Class picard.analysis.CollectWgsMetricsTest
|
100%
successful |
Tests
| Test | Duration | Result |
|---|---|---|
| testAdapterReads[0](false) | 0.119s | passed |
| testAdapterReads[1](true) | 0.105s | passed |
| testExclusions[0](false) | 0.213s | passed |
| testExclusions[1](true) | 0.198s | passed |
| testFailDifferentSequenceDictionaries | 0.013s | passed |
| testGiantDeletion[0](false) | 0.222s | passed |
| testGiantDeletion[1](true) | 0.217s | passed |
| testIntervalOneRead[0](false) | 1.254s | passed |
| testIntervalOneRead[1](true) | 1.222s | passed |
| testLargeIntervals[0](false) | 1.206s | passed |
| testLargeIntervals[1](true) | 1.205s | passed |
| testMetricsFromWGS[0](/tmp/picard.analysis.CollectWgsMetricsTest869842295701644325/setupBuilder18308094214879901259.bam, /mounts/lovelace/software/picard/picard/testdata/picard/reference/chrM.reference.fasta, false) | 0.617s | passed |
| testMetricsFromWGS[1](/tmp/picard.analysis.CollectWgsMetricsTest869842295701644325/setupBuilder18308094214879901259.bam, /mounts/lovelace/software/picard/picard/testdata/picard/reference/chrM.reference.fasta, true) | 0.319s | passed |
| testPoorQualityBases[0](false) | 0.211s | passed |
| testPoorQualityBases[1](true) | 0.209s | passed |
| testSmallIntervals[0](/tmp/picard.analysis.CollectWgsMetricsTest869842295701644325/setupBuilder18308094214879901259.bam, /mounts/lovelace/software/picard/picard/testdata/picard/reference/chrM.reference.fasta, false) | 0.925s | passed |
| testSmallIntervals[1](/tmp/picard.analysis.CollectWgsMetricsTest869842295701644325/setupBuilder18308094214879901259.bam, /mounts/lovelace/software/picard/picard/testdata/picard/reference/chrM.reference.fasta, true) | 0.614s | passed |
Standard error
[Thu Apr 24 12:59:25 EDT 2025] CollectWgsMetrics --INPUT /mounts/lovelace/software/picard/picard/testdata/picard/metrics/AlignedAdapterReads.sam --OUTPUT /tmp/picard.analysis.CollectWgsMetricsTest869842295701644325/testAdapterReads16595133398953341454.wgs_metrics --SAMPLE_SIZE 10 --USE_FAST_ALGORITHM false --REFERENCE_SEQUENCE /mounts/lovelace/software/picard/picard/testdata/picard/reference/chrM.reference.fasta --MINIMUM_MAPPING_QUALITY 20 --MINIMUM_BASE_QUALITY 20 --COVERAGE_CAP 250 --LOCUS_ACCUMULATION_CAP 100000 --STOP_AFTER -1 --INCLUDE_BQ_HISTOGRAM false --COUNT_UNPAIRED 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 --READ_LENGTH 150 --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 12:59:25 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 WARNING 2025-04-24 12:59:25 AbstractLocusIterator SamLocusIterator constructed with samReader that has SortOrder == unsorted. Assuming SAM is coordinate sorted, but exceptions may occur if it is not. INFO 2025-04-24 12:59:25 TheoreticalSensitivity Creating Roulette Wheel INFO 2025-04-24 12:59:25 TheoreticalSensitivity Calculating quality sums from quality sampler INFO 2025-04-24 12:59:25 TheoreticalSensitivity 0 sampling iterations completed INFO 2025-04-24 12:59:25 TheoreticalSensitivity Calculating theoretical het sensitivity [Thu Apr 24 12:59:25 EDT 2025] picard.analysis.CollectWgsMetrics done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 [Thu Apr 24 12:59:25 EDT 2025] CollectWgsMetrics --INPUT /mounts/lovelace/software/picard/picard/testdata/picard/metrics/AlignedAdapterReads.sam --OUTPUT /tmp/picard.analysis.CollectWgsMetricsTest869842295701644325/testAdapterReads17757585203795920351.wgs_metrics --SAMPLE_SIZE 10 --USE_FAST_ALGORITHM true --REFERENCE_SEQUENCE /mounts/lovelace/software/picard/picard/testdata/picard/reference/chrM.reference.fasta --MINIMUM_MAPPING_QUALITY 20 --MINIMUM_BASE_QUALITY 20 --COVERAGE_CAP 250 --LOCUS_ACCUMULATION_CAP 100000 --STOP_AFTER -1 --INCLUDE_BQ_HISTOGRAM false --COUNT_UNPAIRED 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 --READ_LENGTH 150 --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 12:59:25 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 WARNING 2025-04-24 12:59:25 AbstractLocusIterator EdgeReadIterator constructed with samReader that has SortOrder == unsorted. Assuming SAM is coordinate sorted, but exceptions may occur if it is not. INFO 2025-04-24 12:59:25 TheoreticalSensitivity Creating Roulette Wheel INFO 2025-04-24 12:59:25 TheoreticalSensitivity Calculating quality sums from quality sampler INFO 2025-04-24 12:59:25 TheoreticalSensitivity 0 sampling iterations completed INFO 2025-04-24 12:59:25 TheoreticalSensitivity Calculating theoretical het sensitivity [Thu Apr 24 12:59:25 EDT 2025] picard.analysis.CollectWgsMetrics done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 [Thu Apr 24 12:59:25 EDT 2025] CollectWgsMetrics --INPUT /tmp/picard.analysis.CollectWgsMetricsTest869842295701644325/testExclusions14615816803378171532.bam --OUTPUT /tmp/picard.analysis.CollectWgsMetricsTest869842295701644325/testExclusions17502549104755508984.txt --COVERAGE_CAP 3 --INCLUDE_BQ_HISTOGRAM true --USE_FAST_ALGORITHM false --REFERENCE_SEQUENCE /mounts/lovelace/software/picard/picard/testdata/picard/sam/merger.fasta --MINIMUM_MAPPING_QUALITY 20 --MINIMUM_BASE_QUALITY 20 --LOCUS_ACCUMULATION_CAP 100000 --STOP_AFTER -1 --COUNT_UNPAIRED false --SAMPLE_SIZE 10000 --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 --READ_LENGTH 150 --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 12:59:25 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 WARNING 2025-04-24 12:59:25 AbstractLocusIterator SamLocusIterator constructed with samReader that has SortOrder == unsorted. Assuming SAM is coordinate sorted, but exceptions may occur if it is not. INFO 2025-04-24 12:59:25 TheoreticalSensitivity Creating Roulette Wheel INFO 2025-04-24 12:59:25 TheoreticalSensitivity Calculating quality sums from quality sampler INFO 2025-04-24 12:59:25 TheoreticalSensitivity 0 sampling iterations completed INFO 2025-04-24 12:59:25 TheoreticalSensitivity 1000 sampling iterations completed INFO 2025-04-24 12:59:25 TheoreticalSensitivity 2000 sampling iterations completed INFO 2025-04-24 12:59:25 TheoreticalSensitivity 3000 sampling iterations completed INFO 2025-04-24 12:59:25 TheoreticalSensitivity 4000 sampling iterations completed INFO 2025-04-24 12:59:25 TheoreticalSensitivity 5000 sampling iterations completed INFO 2025-04-24 12:59:25 TheoreticalSensitivity 6000 sampling iterations completed INFO 2025-04-24 12:59:25 TheoreticalSensitivity 7000 sampling iterations completed INFO 2025-04-24 12:59:25 TheoreticalSensitivity 8000 sampling iterations completed INFO 2025-04-24 12:59:25 TheoreticalSensitivity 9000 sampling iterations completed INFO 2025-04-24 12:59:25 TheoreticalSensitivity Calculating theoretical het sensitivity [Thu Apr 24 12:59:25 EDT 2025] picard.analysis.CollectWgsMetrics done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 [Thu Apr 24 12:59:25 EDT 2025] CollectWgsMetrics --INPUT /tmp/picard.analysis.CollectWgsMetricsTest869842295701644325/testExclusions1479332077386708370.bam --OUTPUT /tmp/picard.analysis.CollectWgsMetricsTest869842295701644325/testExclusions3460166830973671920.txt --COVERAGE_CAP 3 --INCLUDE_BQ_HISTOGRAM true --USE_FAST_ALGORITHM true --REFERENCE_SEQUENCE /mounts/lovelace/software/picard/picard/testdata/picard/sam/merger.fasta --MINIMUM_MAPPING_QUALITY 20 --MINIMUM_BASE_QUALITY 20 --LOCUS_ACCUMULATION_CAP 100000 --STOP_AFTER -1 --COUNT_UNPAIRED false --SAMPLE_SIZE 10000 --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 --READ_LENGTH 150 --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 12:59:25 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 WARNING 2025-04-24 12:59:25 AbstractLocusIterator EdgeReadIterator constructed with samReader that has SortOrder == unsorted. Assuming SAM is coordinate sorted, but exceptions may occur if it is not. INFO 2025-04-24 12:59:25 TheoreticalSensitivity Creating Roulette Wheel INFO 2025-04-24 12:59:25 TheoreticalSensitivity Calculating quality sums from quality sampler INFO 2025-04-24 12:59:25 TheoreticalSensitivity 0 sampling iterations completed INFO 2025-04-24 12:59:25 TheoreticalSensitivity 1000 sampling iterations completed INFO 2025-04-24 12:59:25 TheoreticalSensitivity 2000 sampling iterations completed INFO 2025-04-24 12:59:25 TheoreticalSensitivity 3000 sampling iterations completed INFO 2025-04-24 12:59:25 TheoreticalSensitivity 4000 sampling iterations completed INFO 2025-04-24 12:59:25 TheoreticalSensitivity 5000 sampling iterations completed INFO 2025-04-24 12:59:25 TheoreticalSensitivity 6000 sampling iterations completed INFO 2025-04-24 12:59:25 TheoreticalSensitivity 7000 sampling iterations completed INFO 2025-04-24 12:59:26 TheoreticalSensitivity 8000 sampling iterations completed INFO 2025-04-24 12:59:26 TheoreticalSensitivity 9000 sampling iterations completed INFO 2025-04-24 12:59:26 TheoreticalSensitivity Calculating theoretical het sensitivity [Thu Apr 24 12:59:26 EDT 2025] picard.analysis.CollectWgsMetrics done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 [Thu Apr 24 12:59:26 EDT 2025] CollectWgsMetrics --INPUT /mounts/lovelace/software/picard/picard/testdata/picard/sam/forMetrics.sam --OUTPUT /tmp/picard.analysis.CollectWgsMetricsTest869842295701644325/test8472368466349823312.wgs_metrics --REFERENCE_SEQUENCE testdata/picard/reference/test.fasta --MINIMUM_MAPPING_QUALITY 20 --MINIMUM_BASE_QUALITY 20 --COVERAGE_CAP 250 --LOCUS_ACCUMULATION_CAP 100000 --STOP_AFTER -1 --INCLUDE_BQ_HISTOGRAM false --COUNT_UNPAIRED false --SAMPLE_SIZE 10000 --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 --USE_FAST_ALGORITHM false --READ_LENGTH 150 --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 12:59:26 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 [Thu Apr 24 12:59:26 EDT 2025] picard.analysis.CollectWgsMetrics done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp [Thu Apr 24 12:59:26 EDT 2025] CollectWgsMetrics --INPUT /tmp/picard.analysis.CollectWgsMetricsTest869842295701644325/testGiantDeletion13005212100998555319.bam --OUTPUT /tmp/picard.analysis.CollectWgsMetricsTest869842295701644325/testGiantDeletion7658248773350240496.txt --COVERAGE_CAP 3 --INCLUDE_BQ_HISTOGRAM true --USE_FAST_ALGORITHM false --REFERENCE_SEQUENCE /mounts/lovelace/software/picard/picard/testdata/picard/reference/chrM.reference.fasta --MINIMUM_MAPPING_QUALITY 20 --MINIMUM_BASE_QUALITY 20 --LOCUS_ACCUMULATION_CAP 100000 --STOP_AFTER -1 --COUNT_UNPAIRED false --SAMPLE_SIZE 10000 --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 --READ_LENGTH 150 --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 12:59:26 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 WARNING 2025-04-24 12:59:26 AbstractLocusIterator SamLocusIterator constructed with samReader that has SortOrder == unsorted. Assuming SAM is coordinate sorted, but exceptions may occur if it is not. INFO 2025-04-24 12:59:26 TheoreticalSensitivity Creating Roulette Wheel INFO 2025-04-24 12:59:26 TheoreticalSensitivity Calculating quality sums from quality sampler INFO 2025-04-24 12:59:26 TheoreticalSensitivity 0 sampling iterations completed INFO 2025-04-24 12:59:26 TheoreticalSensitivity 1000 sampling iterations completed INFO 2025-04-24 12:59:26 TheoreticalSensitivity 2000 sampling iterations completed INFO 2025-04-24 12:59:26 TheoreticalSensitivity 3000 sampling iterations completed INFO 2025-04-24 12:59:26 TheoreticalSensitivity 4000 sampling iterations completed INFO 2025-04-24 12:59:26 TheoreticalSensitivity 5000 sampling iterations completed INFO 2025-04-24 12:59:26 TheoreticalSensitivity 6000 sampling iterations completed INFO 2025-04-24 12:59:26 TheoreticalSensitivity 7000 sampling iterations completed INFO 2025-04-24 12:59:26 TheoreticalSensitivity 8000 sampling iterations completed INFO 2025-04-24 12:59:26 TheoreticalSensitivity 9000 sampling iterations completed INFO 2025-04-24 12:59:26 TheoreticalSensitivity Calculating theoretical het sensitivity [Thu Apr 24 12:59:26 EDT 2025] picard.analysis.CollectWgsMetrics done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 [Thu Apr 24 12:59:26 EDT 2025] CollectWgsMetrics --INPUT /tmp/picard.analysis.CollectWgsMetricsTest869842295701644325/testGiantDeletion4024953304086059223.bam --OUTPUT /tmp/picard.analysis.CollectWgsMetricsTest869842295701644325/testGiantDeletion8880238196058673422.txt --COVERAGE_CAP 3 --INCLUDE_BQ_HISTOGRAM true --USE_FAST_ALGORITHM true --REFERENCE_SEQUENCE /mounts/lovelace/software/picard/picard/testdata/picard/reference/chrM.reference.fasta --MINIMUM_MAPPING_QUALITY 20 --MINIMUM_BASE_QUALITY 20 --LOCUS_ACCUMULATION_CAP 100000 --STOP_AFTER -1 --COUNT_UNPAIRED false --SAMPLE_SIZE 10000 --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 --READ_LENGTH 150 --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 12:59:26 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 WARNING 2025-04-24 12:59:26 AbstractLocusIterator EdgeReadIterator constructed with samReader that has SortOrder == unsorted. Assuming SAM is coordinate sorted, but exceptions may occur if it is not. INFO 2025-04-24 12:59:26 TheoreticalSensitivity Creating Roulette Wheel INFO 2025-04-24 12:59:26 TheoreticalSensitivity Calculating quality sums from quality sampler INFO 2025-04-24 12:59:26 TheoreticalSensitivity 0 sampling iterations completed INFO 2025-04-24 12:59:26 TheoreticalSensitivity 1000 sampling iterations completed INFO 2025-04-24 12:59:26 TheoreticalSensitivity 2000 sampling iterations completed INFO 2025-04-24 12:59:26 TheoreticalSensitivity 3000 sampling iterations completed INFO 2025-04-24 12:59:26 TheoreticalSensitivity 4000 sampling iterations completed INFO 2025-04-24 12:59:26 TheoreticalSensitivity 5000 sampling iterations completed INFO 2025-04-24 12:59:26 TheoreticalSensitivity 6000 sampling iterations completed INFO 2025-04-24 12:59:26 TheoreticalSensitivity 7000 sampling iterations completed INFO 2025-04-24 12:59:26 TheoreticalSensitivity 8000 sampling iterations completed INFO 2025-04-24 12:59:26 TheoreticalSensitivity 9000 sampling iterations completed INFO 2025-04-24 12:59:26 TheoreticalSensitivity Calculating theoretical het sensitivity [Thu Apr 24 12:59:26 EDT 2025] picard.analysis.CollectWgsMetrics done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 [Thu Apr 24 12:59:26 EDT 2025] CollectWgsMetrics --INPUT /tmp/picard.analysis.CollectWgsMetricsTest869842295701644325/testIntervalOneRead7736349648279163209.bam --OUTPUT /tmp/picard.analysis.CollectWgsMetricsTest869842295701644325/testIntervalOneRead11458317286490994378.wgs_metrics --SAMPLE_SIZE 1000 --INTERVALS /mounts/lovelace/software/picard/picard/testdata/picard/sam/smallIntervals.interval_list --USE_FAST_ALGORITHM false --REFERENCE_SEQUENCE /mounts/lovelace/software/picard/picard/testdata/picard/reference/chrM.reference.fasta --MINIMUM_MAPPING_QUALITY 20 --MINIMUM_BASE_QUALITY 20 --COVERAGE_CAP 250 --LOCUS_ACCUMULATION_CAP 100000 --STOP_AFTER -1 --INCLUDE_BQ_HISTOGRAM false --COUNT_UNPAIRED 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 --READ_LENGTH 150 --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 12:59:26 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 WARNING 2025-04-24 12:59:26 AbstractLocusIterator SamLocusIterator constructed with samReader that has SortOrder == unsorted. Assuming SAM is coordinate sorted, but exceptions may occur if it is not. INFO 2025-04-24 12:59:26 TheoreticalSensitivity Creating Roulette Wheel INFO 2025-04-24 12:59:26 TheoreticalSensitivity Calculating quality sums from quality sampler INFO 2025-04-24 12:59:26 TheoreticalSensitivity 0 sampling iterations completed INFO 2025-04-24 12:59:27 TheoreticalSensitivity Calculating theoretical het sensitivity [Thu Apr 24 12:59:27 EDT 2025] picard.analysis.CollectWgsMetrics done. Elapsed time: 0.02 minutes. Runtime.totalMemory()=1073741824 [Thu Apr 24 12:59:27 EDT 2025] CollectWgsMetrics --INPUT /tmp/picard.analysis.CollectWgsMetricsTest869842295701644325/testIntervalOneRead6612476400501991414.bam --OUTPUT /tmp/picard.analysis.CollectWgsMetricsTest869842295701644325/testIntervalOneRead8808335097155050447.wgs_metrics --SAMPLE_SIZE 1000 --INTERVALS /mounts/lovelace/software/picard/picard/testdata/picard/sam/smallIntervals.interval_list --USE_FAST_ALGORITHM true --REFERENCE_SEQUENCE /mounts/lovelace/software/picard/picard/testdata/picard/reference/chrM.reference.fasta --MINIMUM_MAPPING_QUALITY 20 --MINIMUM_BASE_QUALITY 20 --COVERAGE_CAP 250 --LOCUS_ACCUMULATION_CAP 100000 --STOP_AFTER -1 --INCLUDE_BQ_HISTOGRAM false --COUNT_UNPAIRED 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 --READ_LENGTH 150 --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 12:59:27 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 WARNING 2025-04-24 12:59:27 AbstractLocusIterator EdgeReadIterator constructed with samReader that has SortOrder == unsorted. Assuming SAM is coordinate sorted, but exceptions may occur if it is not. INFO 2025-04-24 12:59:27 TheoreticalSensitivity Creating Roulette Wheel INFO 2025-04-24 12:59:27 TheoreticalSensitivity Calculating quality sums from quality sampler INFO 2025-04-24 12:59:27 TheoreticalSensitivity 0 sampling iterations completed INFO 2025-04-24 12:59:28 TheoreticalSensitivity Calculating theoretical het sensitivity [Thu Apr 24 12:59:28 EDT 2025] picard.analysis.CollectWgsMetrics done. Elapsed time: 0.02 minutes. Runtime.totalMemory()=1073741824 [Thu Apr 24 12:59:28 EDT 2025] CollectWgsMetrics --INPUT /mounts/lovelace/software/picard/picard/testdata/picard/sam/forMetrics.sam --OUTPUT /tmp/picard.analysis.CollectWgsMetricsTest869842295701644325/test14673342202125381989.wgs_metrics --SAMPLE_SIZE 1000 --INTERVALS /mounts/lovelace/software/picard/picard/testdata/picard/sam/largeIntervals.interval_list --USE_FAST_ALGORITHM false --REFERENCE_SEQUENCE /mounts/lovelace/software/picard/picard/testdata/picard/sam/merger.fasta --MINIMUM_MAPPING_QUALITY 20 --MINIMUM_BASE_QUALITY 20 --COVERAGE_CAP 250 --LOCUS_ACCUMULATION_CAP 100000 --STOP_AFTER -1 --INCLUDE_BQ_HISTOGRAM false --COUNT_UNPAIRED 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 --READ_LENGTH 150 --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 12:59:28 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 12:59:28 TheoreticalSensitivity Creating Roulette Wheel INFO 2025-04-24 12:59:28 TheoreticalSensitivity Calculating quality sums from quality sampler INFO 2025-04-24 12:59:28 TheoreticalSensitivity 0 sampling iterations completed INFO 2025-04-24 12:59:30 TheoreticalSensitivity Calculating theoretical het sensitivity [Thu Apr 24 12:59:30 EDT 2025] picard.analysis.CollectWgsMetrics done. Elapsed time: 0.02 minutes. Runtime.totalMemory()=1073741824 [Thu Apr 24 12:59:30 EDT 2025] CollectWgsMetrics --INPUT /mounts/lovelace/software/picard/picard/testdata/picard/sam/forMetrics.sam --OUTPUT /tmp/picard.analysis.CollectWgsMetricsTest869842295701644325/test10217951882490145260.wgs_metrics --SAMPLE_SIZE 1000 --INTERVALS /mounts/lovelace/software/picard/picard/testdata/picard/sam/largeIntervals.interval_list --USE_FAST_ALGORITHM true --REFERENCE_SEQUENCE /mounts/lovelace/software/picard/picard/testdata/picard/sam/merger.fasta --MINIMUM_MAPPING_QUALITY 20 --MINIMUM_BASE_QUALITY 20 --COVERAGE_CAP 250 --LOCUS_ACCUMULATION_CAP 100000 --STOP_AFTER -1 --INCLUDE_BQ_HISTOGRAM false --COUNT_UNPAIRED 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 --READ_LENGTH 150 --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 12:59:30 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 12:59:30 TheoreticalSensitivity Creating Roulette Wheel INFO 2025-04-24 12:59:30 TheoreticalSensitivity Calculating quality sums from quality sampler INFO 2025-04-24 12:59:30 TheoreticalSensitivity 0 sampling iterations completed INFO 2025-04-24 12:59:31 TheoreticalSensitivity Calculating theoretical het sensitivity [Thu Apr 24 12:59:31 EDT 2025] picard.analysis.CollectWgsMetrics done. Elapsed time: 0.02 minutes. Runtime.totalMemory()=1073741824 [Thu Apr 24 12:59:31 EDT 2025] CollectWgsMetrics --INPUT /tmp/picard.analysis.CollectWgsMetricsTest869842295701644325/setupBuilder18308094214879901259.bam --OUTPUT /tmp/picard.analysis.CollectWgsMetricsTest869842295701644325/testMetricsFromWGS9476874135358744951.wgs_metrics --SAMPLE_SIZE 1000 --USE_FAST_ALGORITHM false --REFERENCE_SEQUENCE /mounts/lovelace/software/picard/picard/testdata/picard/reference/chrM.reference.fasta --MINIMUM_MAPPING_QUALITY 20 --MINIMUM_BASE_QUALITY 20 --COVERAGE_CAP 250 --LOCUS_ACCUMULATION_CAP 100000 --STOP_AFTER -1 --INCLUDE_BQ_HISTOGRAM false --COUNT_UNPAIRED 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 --READ_LENGTH 150 --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 12:59:31 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 12:59:31 TheoreticalSensitivity Creating Roulette Wheel INFO 2025-04-24 12:59:31 TheoreticalSensitivity Calculating quality sums from quality sampler INFO 2025-04-24 12:59:31 TheoreticalSensitivity 0 sampling iterations completed INFO 2025-04-24 12:59:31 TheoreticalSensitivity Calculating theoretical het sensitivity [Thu Apr 24 12:59:32 EDT 2025] picard.analysis.CollectWgsMetrics done. Elapsed time: 0.01 minutes. Runtime.totalMemory()=1073741824 [Thu Apr 24 12:59:32 EDT 2025] CollectWgsMetrics --INPUT /tmp/picard.analysis.CollectWgsMetricsTest869842295701644325/setupBuilder18308094214879901259.bam --OUTPUT /tmp/picard.analysis.CollectWgsMetricsTest869842295701644325/testMetricsFromWGS7589738202660952137.wgs_metrics --SAMPLE_SIZE 1000 --USE_FAST_ALGORITHM true --REFERENCE_SEQUENCE /mounts/lovelace/software/picard/picard/testdata/picard/reference/chrM.reference.fasta --MINIMUM_MAPPING_QUALITY 20 --MINIMUM_BASE_QUALITY 20 --COVERAGE_CAP 250 --LOCUS_ACCUMULATION_CAP 100000 --STOP_AFTER -1 --INCLUDE_BQ_HISTOGRAM false --COUNT_UNPAIRED 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 --READ_LENGTH 150 --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 12:59:32 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 12:59:32 TheoreticalSensitivity Creating Roulette Wheel INFO 2025-04-24 12:59:32 TheoreticalSensitivity Calculating quality sums from quality sampler INFO 2025-04-24 12:59:32 TheoreticalSensitivity 0 sampling iterations completed INFO 2025-04-24 12:59:32 TheoreticalSensitivity Calculating theoretical het sensitivity [Thu Apr 24 12:59:32 EDT 2025] picard.analysis.CollectWgsMetrics done. Elapsed time: 0.01 minutes. Runtime.totalMemory()=1073741824 [Thu Apr 24 12:59:32 EDT 2025] CollectWgsMetrics --INPUT /tmp/CollectWgsMetrics167158926641919539.bam --OUTPUT /tmp/picard.analysis.CollectWgsMetricsTest869842295701644325/testPoorQualityBases9870342112667179232.txt --COVERAGE_CAP 3 --INCLUDE_BQ_HISTOGRAM true --USE_FAST_ALGORITHM false --REFERENCE_SEQUENCE /mounts/lovelace/software/picard/picard/testdata/picard/reference/chrM.reference.fasta --MINIMUM_MAPPING_QUALITY 20 --MINIMUM_BASE_QUALITY 20 --LOCUS_ACCUMULATION_CAP 100000 --STOP_AFTER -1 --COUNT_UNPAIRED false --SAMPLE_SIZE 10000 --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 --READ_LENGTH 150 --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 12:59:32 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 WARNING 2025-04-24 12:59:32 AbstractLocusIterator SamLocusIterator constructed with samReader that has SortOrder == unsorted. Assuming SAM is coordinate sorted, but exceptions may occur if it is not. INFO 2025-04-24 12:59:32 TheoreticalSensitivity Creating Roulette Wheel INFO 2025-04-24 12:59:32 TheoreticalSensitivity Calculating quality sums from quality sampler INFO 2025-04-24 12:59:32 TheoreticalSensitivity 0 sampling iterations completed INFO 2025-04-24 12:59:32 TheoreticalSensitivity 1000 sampling iterations completed INFO 2025-04-24 12:59:32 TheoreticalSensitivity 2000 sampling iterations completed INFO 2025-04-24 12:59:32 TheoreticalSensitivity 3000 sampling iterations completed INFO 2025-04-24 12:59:32 TheoreticalSensitivity 4000 sampling iterations completed INFO 2025-04-24 12:59:32 TheoreticalSensitivity 5000 sampling iterations completed INFO 2025-04-24 12:59:32 TheoreticalSensitivity 6000 sampling iterations completed INFO 2025-04-24 12:59:32 TheoreticalSensitivity 7000 sampling iterations completed INFO 2025-04-24 12:59:32 TheoreticalSensitivity 8000 sampling iterations completed INFO 2025-04-24 12:59:32 TheoreticalSensitivity 9000 sampling iterations completed INFO 2025-04-24 12:59:32 TheoreticalSensitivity Calculating theoretical het sensitivity [Thu Apr 24 12:59:32 EDT 2025] picard.analysis.CollectWgsMetrics done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 [Thu Apr 24 12:59:32 EDT 2025] CollectWgsMetrics --INPUT /tmp/CollectWgsMetrics16241630922609086211.bam --OUTPUT /tmp/picard.analysis.CollectWgsMetricsTest869842295701644325/testPoorQualityBases6412173062781353422.txt --COVERAGE_CAP 3 --INCLUDE_BQ_HISTOGRAM true --USE_FAST_ALGORITHM true --REFERENCE_SEQUENCE /mounts/lovelace/software/picard/picard/testdata/picard/reference/chrM.reference.fasta --MINIMUM_MAPPING_QUALITY 20 --MINIMUM_BASE_QUALITY 20 --LOCUS_ACCUMULATION_CAP 100000 --STOP_AFTER -1 --COUNT_UNPAIRED false --SAMPLE_SIZE 10000 --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 --READ_LENGTH 150 --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 12:59:32 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 WARNING 2025-04-24 12:59:32 AbstractLocusIterator EdgeReadIterator constructed with samReader that has SortOrder == unsorted. Assuming SAM is coordinate sorted, but exceptions may occur if it is not. INFO 2025-04-24 12:59:32 TheoreticalSensitivity Creating Roulette Wheel INFO 2025-04-24 12:59:32 TheoreticalSensitivity Calculating quality sums from quality sampler INFO 2025-04-24 12:59:32 TheoreticalSensitivity 0 sampling iterations completed INFO 2025-04-24 12:59:32 TheoreticalSensitivity 1000 sampling iterations completed INFO 2025-04-24 12:59:32 TheoreticalSensitivity 2000 sampling iterations completed INFO 2025-04-24 12:59:32 TheoreticalSensitivity 3000 sampling iterations completed INFO 2025-04-24 12:59:32 TheoreticalSensitivity 4000 sampling iterations completed INFO 2025-04-24 12:59:32 TheoreticalSensitivity 5000 sampling iterations completed INFO 2025-04-24 12:59:32 TheoreticalSensitivity 6000 sampling iterations completed INFO 2025-04-24 12:59:32 TheoreticalSensitivity 7000 sampling iterations completed INFO 2025-04-24 12:59:32 TheoreticalSensitivity 8000 sampling iterations completed INFO 2025-04-24 12:59:32 TheoreticalSensitivity 9000 sampling iterations completed INFO 2025-04-24 12:59:32 TheoreticalSensitivity Calculating theoretical het sensitivity [Thu Apr 24 12:59:32 EDT 2025] picard.analysis.CollectWgsMetrics done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 [Thu Apr 24 12:59:32 EDT 2025] CollectWgsMetrics --INPUT /tmp/picard.analysis.CollectWgsMetricsTest869842295701644325/setupBuilder18308094214879901259.bam --OUTPUT /tmp/picard.analysis.CollectWgsMetricsTest869842295701644325/testSmallIntervals232591413768169483.wgs_metrics --COVERAGE_CAP 40000 --SAMPLE_SIZE 1000 --INTERVALS /mounts/lovelace/software/picard/picard/testdata/picard/sam/smallIntervals.interval_list --USE_FAST_ALGORITHM false --REFERENCE_SEQUENCE /mounts/lovelace/software/picard/picard/testdata/picard/reference/chrM.reference.fasta --MINIMUM_MAPPING_QUALITY 20 --MINIMUM_BASE_QUALITY 20 --LOCUS_ACCUMULATION_CAP 100000 --STOP_AFTER -1 --INCLUDE_BQ_HISTOGRAM false --COUNT_UNPAIRED 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 --READ_LENGTH 150 --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 12:59:32 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 12:59:33 TheoreticalSensitivity Creating Roulette Wheel INFO 2025-04-24 12:59:33 TheoreticalSensitivity Calculating quality sums from quality sampler INFO 2025-04-24 12:59:33 TheoreticalSensitivity 0 sampling iterations completed INFO 2025-04-24 12:59:33 TheoreticalSensitivity Calculating theoretical het sensitivity [Thu Apr 24 12:59:33 EDT 2025] picard.analysis.CollectWgsMetrics done. Elapsed time: 0.01 minutes. Runtime.totalMemory()=1073741824 [Thu Apr 24 12:59:33 EDT 2025] CollectWgsMetrics --INPUT /tmp/picard.analysis.CollectWgsMetricsTest869842295701644325/setupBuilder18308094214879901259.bam --OUTPUT /tmp/picard.analysis.CollectWgsMetricsTest869842295701644325/testSmallIntervals959923825708010285.wgs_metrics --COVERAGE_CAP 40000 --SAMPLE_SIZE 1000 --INTERVALS /mounts/lovelace/software/picard/picard/testdata/picard/sam/smallIntervals.interval_list --USE_FAST_ALGORITHM true --REFERENCE_SEQUENCE /mounts/lovelace/software/picard/picard/testdata/picard/reference/chrM.reference.fasta --MINIMUM_MAPPING_QUALITY 20 --MINIMUM_BASE_QUALITY 20 --LOCUS_ACCUMULATION_CAP 100000 --STOP_AFTER -1 --INCLUDE_BQ_HISTOGRAM false --COUNT_UNPAIRED 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 --READ_LENGTH 150 --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 12:59:33 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 12:59:33 TheoreticalSensitivity Creating Roulette Wheel INFO 2025-04-24 12:59:33 TheoreticalSensitivity Calculating quality sums from quality sampler INFO 2025-04-24 12:59:33 TheoreticalSensitivity 0 sampling iterations completed INFO 2025-04-24 12:59:34 TheoreticalSensitivity Calculating theoretical het sensitivity [Thu Apr 24 12:59:34 EDT 2025] picard.analysis.CollectWgsMetrics done. Elapsed time: 0.01 minutes. Runtime.totalMemory()=1073741824