUALITY=0 MINIMUM_BASE_QUALITY=0 CLIP_OVERLAPPING_READS=false TARGET_INTERVALS=[testdata/picard/analysis/directed/CollectHsMetrics/chrM.interval_list] INPUT=testdata/picard/analysis/directed/CollectHsMetrics/overlapping.sam OUTPUT=testdata/picard/analysis/directed/CollectHsMetrics/CollectHsMetrics7658625444802430786.hs_metrics SAMPLE_SIZE=1000    METRIC_ACCUMULATION_LEVEL=[ALL_READS] NEAR_DISTANCE=250 COVERAGE_CAP=200 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
[Tue Aug 16 04:11:22 CDT 2016] Executing as jli@corona on Linux 3.19.0-61-generic amd64; Java HotSpot(TM) 64-Bit Server VM 1.8.0_91-b14; Picard version: null
INFO	2016-08-16 04:11:22	TheoreticalSensitivity	Creating Roulette Wheel
INFO	2016-08-16 04:11:22	TheoreticalSensitivity	Calculating quality sums from quality sampler
INFO	2016-08-16 04:11:22	TheoreticalSensitivity	0 sampling iterations completed
INFO	2016-08-16 04:11:23	TheoreticalSensitivity	Calculating theoretical het sensitivity
[Tue Aug 16 04:11:23 CDT 2016] picard.analysis.directed.CollectHsMetrics done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=1829765120