Class picard.analysis.directed.CollectHsMetricsTest
|
100%
successful |
Tests
| Test | Duration | Result |
|---|---|---|
| runCollectHsMetricsTest[0](testdata/picard/analysis/directed/CollectHsMetrics/lowbaseq.sam, testdata/picard/analysis/directed/CollectHsMetrics/chrM.interval_list, 1, 10, true, 2, 200, 0.5, 0.0, 0.0, 0.5, 0.0, 1, 0, 200, 1000) | 0.991s | passed |
| runCollectHsMetricsTest[1](testdata/picard/analysis/directed/CollectHsMetrics/lowbaseq.sam, testdata/picard/analysis/directed/CollectHsMetrics/chrM_100bp.interval_list, 1, 10, true, 2, 200, 0.5, 0.0, 0.0, 1.0, 0.0, 1, 1, 200, 1000) | 0.980s | passed |
| runCollectHsMetricsTest[2](testdata/picard/analysis/directed/CollectHsMetrics/lowmapq.sam, testdata/picard/analysis/directed/CollectHsMetrics/chrM.interval_list, 2, 0, true, 2, 202, 0, 0.0, 0.0, 0.505, 0.0, 1, 0, 202, 1000) | 0.331s | passed |
| runCollectHsMetricsTest[3](testdata/picard/analysis/directed/CollectHsMetrics/lowmapq.sam, testdata/picard/analysis/directed/CollectHsMetrics/chrM_100bp.interval_list, 2, 0, true, 2, 202, 0, 0.0, 0.00495, 1.0, 0.0, 1, 1, 202, 1000) | 0.334s | passed |
| runCollectHsMetricsTest[4](testdata/picard/analysis/directed/CollectHsMetrics/overlapping.sam, testdata/picard/analysis/directed/CollectHsMetrics/chrM.interval_list, 0, 0, true, 2, 202, 0, 0.5, 0.0, 0.505, 0, 1, 0, 202, 1000) | 0.337s | passed |
| runCollectHsMetricsTest[5](testdata/picard/analysis/directed/CollectHsMetrics/overlapping.sam, testdata/picard/analysis/directed/CollectHsMetrics/chrM.interval_list, 0, 0, false, 2, 202, 0, 0.0, 0.0, 0.505, 0.505, 2, 0, 202, 1000) | 0.342s | passed |
| runCollectHsMetricsTest[6](testdata/picard/analysis/directed/CollectHsMetrics/overlapping.sam, testdata/picard/analysis/directed/CollectHsMetrics/chrM_100bp.interval_list, 0, 0, true, 2, 202, 0, 0.5, 0.00495, 1.0, 0, 1, 1, 202, 1000) | 0.341s | passed |
| runCollectHsMetricsTest[7](testdata/picard/analysis/directed/CollectHsMetrics/overlapping.sam, testdata/picard/analysis/directed/CollectHsMetrics/chrM_100bp.interval_list, 0, 0, false, 2, 202, 0, 0.0, 0.009901, 1.0, 1.0, 2, 2, 202, 1000) | 0.333s | passed |
| runCollectHsMetricsTest[8](testdata/picard/analysis/directed/CollectHsMetrics/single-short-read.sam, testdata/picard/analysis/directed/CollectHsMetrics/two-small.interval_list, 20, 20, true, 1, 10, 0.0, 0.0, 0.0, 0.5, 0.0, 1, 0, 10, 1000) | 0.973s | passed |
| runCollectHsMetricsTest[9](testdata/picard/analysis/directed/CollectHsMetrics/someLowbaseq.sam, testdata/picard/analysis/directed/CollectHsMetrics/two-small.interval_list, 0, 21, true, 2, 200, 0.75, 0.0, 0.2, 0.5, 0.0, 1, 0, 200, 1000) | 0.497s | passed |
| testCoverageHistogram | 0.021s | passed |
| testHsMetricsF80DoesNotUseCovCap | 4.774s | passed |
| testHsMetricsHandlesIndelsAppropriately | 0.092s | passed |
| testHsMetricsHighTargetCoverage | 4.220s | passed |
Standard error
[Thu Apr 24 12:59:53 EDT 2025] CollectHsMetrics --BAIT_INTERVALS testdata/picard/analysis/directed/CollectHsMetrics/chrM.interval_list --TARGET_INTERVALS testdata/picard/analysis/directed/CollectHsMetrics/chrM.interval_list --INPUT testdata/picard/analysis/directed/CollectHsMetrics/lowbaseq.sam --OUTPUT testdata/picard/analysis/directed/CollectHsMetrics/CollectHsMetrics5559692479952495772.hs_metrics --MINIMUM_MAPPING_QUALITY 1 --MINIMUM_BASE_QUALITY 10 --CLIP_OVERLAPPING_READS true --SAMPLE_SIZE 1000 --METRIC_ACCUMULATION_LEVEL ALL_READS --NEAR_DISTANCE 250 --INCLUDE_INDELS false --COVERAGE_CAP 200 --ALLELE_FRACTION 0.001 --ALLELE_FRACTION 0.005 --ALLELE_FRACTION 0.01 --ALLELE_FRACTION 0.02 --ALLELE_FRACTION 0.05 --ALLELE_FRACTION 0.1 --ALLELE_FRACTION 0.2 --ALLELE_FRACTION 0.3 --ALLELE_FRACTION 0.5 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 12:59:53 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null INFO 2025-04-24 12:59:53 TheoreticalSensitivity Creating Roulette Wheel INFO 2025-04-24 12:59:53 TheoreticalSensitivity Calculating quality sums from quality sampler INFO 2025-04-24 12:59:53 TheoreticalSensitivity 0 sampling iterations completed INFO 2025-04-24 12:59:54 TheoreticalSensitivity Calculating theoretical het sensitivity [Thu Apr 24 12:59:54 EDT 2025] picard.analysis.directed.CollectHsMetrics done. Elapsed time: 0.02 minutes. Runtime.totalMemory()=1073741824 [Thu Apr 24 12:59:54 EDT 2025] CollectHsMetrics --BAIT_INTERVALS testdata/picard/analysis/directed/CollectHsMetrics/chrM_100bp.interval_list --TARGET_INTERVALS testdata/picard/analysis/directed/CollectHsMetrics/chrM_100bp.interval_list --INPUT testdata/picard/analysis/directed/CollectHsMetrics/lowbaseq.sam --OUTPUT testdata/picard/analysis/directed/CollectHsMetrics/CollectHsMetrics1018775218518173589.hs_metrics --MINIMUM_MAPPING_QUALITY 1 --MINIMUM_BASE_QUALITY 10 --CLIP_OVERLAPPING_READS true --SAMPLE_SIZE 1000 --METRIC_ACCUMULATION_LEVEL ALL_READS --NEAR_DISTANCE 250 --INCLUDE_INDELS false --COVERAGE_CAP 200 --ALLELE_FRACTION 0.001 --ALLELE_FRACTION 0.005 --ALLELE_FRACTION 0.01 --ALLELE_FRACTION 0.02 --ALLELE_FRACTION 0.05 --ALLELE_FRACTION 0.1 --ALLELE_FRACTION 0.2 --ALLELE_FRACTION 0.3 --ALLELE_FRACTION 0.5 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 12:59:54 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null INFO 2025-04-24 12:59:54 TheoreticalSensitivity Creating Roulette Wheel INFO 2025-04-24 12:59:54 TheoreticalSensitivity Calculating quality sums from quality sampler INFO 2025-04-24 12:59:54 TheoreticalSensitivity 0 sampling iterations completed INFO 2025-04-24 12:59:55 TheoreticalSensitivity Calculating theoretical het sensitivity [Thu Apr 24 12:59:55 EDT 2025] picard.analysis.directed.CollectHsMetrics done. Elapsed time: 0.02 minutes. Runtime.totalMemory()=1073741824 [Thu Apr 24 12:59:55 EDT 2025] CollectHsMetrics --BAIT_INTERVALS testdata/picard/analysis/directed/CollectHsMetrics/chrM.interval_list --TARGET_INTERVALS testdata/picard/analysis/directed/CollectHsMetrics/chrM.interval_list --INPUT testdata/picard/analysis/directed/CollectHsMetrics/lowmapq.sam --OUTPUT testdata/picard/analysis/directed/CollectHsMetrics/CollectHsMetrics7374097903359667862.hs_metrics --MINIMUM_MAPPING_QUALITY 2 --MINIMUM_BASE_QUALITY 0 --CLIP_OVERLAPPING_READS true --SAMPLE_SIZE 1000 --METRIC_ACCUMULATION_LEVEL ALL_READS --NEAR_DISTANCE 250 --INCLUDE_INDELS false --COVERAGE_CAP 200 --ALLELE_FRACTION 0.001 --ALLELE_FRACTION 0.005 --ALLELE_FRACTION 0.01 --ALLELE_FRACTION 0.02 --ALLELE_FRACTION 0.05 --ALLELE_FRACTION 0.1 --ALLELE_FRACTION 0.2 --ALLELE_FRACTION 0.3 --ALLELE_FRACTION 0.5 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 12:59:55 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null INFO 2025-04-24 12:59:55 TheoreticalSensitivity Creating Roulette Wheel INFO 2025-04-24 12:59:55 TheoreticalSensitivity Calculating quality sums from quality sampler INFO 2025-04-24 12:59:55 TheoreticalSensitivity 0 sampling iterations completed INFO 2025-04-24 12:59:55 TheoreticalSensitivity Calculating theoretical het sensitivity [Thu Apr 24 12:59:55 EDT 2025] picard.analysis.directed.CollectHsMetrics done. Elapsed time: 0.01 minutes. Runtime.totalMemory()=1073741824 [Thu Apr 24 12:59:55 EDT 2025] CollectHsMetrics --BAIT_INTERVALS testdata/picard/analysis/directed/CollectHsMetrics/chrM_100bp.interval_list --TARGET_INTERVALS testdata/picard/analysis/directed/CollectHsMetrics/chrM_100bp.interval_list --INPUT testdata/picard/analysis/directed/CollectHsMetrics/lowmapq.sam --OUTPUT testdata/picard/analysis/directed/CollectHsMetrics/CollectHsMetrics10094248078232660826.hs_metrics --MINIMUM_MAPPING_QUALITY 2 --MINIMUM_BASE_QUALITY 0 --CLIP_OVERLAPPING_READS true --SAMPLE_SIZE 1000 --METRIC_ACCUMULATION_LEVEL ALL_READS --NEAR_DISTANCE 250 --INCLUDE_INDELS false --COVERAGE_CAP 200 --ALLELE_FRACTION 0.001 --ALLELE_FRACTION 0.005 --ALLELE_FRACTION 0.01 --ALLELE_FRACTION 0.02 --ALLELE_FRACTION 0.05 --ALLELE_FRACTION 0.1 --ALLELE_FRACTION 0.2 --ALLELE_FRACTION 0.3 --ALLELE_FRACTION 0.5 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 12:59:55 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null INFO 2025-04-24 12:59:55 TheoreticalSensitivity Creating Roulette Wheel INFO 2025-04-24 12:59:55 TheoreticalSensitivity Calculating quality sums from quality sampler INFO 2025-04-24 12:59:55 TheoreticalSensitivity 0 sampling iterations completed INFO 2025-04-24 12:59:56 TheoreticalSensitivity Calculating theoretical het sensitivity [Thu Apr 24 12:59:56 EDT 2025] picard.analysis.directed.CollectHsMetrics done. Elapsed time: 0.01 minutes. Runtime.totalMemory()=1073741824 [Thu Apr 24 12:59:56 EDT 2025] CollectHsMetrics --BAIT_INTERVALS testdata/picard/analysis/directed/CollectHsMetrics/chrM.interval_list --TARGET_INTERVALS testdata/picard/analysis/directed/CollectHsMetrics/chrM.interval_list --INPUT testdata/picard/analysis/directed/CollectHsMetrics/overlapping.sam --OUTPUT testdata/picard/analysis/directed/CollectHsMetrics/CollectHsMetrics11548507245658428894.hs_metrics --MINIMUM_MAPPING_QUALITY 0 --MINIMUM_BASE_QUALITY 0 --CLIP_OVERLAPPING_READS true --SAMPLE_SIZE 1000 --METRIC_ACCUMULATION_LEVEL ALL_READS --NEAR_DISTANCE 250 --INCLUDE_INDELS false --COVERAGE_CAP 200 --ALLELE_FRACTION 0.001 --ALLELE_FRACTION 0.005 --ALLELE_FRACTION 0.01 --ALLELE_FRACTION 0.02 --ALLELE_FRACTION 0.05 --ALLELE_FRACTION 0.1 --ALLELE_FRACTION 0.2 --ALLELE_FRACTION 0.3 --ALLELE_FRACTION 0.5 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 12:59:56 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null INFO 2025-04-24 12:59:56 TheoreticalSensitivity Creating Roulette Wheel INFO 2025-04-24 12:59:56 TheoreticalSensitivity Calculating quality sums from quality sampler INFO 2025-04-24 12:59:56 TheoreticalSensitivity 0 sampling iterations completed INFO 2025-04-24 12:59:56 TheoreticalSensitivity Calculating theoretical het sensitivity [Thu Apr 24 12:59:56 EDT 2025] picard.analysis.directed.CollectHsMetrics done. Elapsed time: 0.01 minutes. Runtime.totalMemory()=1073741824 [Thu Apr 24 12:59:56 EDT 2025] CollectHsMetrics --BAIT_INTERVALS testdata/picard/analysis/directed/CollectHsMetrics/chrM.interval_list --TARGET_INTERVALS testdata/picard/analysis/directed/CollectHsMetrics/chrM.interval_list --INPUT testdata/picard/analysis/directed/CollectHsMetrics/overlapping.sam --OUTPUT testdata/picard/analysis/directed/CollectHsMetrics/CollectHsMetrics6671618781306470719.hs_metrics --MINIMUM_MAPPING_QUALITY 0 --MINIMUM_BASE_QUALITY 0 --CLIP_OVERLAPPING_READS false --SAMPLE_SIZE 1000 --METRIC_ACCUMULATION_LEVEL ALL_READS --NEAR_DISTANCE 250 --INCLUDE_INDELS false --COVERAGE_CAP 200 --ALLELE_FRACTION 0.001 --ALLELE_FRACTION 0.005 --ALLELE_FRACTION 0.01 --ALLELE_FRACTION 0.02 --ALLELE_FRACTION 0.05 --ALLELE_FRACTION 0.1 --ALLELE_FRACTION 0.2 --ALLELE_FRACTION 0.3 --ALLELE_FRACTION 0.5 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 12:59:56 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null INFO 2025-04-24 12:59:56 TheoreticalSensitivity Creating Roulette Wheel INFO 2025-04-24 12:59:56 TheoreticalSensitivity Calculating quality sums from quality sampler INFO 2025-04-24 12:59:56 TheoreticalSensitivity 0 sampling iterations completed INFO 2025-04-24 12:59:56 TheoreticalSensitivity Calculating theoretical het sensitivity [Thu Apr 24 12:59:56 EDT 2025] picard.analysis.directed.CollectHsMetrics done. Elapsed time: 0.01 minutes. Runtime.totalMemory()=1073741824 [Thu Apr 24 12:59:56 EDT 2025] CollectHsMetrics --BAIT_INTERVALS testdata/picard/analysis/directed/CollectHsMetrics/chrM_100bp.interval_list --TARGET_INTERVALS testdata/picard/analysis/directed/CollectHsMetrics/chrM_100bp.interval_list --INPUT testdata/picard/analysis/directed/CollectHsMetrics/overlapping.sam --OUTPUT testdata/picard/analysis/directed/CollectHsMetrics/CollectHsMetrics10301438408592622402.hs_metrics --MINIMUM_MAPPING_QUALITY 0 --MINIMUM_BASE_QUALITY 0 --CLIP_OVERLAPPING_READS true --SAMPLE_SIZE 1000 --METRIC_ACCUMULATION_LEVEL ALL_READS --NEAR_DISTANCE 250 --INCLUDE_INDELS false --COVERAGE_CAP 200 --ALLELE_FRACTION 0.001 --ALLELE_FRACTION 0.005 --ALLELE_FRACTION 0.01 --ALLELE_FRACTION 0.02 --ALLELE_FRACTION 0.05 --ALLELE_FRACTION 0.1 --ALLELE_FRACTION 0.2 --ALLELE_FRACTION 0.3 --ALLELE_FRACTION 0.5 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 12:59:56 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null INFO 2025-04-24 12:59:56 TheoreticalSensitivity Creating Roulette Wheel INFO 2025-04-24 12:59:56 TheoreticalSensitivity Calculating quality sums from quality sampler INFO 2025-04-24 12:59:56 TheoreticalSensitivity 0 sampling iterations completed INFO 2025-04-24 12:59:57 TheoreticalSensitivity Calculating theoretical het sensitivity [Thu Apr 24 12:59:57 EDT 2025] picard.analysis.directed.CollectHsMetrics done. Elapsed time: 0.01 minutes. Runtime.totalMemory()=1073741824 [Thu Apr 24 12:59:57 EDT 2025] CollectHsMetrics --BAIT_INTERVALS testdata/picard/analysis/directed/CollectHsMetrics/chrM_100bp.interval_list --TARGET_INTERVALS testdata/picard/analysis/directed/CollectHsMetrics/chrM_100bp.interval_list --INPUT testdata/picard/analysis/directed/CollectHsMetrics/overlapping.sam --OUTPUT testdata/picard/analysis/directed/CollectHsMetrics/CollectHsMetrics13338411791343933191.hs_metrics --MINIMUM_MAPPING_QUALITY 0 --MINIMUM_BASE_QUALITY 0 --CLIP_OVERLAPPING_READS false --SAMPLE_SIZE 1000 --METRIC_ACCUMULATION_LEVEL ALL_READS --NEAR_DISTANCE 250 --INCLUDE_INDELS false --COVERAGE_CAP 200 --ALLELE_FRACTION 0.001 --ALLELE_FRACTION 0.005 --ALLELE_FRACTION 0.01 --ALLELE_FRACTION 0.02 --ALLELE_FRACTION 0.05 --ALLELE_FRACTION 0.1 --ALLELE_FRACTION 0.2 --ALLELE_FRACTION 0.3 --ALLELE_FRACTION 0.5 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 12:59:57 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null INFO 2025-04-24 12:59:57 TheoreticalSensitivity Creating Roulette Wheel INFO 2025-04-24 12:59:57 TheoreticalSensitivity Calculating quality sums from quality sampler INFO 2025-04-24 12:59:57 TheoreticalSensitivity 0 sampling iterations completed INFO 2025-04-24 12:59:57 TheoreticalSensitivity Calculating theoretical het sensitivity [Thu Apr 24 12:59:57 EDT 2025] picard.analysis.directed.CollectHsMetrics done. Elapsed time: 0.01 minutes. Runtime.totalMemory()=1073741824 [Thu Apr 24 12:59:57 EDT 2025] CollectHsMetrics --BAIT_INTERVALS testdata/picard/analysis/directed/CollectHsMetrics/two-small.interval_list --TARGET_INTERVALS testdata/picard/analysis/directed/CollectHsMetrics/two-small.interval_list --INPUT testdata/picard/analysis/directed/CollectHsMetrics/single-short-read.sam --OUTPUT testdata/picard/analysis/directed/CollectHsMetrics/CollectHsMetrics7019726897849690229.hs_metrics --MINIMUM_MAPPING_QUALITY 20 --MINIMUM_BASE_QUALITY 20 --CLIP_OVERLAPPING_READS true --SAMPLE_SIZE 1000 --METRIC_ACCUMULATION_LEVEL ALL_READS --NEAR_DISTANCE 250 --INCLUDE_INDELS false --COVERAGE_CAP 200 --ALLELE_FRACTION 0.001 --ALLELE_FRACTION 0.005 --ALLELE_FRACTION 0.01 --ALLELE_FRACTION 0.02 --ALLELE_FRACTION 0.05 --ALLELE_FRACTION 0.1 --ALLELE_FRACTION 0.2 --ALLELE_FRACTION 0.3 --ALLELE_FRACTION 0.5 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 12:59:57 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null INFO 2025-04-24 12:59:57 TheoreticalSensitivity Creating Roulette Wheel INFO 2025-04-24 12:59:57 TheoreticalSensitivity Calculating quality sums from quality sampler INFO 2025-04-24 12:59:57 TheoreticalSensitivity 0 sampling iterations completed INFO 2025-04-24 12:59:58 TheoreticalSensitivity Calculating theoretical het sensitivity [Thu Apr 24 12:59:58 EDT 2025] picard.analysis.directed.CollectHsMetrics done. Elapsed time: 0.02 minutes. Runtime.totalMemory()=1073741824 [Thu Apr 24 12:59:58 EDT 2025] CollectHsMetrics --BAIT_INTERVALS testdata/picard/analysis/directed/CollectHsMetrics/two-small.interval_list --TARGET_INTERVALS testdata/picard/analysis/directed/CollectHsMetrics/two-small.interval_list --INPUT testdata/picard/analysis/directed/CollectHsMetrics/someLowbaseq.sam --OUTPUT testdata/picard/analysis/directed/CollectHsMetrics/CollectHsMetrics7303409287879222183.hs_metrics --MINIMUM_MAPPING_QUALITY 0 --MINIMUM_BASE_QUALITY 21 --CLIP_OVERLAPPING_READS true --SAMPLE_SIZE 1000 --METRIC_ACCUMULATION_LEVEL ALL_READS --NEAR_DISTANCE 250 --INCLUDE_INDELS false --COVERAGE_CAP 200 --ALLELE_FRACTION 0.001 --ALLELE_FRACTION 0.005 --ALLELE_FRACTION 0.01 --ALLELE_FRACTION 0.02 --ALLELE_FRACTION 0.05 --ALLELE_FRACTION 0.1 --ALLELE_FRACTION 0.2 --ALLELE_FRACTION 0.3 --ALLELE_FRACTION 0.5 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 12:59:58 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null INFO 2025-04-24 12:59:58 TheoreticalSensitivity Creating Roulette Wheel INFO 2025-04-24 12:59:58 TheoreticalSensitivity Calculating quality sums from quality sampler INFO 2025-04-24 12:59:58 TheoreticalSensitivity 0 sampling iterations completed INFO 2025-04-24 12:59:59 TheoreticalSensitivity Calculating theoretical het sensitivity [Thu Apr 24 12:59:59 EDT 2025] picard.analysis.directed.CollectHsMetrics done. Elapsed time: 0.01 minutes. Runtime.totalMemory()=1073741824 [Thu Apr 24 12:59:59 EDT 2025] CollectHsMetrics --BAIT_INTERVALS testdata/picard/analysis/directed/CollectHsMetrics/two-small.interval_list --TARGET_INTERVALS testdata/picard/analysis/directed/CollectHsMetrics/two-small.interval_list --INPUT testdata/picard/analysis/directed/CollectHsMetrics/single-short-read.sam --OUTPUT testdata/picard/analysis/directed/CollectHsMetrics/testCoverageHistogram4510557967140881859.hs_metrics --MINIMUM_MAPPING_QUALITY 20 --MINIMUM_BASE_QUALITY 20 --CLIP_OVERLAPPING_READS true --SAMPLE_SIZE 10 --METRIC_ACCUMULATION_LEVEL ALL_READS --NEAR_DISTANCE 250 --INCLUDE_INDELS false --COVERAGE_CAP 200 --ALLELE_FRACTION 0.001 --ALLELE_FRACTION 0.005 --ALLELE_FRACTION 0.01 --ALLELE_FRACTION 0.02 --ALLELE_FRACTION 0.05 --ALLELE_FRACTION 0.1 --ALLELE_FRACTION 0.2 --ALLELE_FRACTION 0.3 --ALLELE_FRACTION 0.5 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 12:59:59 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null INFO 2025-04-24 12:59:59 TheoreticalSensitivity Creating Roulette Wheel INFO 2025-04-24 12:59:59 TheoreticalSensitivity Calculating quality sums from quality sampler INFO 2025-04-24 12:59:59 TheoreticalSensitivity 0 sampling iterations completed INFO 2025-04-24 12:59:59 TheoreticalSensitivity Calculating theoretical het sensitivity [Thu Apr 24 12:59:59 EDT 2025] picard.analysis.directed.CollectHsMetrics done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 [Thu Apr 24 13:00:00 EDT 2025] CollectHsMetrics --BAIT_INTERVALS /tmp/hsmetrics.test4793257302622306392/baits.interval_list --TARGET_INTERVALS /tmp/hsmetrics.test4793257302622306392/targets.interval_list --INPUT /tmp/hsmetrics.test4793257302622306392/fold_80.bam --OUTPUT /tmp/hsmetrics_high_coverage.10853701278876015258.txt --COVERAGE_CAP 10 --SAMPLE_SIZE 0 --METRIC_ACCUMULATION_LEVEL ALL_READS --NEAR_DISTANCE 250 --MINIMUM_MAPPING_QUALITY 20 --MINIMUM_BASE_QUALITY 20 --CLIP_OVERLAPPING_READS true --INCLUDE_INDELS false --ALLELE_FRACTION 0.001 --ALLELE_FRACTION 0.005 --ALLELE_FRACTION 0.01 --ALLELE_FRACTION 0.02 --ALLELE_FRACTION 0.05 --ALLELE_FRACTION 0.1 --ALLELE_FRACTION 0.2 --ALLELE_FRACTION 0.3 --ALLELE_FRACTION 0.5 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:00:00 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null INFO 2025-04-24 13:00:03 TheoreticalSensitivity Creating Roulette Wheel INFO 2025-04-24 13:00:03 TheoreticalSensitivity Calculating quality sums from quality sampler INFO 2025-04-24 13:00:03 TheoreticalSensitivity Calculating theoretical het sensitivity [Thu Apr 24 13:00:03 EDT 2025] picard.analysis.directed.CollectHsMetrics done. Elapsed time: 0.05 minutes. Runtime.totalMemory()=1073741824 [Thu Apr 24 13:00:03 EDT 2025] CollectHsMetrics --BAIT_INTERVALS /tmp/hsmetrics.test2945312596196336173/baits.interval_list --TARGET_INTERVALS /tmp/hsmetrics.test2945312596196336173/targets.interval_list --INPUT /tmp/hsmetrics.test2945312596196336173/with_del.bam --OUTPUT /tmp/hsmetrics.1776933336461995093.txt --INCLUDE_INDELS false --SAMPLE_SIZE 0 --METRIC_ACCUMULATION_LEVEL ALL_READS --NEAR_DISTANCE 250 --MINIMUM_MAPPING_QUALITY 20 --MINIMUM_BASE_QUALITY 20 --CLIP_OVERLAPPING_READS true --COVERAGE_CAP 200 --ALLELE_FRACTION 0.001 --ALLELE_FRACTION 0.005 --ALLELE_FRACTION 0.01 --ALLELE_FRACTION 0.02 --ALLELE_FRACTION 0.05 --ALLELE_FRACTION 0.1 --ALLELE_FRACTION 0.2 --ALLELE_FRACTION 0.3 --ALLELE_FRACTION 0.5 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:00:03 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null INFO 2025-04-24 13:00:03 TheoreticalSensitivity Creating Roulette Wheel INFO 2025-04-24 13:00:03 TheoreticalSensitivity Calculating quality sums from quality sampler INFO 2025-04-24 13:00:03 TheoreticalSensitivity Calculating theoretical het sensitivity [Thu Apr 24 13:00:03 EDT 2025] picard.analysis.directed.CollectHsMetrics done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 [Thu Apr 24 13:00:03 EDT 2025] CollectHsMetrics --BAIT_INTERVALS /tmp/hsmetrics.test2945312596196336173/baits.interval_list --TARGET_INTERVALS /tmp/hsmetrics.test2945312596196336173/targets.interval_list --INPUT /tmp/hsmetrics.test2945312596196336173/with_del.bam --OUTPUT /tmp/hsmetrics.1776933336461995093.txt --INCLUDE_INDELS true --SAMPLE_SIZE 0 --METRIC_ACCUMULATION_LEVEL ALL_READS --NEAR_DISTANCE 250 --MINIMUM_MAPPING_QUALITY 20 --MINIMUM_BASE_QUALITY 20 --CLIP_OVERLAPPING_READS true --COVERAGE_CAP 200 --ALLELE_FRACTION 0.001 --ALLELE_FRACTION 0.005 --ALLELE_FRACTION 0.01 --ALLELE_FRACTION 0.02 --ALLELE_FRACTION 0.05 --ALLELE_FRACTION 0.1 --ALLELE_FRACTION 0.2 --ALLELE_FRACTION 0.3 --ALLELE_FRACTION 0.5 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:00:03 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null INFO 2025-04-24 13:00:03 TheoreticalSensitivity Creating Roulette Wheel INFO 2025-04-24 13:00:03 TheoreticalSensitivity Calculating quality sums from quality sampler INFO 2025-04-24 13:00:03 TheoreticalSensitivity Calculating theoretical het sensitivity [Thu Apr 24 13:00:03 EDT 2025] picard.analysis.directed.CollectHsMetrics done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 [Thu Apr 24 13:00:03 EDT 2025] CollectHsMetrics --BAIT_INTERVALS /tmp/hsmetrics.test2945312596196336173/baits.interval_list --TARGET_INTERVALS /tmp/hsmetrics.test2945312596196336173/targets.interval_list --INPUT /tmp/hsmetrics.test2945312596196336173/with_ins.bam --OUTPUT /tmp/hsmetrics.1776933336461995093.txt --INCLUDE_INDELS false --SAMPLE_SIZE 0 --METRIC_ACCUMULATION_LEVEL ALL_READS --NEAR_DISTANCE 250 --MINIMUM_MAPPING_QUALITY 20 --MINIMUM_BASE_QUALITY 20 --CLIP_OVERLAPPING_READS true --COVERAGE_CAP 200 --ALLELE_FRACTION 0.001 --ALLELE_FRACTION 0.005 --ALLELE_FRACTION 0.01 --ALLELE_FRACTION 0.02 --ALLELE_FRACTION 0.05 --ALLELE_FRACTION 0.1 --ALLELE_FRACTION 0.2 --ALLELE_FRACTION 0.3 --ALLELE_FRACTION 0.5 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:00:03 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null INFO 2025-04-24 13:00:03 TheoreticalSensitivity Creating Roulette Wheel INFO 2025-04-24 13:00:03 TheoreticalSensitivity Calculating quality sums from quality sampler INFO 2025-04-24 13:00:03 TheoreticalSensitivity Calculating theoretical het sensitivity [Thu Apr 24 13:00:03 EDT 2025] picard.analysis.directed.CollectHsMetrics done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 [Thu Apr 24 13:00:03 EDT 2025] CollectHsMetrics --BAIT_INTERVALS /tmp/hsmetrics.test2945312596196336173/baits.interval_list --TARGET_INTERVALS /tmp/hsmetrics.test2945312596196336173/targets.interval_list --INPUT /tmp/hsmetrics.test2945312596196336173/with_ins.bam --OUTPUT /tmp/hsmetrics.1776933336461995093.txt --INCLUDE_INDELS true --SAMPLE_SIZE 0 --METRIC_ACCUMULATION_LEVEL ALL_READS --NEAR_DISTANCE 250 --MINIMUM_MAPPING_QUALITY 20 --MINIMUM_BASE_QUALITY 20 --CLIP_OVERLAPPING_READS true --COVERAGE_CAP 200 --ALLELE_FRACTION 0.001 --ALLELE_FRACTION 0.005 --ALLELE_FRACTION 0.01 --ALLELE_FRACTION 0.02 --ALLELE_FRACTION 0.05 --ALLELE_FRACTION 0.1 --ALLELE_FRACTION 0.2 --ALLELE_FRACTION 0.3 --ALLELE_FRACTION 0.5 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:00:03 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null INFO 2025-04-24 13:00:04 TheoreticalSensitivity Creating Roulette Wheel INFO 2025-04-24 13:00:04 TheoreticalSensitivity Calculating quality sums from quality sampler INFO 2025-04-24 13:00:04 TheoreticalSensitivity Calculating theoretical het sensitivity [Thu Apr 24 13:00:04 EDT 2025] picard.analysis.directed.CollectHsMetrics done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 [Thu Apr 24 13:00:05 EDT 2025] CollectHsMetrics --BAIT_INTERVALS /tmp/hsmetrics.test17512865183852561276/baits.interval_list --TARGET_INTERVALS /tmp/hsmetrics.test17512865183852561276/targets.interval_list --INPUT /tmp/hsmetrics.test17512865183852561276/high_coverage.bam --OUTPUT /tmp/hsmetrics_high_coverage.6125719176989247299.txt --SAMPLE_SIZE 0 --METRIC_ACCUMULATION_LEVEL ALL_READS --NEAR_DISTANCE 250 --MINIMUM_MAPPING_QUALITY 20 --MINIMUM_BASE_QUALITY 20 --CLIP_OVERLAPPING_READS true --INCLUDE_INDELS false --COVERAGE_CAP 200 --ALLELE_FRACTION 0.001 --ALLELE_FRACTION 0.005 --ALLELE_FRACTION 0.01 --ALLELE_FRACTION 0.02 --ALLELE_FRACTION 0.05 --ALLELE_FRACTION 0.1 --ALLELE_FRACTION 0.2 --ALLELE_FRACTION 0.3 --ALLELE_FRACTION 0.5 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:00:05 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null INFO 2025-04-24 13:00:08 TheoreticalSensitivity Creating Roulette Wheel INFO 2025-04-24 13:00:08 TheoreticalSensitivity Calculating quality sums from quality sampler INFO 2025-04-24 13:00:08 TheoreticalSensitivity Calculating theoretical het sensitivity [Thu Apr 24 13:00:08 EDT 2025] picard.analysis.directed.CollectHsMetrics done. Elapsed time: 0.05 minutes. Runtime.totalMemory()=1073741824