Class picard.analysis.directed.CollectTargetedMetricsTest
Tests
| Test |
Duration |
Result |
| runCollectTargetedMetricsTest[0](/tmp/CollectTargetedMetrics3165096477504688295.bam, /tmp/test10629172057974704282.TargetedMetrics_Coverage, /tmp/perTarget9671349733280231197.perTargetCoverage, /mounts/lovelace/software/picard/picard/testdata/picard/reference/chrM.reference.fasta, testdata/picard/quality/chrM.single.interval_list, 1000) |
0.371s |
passed |
| runCollectTargetedMetricsTest[1](/tmp/CollectTargetedMetrics3165096477504688295.bam, /tmp/test10629172057974704282.TargetedMetrics_Coverage, /tmp/perTarget9671349733280231197.perTargetCoverage, /mounts/lovelace/software/picard/picard/testdata/picard/reference/chrM.reference.fasta, testdata/picard/quality/chrM.empty.interval_list, 1000) |
0.275s |
passed |
| runCollectTargetedMetricsTheoreticalSensitivityTest[0](/tmp/CollectTargetedMetrics3165096477504688295.bam, /tmp/test10629172057974704282.TargetedMetrics_Coverage, /tmp/test9186133411572913995.TheoreticalSensitivityMetrics, /tmp/perTarget9671349733280231197.perTargetCoverage, /mounts/lovelace/software/picard/picard/testdata/picard/reference/chrM.reference.fasta, testdata/picard/quality/chrM.single.interval_list, 2000, [0.01, 0.05, 0.1, 0.3, 0.5], [0.01, 0.54, 0.93, 0.99, 0.99]) |
3.082s |
passed |
| testCoverageGetTotalOverflow |
0s |
passed |
| testRawBqDistributionWithSoftClips |
0.015s |
passed |
Standard error
[Thu Apr 24 13:00:08 EDT 2025] CollectTargetedPcrMetrics --AMPLICON_INTERVALS testdata/picard/quality/chrM.single.interval_list --TARGET_INTERVALS testdata/picard/quality/chrM.single.interval_list --INPUT /tmp/CollectTargetedMetrics3165096477504688295.bam --OUTPUT /tmp/test10629172057974704282.TargetedMetrics_Coverage --METRIC_ACCUMULATION_LEVEL ALL_READS --PER_TARGET_COVERAGE /tmp/perTarget9671349733280231197.perTargetCoverage --SAMPLE_SIZE 1000 --REFERENCE_SEQUENCE /mounts/lovelace/software/picard/picard/testdata/picard/reference/chrM.reference.fasta --NEAR_DISTANCE 250 --MINIMUM_MAPPING_QUALITY 1 --MINIMUM_BASE_QUALITY 0 --CLIP_OVERLAPPING_READS false --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 13:00:08 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 0 sampling iterations completed
INFO 2025-04-24 13:00:08 TheoreticalSensitivity Calculating theoretical het sensitivity
INFO 2025-04-24 13:00:08 TargetMetricsCollector Calculating GC metrics
[Thu Apr 24 13:00:08 EDT 2025] picard.analysis.directed.CollectTargetedPcrMetrics done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 13:00:08 EDT 2025] CollectTargetedPcrMetrics --AMPLICON_INTERVALS testdata/picard/quality/chrM.empty.interval_list --TARGET_INTERVALS testdata/picard/quality/chrM.empty.interval_list --INPUT /tmp/CollectTargetedMetrics3165096477504688295.bam --OUTPUT /tmp/test10629172057974704282.TargetedMetrics_Coverage --METRIC_ACCUMULATION_LEVEL ALL_READS --PER_TARGET_COVERAGE /tmp/perTarget9671349733280231197.perTargetCoverage --SAMPLE_SIZE 1000 --REFERENCE_SEQUENCE /mounts/lovelace/software/picard/picard/testdata/picard/reference/chrM.reference.fasta --NEAR_DISTANCE 250 --MINIMUM_MAPPING_QUALITY 1 --MINIMUM_BASE_QUALITY 0 --CLIP_OVERLAPPING_READS false --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 13:00:08 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 0 sampling iterations completed
INFO 2025-04-24 13:00:08 TheoreticalSensitivity Calculating theoretical het sensitivity
INFO 2025-04-24 13:00:08 TargetMetricsCollector Calculating GC metrics
WARNING 2025-04-24 13:00:08 TargetMetricsCollector interval of length zero found: chrM:2-1 + interval-1 skipped.
[Thu Apr 24 13:00:08 EDT 2025] picard.analysis.directed.CollectTargetedPcrMetrics done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 13:00:08 EDT 2025] CollectTargetedPcrMetrics --AMPLICON_INTERVALS testdata/picard/quality/chrM.single.interval_list --TARGET_INTERVALS testdata/picard/quality/chrM.single.interval_list --INPUT /tmp/CollectTargetedMetrics3165096477504688295.bam --OUTPUT /tmp/test10629172057974704282.TargetedMetrics_Coverage --METRIC_ACCUMULATION_LEVEL ALL_READS --PER_TARGET_COVERAGE /tmp/perTarget9671349733280231197.perTargetCoverage --SAMPLE_SIZE 2000 --THEORETICAL_SENSITIVITY_OUTPUT /tmp/test9186133411572913995.TheoreticalSensitivityMetrics --REFERENCE_SEQUENCE /mounts/lovelace/software/picard/picard/testdata/picard/reference/chrM.reference.fasta --NEAR_DISTANCE 250 --MINIMUM_MAPPING_QUALITY 1 --MINIMUM_BASE_QUALITY 0 --CLIP_OVERLAPPING_READS false --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 13:00:08 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 13:00:09 TheoreticalSensitivity Creating Roulette Wheel
INFO 2025-04-24 13:00:09 TheoreticalSensitivity Calculating quality sums from quality sampler
INFO 2025-04-24 13:00:09 TheoreticalSensitivity 0 sampling iterations completed
INFO 2025-04-24 13:00:09 TheoreticalSensitivity 1000 sampling iterations completed
INFO 2025-04-24 13:00:09 TheoreticalSensitivity Calculating theoretical het sensitivity
INFO 2025-04-24 13:00:09 TargetMetricsCollector Calculating GC metrics
INFO 2025-04-24 13:00:09 CollectTargetedPcrMetrics Calculating theoretical sentitivity at 9 allele fractions.
[Thu Apr 24 13:00:11 EDT 2025] picard.analysis.directed.CollectTargetedPcrMetrics done. Elapsed time: 0.05 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 13:00:11 EDT 2025] CollectTargetedPcrMetrics --AMPLICON_INTERVALS testdata/picard/quality/chrM.single.interval_list --TARGET_INTERVALS testdata/picard/quality/chrM.single.interval_list --INPUT testdata/picard/quality/chrMReadsWithClips.sam --OUTPUT /tmp/test657209322347212772.TargetedMetrics_Coverage --METRIC_ACCUMULATION_LEVEL ALL_READS --SAMPLE_SIZE 0 --REFERENCE_SEQUENCE /mounts/lovelace/software/picard/picard/testdata/picard/reference/chrM.reference.fasta --NEAR_DISTANCE 250 --MINIMUM_MAPPING_QUALITY 1 --MINIMUM_BASE_QUALITY 0 --CLIP_OVERLAPPING_READS false --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 13:00:11 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 13:00:11 TheoreticalSensitivity Creating Roulette Wheel
INFO 2025-04-24 13:00:11 TheoreticalSensitivity Calculating quality sums from quality sampler
INFO 2025-04-24 13:00:11 TheoreticalSensitivity Calculating theoretical het sensitivity
INFO 2025-04-24 13:00:11 TargetMetricsCollector Calculating GC metrics
[Thu Apr 24 13:00:11 EDT 2025] picard.analysis.directed.CollectTargetedPcrMetrics done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824