Class picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigarTest
|
100%
successful |
Tests
| Test | Duration | Result |
|---|---|---|
| testBulkFragmentsNoDuplicates[0](.sam) | 0.532s | passed |
| testBulkFragmentsNoDuplicates[1](.bam) | 0.540s | passed |
| testBulkFragmentsNoDuplicates[2](.cram) | 0.951s | passed |
| testBulkFragmentsWithDuplicates[0](.sam) | 0.753s | passed |
| testBulkFragmentsWithDuplicates[1](.bam) | 0.807s | passed |
| testBulkFragmentsWithDuplicates[2](.cram) | 1.441s | passed |
| testBulkPairsNoDuplicates[0](.sam) | 0.883s | passed |
| testBulkPairsNoDuplicates[1](.bam) | 0.916s | passed |
| testBulkPairsNoDuplicates[2](.cram) | 1.560s | passed |
| testBulkPairsWithDuplicates[0](.sam) | 0.491s | passed |
| testBulkPairsWithDuplicates[1](.bam) | 0.547s | passed |
| testBulkPairsWithDuplicates[2](.cram) | 0.775s | passed |
| testDifferentChromosomesInOppositeOrder | 0.010s | passed |
| testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[0](true, true, true) | 0.009s | passed |
| testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[1](true, false, true) | 0.008s | passed |
| testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[2](false, true, true) | 0.007s | passed |
| testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[3](true, true, false) | 0.007s | passed |
| testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[4](true, false, false) | 0.007s | passed |
| testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[5](false, true, false) | 0.007s | passed |
| testMappedFragmentAndMappedPairFirstOfPairNonPrimary | 0.006s | passed |
| testMappedFragmentAndMatePairFirstUnmapped | 0.007s | passed |
| testMappedFragmentAndMatePairSecondUnmapped | 0.007s | passed |
| testMappedPairAndMappedFragmentAndMatePairFirstUnmapped | 0.007s | passed |
| testMappedPairAndMappedFragmentAndMatePairSecondUnmapped | 0.007s | passed |
| testMappedPairAndMatePairFirstOppositeStrandSecondUnmapped | 0.007s | passed |
| testMappedPairAndMatePairFirstUnmapped | 0.007s | passed |
| testMappedPairAndMatePairSecondUnmapped | 0.007s | passed |
| testMappedPairWithFirstEndSamePositionAndOther | 0.007s | passed |
| testMappedPairWithSamePosition | 0.007s | passed |
| testMappedPairWithSamePositionSameCigar | 0.006s | passed |
| testMatePairFirstUnmapped | 0.006s | passed |
| testMatePairSecondUnmapped | 0.006s | passed |
| testOpticalDuplicateBehaviorNullRegex | 0.007s | passed |
| testOpticalDuplicateClusterOneEndSamePositionOneCluster | 0.007s | passed |
| testOpticalDuplicateClusterSamePositionNoOpticalDuplicatesWithinPixelDistance | 0.007s | passed |
| testOpticalDuplicateClusterSamePositionOneOpticalDuplicatesWithinPixelDistance | 0.007s | passed |
| testOpticalDuplicateClustersAddingSecondEndFirstSameCoordinate | 0.006s | passed |
| testOpticalDuplicateFinding | 0.007s | passed |
| testPathologicalOrderingAtTheSamePosition | 0.007s | passed |
| testSecondEndIsBeforeFirstInCoordinate | 0.007s | passed |
| testSingleMappedFragment | 0.007s | passed |
| testSingleMappedFragmentAndSingleMappedPair | 0.006s | passed |
| testSingleMappedFragmentAndTwoMappedPairs | 0.007s | passed |
| testSingleMappedPair | 0.006s | passed |
| testSingleUnmappedFragment | 0.006s | passed |
| testSingleUnmappedPair | 0.007s | passed |
| testStackOverFlowPairSetSwap | 0.008s | passed |
| testThreeGroupsOnDifferentChromosomesOfThreeMappedPairs | 0.008s | passed |
| testThreeMappedPairs | 0.008s | passed |
| testThreeMappedPairsWithMatchingSecondMate | 0.007s | passed |
| testTwoGroupsOnDifferentChromosomesOfThreeMappedPairs | 0.008s | passed |
| testTwoGroupsOnDifferentChromosomesOfTwoFragments | 0.007s | passed |
| testTwoGroupsOnDifferentChromosomesOfTwoMappedPairs | 0.007s | passed |
| testTwoMappedFragments | 0.007s | passed |
| testTwoMappedPairWithSamePosition | 0.007s | passed |
| testTwoMappedPairWithSamePositionDifferentStrands | 0.007s | passed |
| testTwoMappedPairWithSamePositionDifferentStrands2 | 0.007s | passed |
| testTwoMappedPairs | 0.007s | passed |
| testTwoMappedPairsAndMappedSecondaryFragment | 0.007s | passed |
| testTwoMappedPairsAndTerminalUnmappedFragment | 0.007s | passed |
| testTwoMappedPairsAndTerminalUnmappedPair | 0.008s | passed |
| testTwoMappedPairsMatesSoftClipped | 0.007s | passed |
| testTwoMappedPairsWithOppositeOrientations | 0.007s | passed |
| testTwoMappedPairsWithOppositeOrientationsNumberTwo | 0.007s | passed |
| testTwoMappedPairsWithSoftClipping | 0.008s | passed |
| testTwoMappedPairsWithSoftClippingBoth | 0.007s | passed |
| testTwoMappedPairsWithSoftClippingFirstOfPairOnlyNoMateCigar | 0.007s | passed |
| testTwoMappedPairsWithSupplementaryReadsAfterCanonical[0](true, true, true) | 0.007s | passed |
| testTwoMappedPairsWithSupplementaryReadsAfterCanonical[1](true, false, true) | 0.007s | passed |
| testTwoMappedPairsWithSupplementaryReadsAfterCanonical[2](false, true, true) | 0.006s | passed |
| testTwoMappedPairsWithSupplementaryReadsAfterCanonical[3](true, true, false) | 0.008s | passed |
| testTwoMappedPairsWithSupplementaryReadsAfterCanonical[4](true, false, false) | 0.007s | passed |
| testTwoMappedPairsWithSupplementaryReadsAfterCanonical[5](false, true, false) | 0.006s | passed |
| testTwoMappedPairsWithSupplementaryReads[0](true, true, true) | 0.006s | passed |
| testTwoMappedPairsWithSupplementaryReads[1](true, false, true) | 0.007s | passed |
| testTwoMappedPairsWithSupplementaryReads[2](false, true, true) | 0.007s | passed |
| testTwoMappedPairsWithSupplementaryReads[3](true, true, false) | 0.007s | passed |
| testTwoMappedPairsWithSupplementaryReads[4](true, false, false) | 0.007s | passed |
| testTwoMappedPairsWithSupplementaryReads[5](false, true, false) | 0.007s | passed |
| testTwoUnmappedFragments | 0.006s | passed |
Standard error
[Thu Apr 24 13:17:13 EDT 2025] SimpleMarkDuplicatesWithMateCigar --INPUT /tmp/SimpleMarkDuplicatesWithMateCigarTester.tmp1919594112961887208/input.sam --OUTPUT /tmp/SimpleMarkDuplicatesWithMateCigarTester.tmp1919594112961887208/output.sam --METRICS_FILE /tmp/SimpleMarkDuplicatesWithMateCigarTester.tmp1919594112961887208/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_RECORDS_IN_RAM 1000 --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --TAGGING_POLICY DontTag --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_END_IN_UNPAIRED_READS false --FLOW_USE_UNPAIRED_CLIPPED_END false --FLOW_UNPAIRED_END_UNCERTAINTY 0 --FLOW_UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME SimpleMarkDuplicatesWithMateCigar --READ_NAME_REGEX <optimized capture of last three ':' separated fields as numeric values> --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:17:13 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 13:17:13 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. INFO 2025-04-24 13:17:13 MarkDuplicatesWithMateCigar Processed 10000 records INFO 2025-04-24 13:17:13 MarkDuplicatesWithMateCigar Marking 0 records as duplicates. [Thu Apr 24 13:17:13 EDT 2025] picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigar done. Elapsed time: 0.01 minutes. Runtime.totalMemory()=1073741824 [Thu Apr 24 13:17:13 EDT 2025] SimpleMarkDuplicatesWithMateCigar --INPUT /tmp/SimpleMarkDuplicatesWithMateCigarTester.tmp9634810031178437045/input.bam --OUTPUT /tmp/SimpleMarkDuplicatesWithMateCigarTester.tmp9634810031178437045/output.sam --METRICS_FILE /tmp/SimpleMarkDuplicatesWithMateCigarTester.tmp9634810031178437045/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_RECORDS_IN_RAM 1000 --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --TAGGING_POLICY DontTag --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_END_IN_UNPAIRED_READS false --FLOW_USE_UNPAIRED_CLIPPED_END false --FLOW_UNPAIRED_END_UNCERTAINTY 0 --FLOW_UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME SimpleMarkDuplicatesWithMateCigar --READ_NAME_REGEX <optimized capture of last three ':' separated fields as numeric values> --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:17:13 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 13:17:14 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. INFO 2025-04-24 13:17:14 MarkDuplicatesWithMateCigar Processed 10000 records INFO 2025-04-24 13:17:14 MarkDuplicatesWithMateCigar Marking 0 records as duplicates. [Thu Apr 24 13:17:14 EDT 2025] picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigar done. Elapsed time: 0.01 minutes. Runtime.totalMemory()=1073741824 [Thu Apr 24 13:17:14 EDT 2025] SimpleMarkDuplicatesWithMateCigar --INPUT /tmp/SimpleMarkDuplicatesWithMateCigarTester.tmp4457060519207763634/input.cram --OUTPUT /tmp/SimpleMarkDuplicatesWithMateCigarTester.tmp4457060519207763634/output.sam --METRICS_FILE /tmp/SimpleMarkDuplicatesWithMateCigarTester.tmp4457060519207763634/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_RECORDS_IN_RAM 1000 --REFERENCE_SEQUENCE /tmp/SamFileTester12223679953548937998/input.fasta --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --TAGGING_POLICY DontTag --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_END_IN_UNPAIRED_READS false --FLOW_USE_UNPAIRED_CLIPPED_END false --FLOW_UNPAIRED_END_UNCERTAINTY 0 --FLOW_UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME SimpleMarkDuplicatesWithMateCigar --READ_NAME_REGEX <optimized capture of last three ':' separated fields as numeric values> --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:17:14 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 13:17:15 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. INFO 2025-04-24 13:17:15 MarkDuplicatesWithMateCigar Processed 10000 records INFO 2025-04-24 13:17:15 MarkDuplicatesWithMateCigar Marking 0 records as duplicates. [Thu Apr 24 13:17:15 EDT 2025] picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigar done. Elapsed time: 0.01 minutes. Runtime.totalMemory()=1073741824 [Thu Apr 24 13:17:15 EDT 2025] SimpleMarkDuplicatesWithMateCigar --INPUT /tmp/SimpleMarkDuplicatesWithMateCigarTester.tmp10439788063084926910/input.sam --OUTPUT /tmp/SimpleMarkDuplicatesWithMateCigarTester.tmp10439788063084926910/output.sam --METRICS_FILE /tmp/SimpleMarkDuplicatesWithMateCigarTester.tmp10439788063084926910/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_RECORDS_IN_RAM 1000 --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --TAGGING_POLICY DontTag --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_END_IN_UNPAIRED_READS false --FLOW_USE_UNPAIRED_CLIPPED_END false --FLOW_UNPAIRED_END_UNCERTAINTY 0 --FLOW_UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME SimpleMarkDuplicatesWithMateCigar --READ_NAME_REGEX <optimized capture of last three ':' separated fields as numeric values> --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:17:15 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 13:17:16 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. INFO 2025-04-24 13:17:16 MarkDuplicatesWithMateCigar Processed 21000 records INFO 2025-04-24 13:17:16 MarkDuplicatesWithMateCigar Marking 20000 records as duplicates. [Thu Apr 24 13:17:16 EDT 2025] picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigar done. Elapsed time: 0.01 minutes. Runtime.totalMemory()=1073741824 [Thu Apr 24 13:17:16 EDT 2025] SimpleMarkDuplicatesWithMateCigar --INPUT /tmp/SimpleMarkDuplicatesWithMateCigarTester.tmp6991762697347916319/input.bam --OUTPUT /tmp/SimpleMarkDuplicatesWithMateCigarTester.tmp6991762697347916319/output.sam --METRICS_FILE /tmp/SimpleMarkDuplicatesWithMateCigarTester.tmp6991762697347916319/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_RECORDS_IN_RAM 1000 --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --TAGGING_POLICY DontTag --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_END_IN_UNPAIRED_READS false --FLOW_USE_UNPAIRED_CLIPPED_END false --FLOW_UNPAIRED_END_UNCERTAINTY 0 --FLOW_UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME SimpleMarkDuplicatesWithMateCigar --READ_NAME_REGEX <optimized capture of last three ':' separated fields as numeric values> --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:17:16 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 13:17:16 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. INFO 2025-04-24 13:17:16 MarkDuplicatesWithMateCigar Processed 21000 records INFO 2025-04-24 13:17:16 MarkDuplicatesWithMateCigar Marking 20000 records as duplicates. [Thu Apr 24 13:17:16 EDT 2025] picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigar done. Elapsed time: 0.01 minutes. Runtime.totalMemory()=1073741824 [Thu Apr 24 13:17:17 EDT 2025] SimpleMarkDuplicatesWithMateCigar --INPUT /tmp/SimpleMarkDuplicatesWithMateCigarTester.tmp10551245355813574042/input.cram --OUTPUT /tmp/SimpleMarkDuplicatesWithMateCigarTester.tmp10551245355813574042/output.sam --METRICS_FILE /tmp/SimpleMarkDuplicatesWithMateCigarTester.tmp10551245355813574042/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_RECORDS_IN_RAM 1000 --REFERENCE_SEQUENCE /tmp/SamFileTester7865029592334370029/input.fasta --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --TAGGING_POLICY DontTag --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_END_IN_UNPAIRED_READS false --FLOW_USE_UNPAIRED_CLIPPED_END false --FLOW_UNPAIRED_END_UNCERTAINTY 0 --FLOW_UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME SimpleMarkDuplicatesWithMateCigar --READ_NAME_REGEX <optimized capture of last three ':' separated fields as numeric values> --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:17:17 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 13:17:18 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. INFO 2025-04-24 13:17:18 MarkDuplicatesWithMateCigar Processed 21000 records INFO 2025-04-24 13:17:18 MarkDuplicatesWithMateCigar Marking 20000 records as duplicates. [Thu Apr 24 13:17:18 EDT 2025] picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigar done. Elapsed time: 0.01 minutes. Runtime.totalMemory()=1073741824 [Thu Apr 24 13:17:18 EDT 2025] SimpleMarkDuplicatesWithMateCigar --INPUT /tmp/SimpleMarkDuplicatesWithMateCigarTester.tmp9315695296917035731/input.sam --OUTPUT /tmp/SimpleMarkDuplicatesWithMateCigarTester.tmp9315695296917035731/output.sam --METRICS_FILE /tmp/SimpleMarkDuplicatesWithMateCigarTester.tmp9315695296917035731/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_RECORDS_IN_RAM 1000 --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --TAGGING_POLICY DontTag --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_END_IN_UNPAIRED_READS false --FLOW_USE_UNPAIRED_CLIPPED_END false --FLOW_UNPAIRED_END_UNCERTAINTY 0 --FLOW_UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME SimpleMarkDuplicatesWithMateCigar --READ_NAME_REGEX <optimized capture of last three ':' separated fields as numeric values> --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:17:18 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 13:17:18 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. INFO 2025-04-24 13:17:19 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. INFO 2025-04-24 13:17:19 MarkDuplicatesWithMateCigar Processed 20200 records INFO 2025-04-24 13:17:19 MarkDuplicatesWithMateCigar Marking 0 records as duplicates. [Thu Apr 24 13:17:19 EDT 2025] picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigar done. Elapsed time: 0.01 minutes. Runtime.totalMemory()=1073741824 [Thu Apr 24 13:17:19 EDT 2025] SimpleMarkDuplicatesWithMateCigar --INPUT /tmp/SimpleMarkDuplicatesWithMateCigarTester.tmp9629477509729920846/input.bam --OUTPUT /tmp/SimpleMarkDuplicatesWithMateCigarTester.tmp9629477509729920846/output.sam --METRICS_FILE /tmp/SimpleMarkDuplicatesWithMateCigarTester.tmp9629477509729920846/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_RECORDS_IN_RAM 1000 --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --TAGGING_POLICY DontTag --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_END_IN_UNPAIRED_READS false --FLOW_USE_UNPAIRED_CLIPPED_END false --FLOW_UNPAIRED_END_UNCERTAINTY 0 --FLOW_UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME SimpleMarkDuplicatesWithMateCigar --READ_NAME_REGEX <optimized capture of last three ':' separated fields as numeric values> --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:17:19 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 13:17:19 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. INFO 2025-04-24 13:17:20 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. INFO 2025-04-24 13:17:20 MarkDuplicatesWithMateCigar Processed 20200 records INFO 2025-04-24 13:17:20 MarkDuplicatesWithMateCigar Marking 0 records as duplicates. [Thu Apr 24 13:17:20 EDT 2025] picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigar done. Elapsed time: 0.01 minutes. Runtime.totalMemory()=1073741824 [Thu Apr 24 13:17:20 EDT 2025] SimpleMarkDuplicatesWithMateCigar --INPUT /tmp/SimpleMarkDuplicatesWithMateCigarTester.tmp3913484232991751205/input.cram --OUTPUT /tmp/SimpleMarkDuplicatesWithMateCigarTester.tmp3913484232991751205/output.sam --METRICS_FILE /tmp/SimpleMarkDuplicatesWithMateCigarTester.tmp3913484232991751205/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_RECORDS_IN_RAM 1000 --REFERENCE_SEQUENCE /tmp/SamFileTester18411208722120017735/input.fasta --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --TAGGING_POLICY DontTag --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_END_IN_UNPAIRED_READS false --FLOW_USE_UNPAIRED_CLIPPED_END false --FLOW_UNPAIRED_END_UNCERTAINTY 0 --FLOW_UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME SimpleMarkDuplicatesWithMateCigar --READ_NAME_REGEX <optimized capture of last three ':' separated fields as numeric values> --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:17:20 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 13:17:21 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. INFO 2025-04-24 13:17:21 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. INFO 2025-04-24 13:17:21 MarkDuplicatesWithMateCigar Processed 20200 records INFO 2025-04-24 13:17:21 MarkDuplicatesWithMateCigar Marking 0 records as duplicates. [Thu Apr 24 13:17:21 EDT 2025] picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigar done. Elapsed time: 0.01 minutes. Runtime.totalMemory()=1073741824 [Thu Apr 24 13:17:21 EDT 2025] SimpleMarkDuplicatesWithMateCigar --INPUT /tmp/SimpleMarkDuplicatesWithMateCigarTester.tmp9254464258706891338/input.sam --OUTPUT /tmp/SimpleMarkDuplicatesWithMateCigarTester.tmp9254464258706891338/output.sam --METRICS_FILE /tmp/SimpleMarkDuplicatesWithMateCigarTester.tmp9254464258706891338/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_RECORDS_IN_RAM 1000 --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --TAGGING_POLICY DontTag --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_END_IN_UNPAIRED_READS false --FLOW_USE_UNPAIRED_CLIPPED_END false --FLOW_UNPAIRED_END_UNCERTAINTY 0 --FLOW_UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME SimpleMarkDuplicatesWithMateCigar --READ_NAME_REGEX <optimized capture of last three ':' separated fields as numeric values> --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:17:21 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 13:17:21 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. INFO 2025-04-24 13:17:22 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. INFO 2025-04-24 13:17:22 MarkDuplicatesWithMateCigar Processed 6820 records INFO 2025-04-24 13:17:22 MarkDuplicatesWithMateCigar Marking 6200 records as duplicates. [Thu Apr 24 13:17:22 EDT 2025] picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigar done. Elapsed time: 0.01 minutes. Runtime.totalMemory()=1073741824 [Thu Apr 24 13:17:22 EDT 2025] SimpleMarkDuplicatesWithMateCigar --INPUT /tmp/SimpleMarkDuplicatesWithMateCigarTester.tmp11561636090238426134/input.bam --OUTPUT /tmp/SimpleMarkDuplicatesWithMateCigarTester.tmp11561636090238426134/output.sam --METRICS_FILE /tmp/SimpleMarkDuplicatesWithMateCigarTester.tmp11561636090238426134/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_RECORDS_IN_RAM 1000 --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --TAGGING_POLICY DontTag --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_END_IN_UNPAIRED_READS false --FLOW_USE_UNPAIRED_CLIPPED_END false --FLOW_UNPAIRED_END_UNCERTAINTY 0 --FLOW_UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME SimpleMarkDuplicatesWithMateCigar --READ_NAME_REGEX <optimized capture of last three ':' separated fields as numeric values> --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:17:22 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 13:17:22 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. INFO 2025-04-24 13:17:22 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. INFO 2025-04-24 13:17:22 MarkDuplicatesWithMateCigar Processed 6820 records INFO 2025-04-24 13:17:22 MarkDuplicatesWithMateCigar Marking 6200 records as duplicates. [Thu Apr 24 13:17:22 EDT 2025] picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigar done. Elapsed time: 0.01 minutes. Runtime.totalMemory()=1073741824 [Thu Apr 24 13:17:23 EDT 2025] SimpleMarkDuplicatesWithMateCigar --INPUT /tmp/SimpleMarkDuplicatesWithMateCigarTester.tmp15856242783122561197/input.cram --OUTPUT /tmp/SimpleMarkDuplicatesWithMateCigarTester.tmp15856242783122561197/output.sam --METRICS_FILE /tmp/SimpleMarkDuplicatesWithMateCigarTester.tmp15856242783122561197/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_RECORDS_IN_RAM 1000 --REFERENCE_SEQUENCE /tmp/SamFileTester17695884752373913413/input.fasta --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --TAGGING_POLICY DontTag --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_END_IN_UNPAIRED_READS false --FLOW_USE_UNPAIRED_CLIPPED_END false --FLOW_UNPAIRED_END_UNCERTAINTY 0 --FLOW_UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME SimpleMarkDuplicatesWithMateCigar --READ_NAME_REGEX <optimized capture of last three ':' separated fields as numeric values> --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:17:23 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 13:17:23 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. INFO 2025-04-24 13:17:23 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. INFO 2025-04-24 13:17:23 MarkDuplicatesWithMateCigar Processed 6820 records INFO 2025-04-24 13:17:23 MarkDuplicatesWithMateCigar Marking 6200 records as duplicates. [Thu Apr 24 13:17:23 EDT 2025] picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigar done. Elapsed time: 0.01 minutes. Runtime.totalMemory()=1073741824 [Thu Apr 24 13:17:23 EDT 2025] SimpleMarkDuplicatesWithMateCigar --INPUT /tmp/SimpleMarkDuplicatesWithMateCigarTester.tmp15286323640500617313/input.sam --OUTPUT /tmp/SimpleMarkDuplicatesWithMateCigarTester.tmp15286323640500617313/output.sam --METRICS_FILE /tmp/SimpleMarkDuplicatesWithMateCigarTester.tmp15286323640500617313/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_RECORDS_IN_RAM 1000 --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --TAGGING_POLICY DontTag --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_END_IN_UNPAIRED_READS false --FLOW_USE_UNPAIRED_CLIPPED_END false --FLOW_UNPAIRED_END_UNCERTAINTY 0 --FLOW_UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME SimpleMarkDuplicatesWithMateCigar --READ_NAME_REGEX <optimized capture of last three ':' separated fields as numeric values> --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:17:23 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 13:17:23 MarkDuplicatesWithMateCigar Found 1 optical duplicate clusters. INFO 2025-04-24 13:17:23 MarkDuplicatesWithMateCigar Processed 4 records INFO 2025-04-24 13:17:23 MarkDuplicatesWithMateCigar Marking 2 records as duplicates. [Thu Apr 24 13:17:23 EDT 2025] picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 [Thu Apr 24 13:17:23 EDT 2025] SimpleMarkDuplicatesWithMateCigar --INPUT /tmp/SimpleMarkDuplicatesWithMateCigarTester.tmp822859637917635055/input.sam --OUTPUT /tmp/SimpleMarkDuplicatesWithMateCigarTester.tmp822859637917635055/output.sam --METRICS_FILE /tmp/SimpleMarkDuplicatesWithMateCigarTester.tmp822859637917635055/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_RECORDS_IN_RAM 1000 --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --TAGGING_POLICY DontTag --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_END_IN_UNPAIRED_READS false --FLOW_USE_UNPAIRED_CLIPPED_END false --FLOW_UNPAIRED_END_UNCERTAINTY 0 --FLOW_UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME SimpleMarkDuplicatesWithMateCigar --READ_NAME_REGEX <optimized capture of last three ':' separated fields as numeric values> --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:17:23 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 13:17:23 MarkDuplicatesWithMateCigar Found 2 optical duplicate clusters. INFO 2025-04-24 13:17:23 MarkDuplicatesWithMateCigar Processed 11 records INFO 2025-04-24 13:17:23 MarkDuplicatesWithMateCigar Marking 8 records as duplicates. [Thu Apr 24 13:17:23 EDT 2025] picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 [Thu Apr 24 13:17:23 EDT 2025] SimpleMarkDuplicatesWithMateCigar --INPUT /tmp/SimpleMarkDuplicatesWithMateCigarTester.tmp1706323941824017718/input.sam --OUTPUT /tmp/SimpleMarkDuplicatesWithMateCigarTester.tmp1706323941824017718/output.sam --METRICS_FILE /tmp/SimpleMarkDuplicatesWithMateCigarTester.tmp1706323941824017718/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_RECORDS_IN_RAM 1000 --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --TAGGING_POLICY DontTag --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_END_IN_UNPAIRED_READS false --FLOW_USE_UNPAIRED_CLIPPED_END false --FLOW_UNPAIRED_END_UNCERTAINTY 0 --FLOW_UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME SimpleMarkDuplicatesWithMateCigar --READ_NAME_REGEX <optimized capture of last three ':' separated fields as numeric values> --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:17:23 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 13:17:23 MarkDuplicatesWithMateCigar Found 2 optical duplicate clusters. INFO 2025-04-24 13:17:23 MarkDuplicatesWithMateCigar Processed 11 records INFO 2025-04-24 13:17:23 MarkDuplicatesWithMateCigar Marking 8 records as duplicates. [Thu Apr 24 13:17:23 EDT 2025] picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 [Thu Apr 24 13:17:23 EDT 2025] SimpleMarkDuplicatesWithMateCigar --INPUT /tmp/SimpleMarkDuplicatesWithMateCigarTester.tmp2655200166966586498/input.sam --OUTPUT /tmp/SimpleMarkDuplicatesWithMateCigarTester.tmp2655200166966586498/output.sam --METRICS_FILE /tmp/SimpleMarkDuplicatesWithMateCigarTester.tmp2655200166966586498/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_RECORDS_IN_RAM 1000 --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --TAGGING_POLICY DontTag --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_END_IN_UNPAIRED_READS false --FLOW_USE_UNPAIRED_CLIPPED_END false --FLOW_UNPAIRED_END_UNCERTAINTY 0 --FLOW_UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME SimpleMarkDuplicatesWithMateCigar --READ_NAME_REGEX <optimized capture of last three ':' separated fields as numeric values> --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:17:23 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 13:17:23 MarkDuplicatesWithMateCigar Found 2 optical duplicate clusters. INFO 2025-04-24 13:17:23 MarkDuplicatesWithMateCigar Processed 11 records INFO 2025-04-24 13:17:23 MarkDuplicatesWithMateCigar Marking 8 records as duplicates. [Thu Apr 24 13:17:23 EDT 2025] picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 [Thu Apr 24 13:17:23 EDT 2025] SimpleMarkDuplicatesWithMateCigar --INPUT /tmp/SimpleMarkDuplicatesWithMateCigarTester.tmp9685835568624545040/input.sam --OUTPUT /tmp/SimpleMarkDuplicatesWithMateCigarTester.tmp9685835568624545040/output.sam --METRICS_FILE /tmp/SimpleMarkDuplicatesWithMateCigarTester.tmp9685835568624545040/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_RECORDS_IN_RAM 1000 --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --TAGGING_POLICY DontTag --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_END_IN_UNPAIRED_READS false --FLOW_USE_UNPAIRED_CLIPPED_END false --FLOW_UNPAIRED_END_UNCERTAINTY 0 --FLOW_UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME SimpleMarkDuplicatesWithMateCigar --READ_NAME_REGEX <optimized capture of last three ':' separated fields as numeric values> --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:17:23 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 13:17:23 MarkDuplicatesWithMateCigar Found 2 optical duplicate clusters. INFO 2025-04-24 13:17:23 MarkDuplicatesWithMateCigar Processed 11 records INFO 2025-04-24 13:17:23 MarkDuplicatesWithMateCigar Marking 8 records as duplicates. [Thu Apr 24 13:17:23 EDT 2025] picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 [Thu Apr 24 13:17:23 EDT 2025] SimpleMarkDuplicatesWithMateCigar --INPUT /tmp/SimpleMarkDuplicatesWithMateCigarTester.tmp7774958212182713931/input.sam --OUTPUT /tmp/SimpleMarkDuplicatesWithMateCigarTester.tmp7774958212182713931/output.sam --METRICS_FILE /tmp/SimpleMarkDuplicatesWithMateCigarTester.tmp7774958212182713931/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_RECORDS_IN_RAM 1000 --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --TAGGING_POLICY DontTag --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_END_IN_UNPAIRED_READS false --FLOW_USE_UNPAIRED_CLIPPED_END false --FLOW_UNPAIRED_END_UNCERTAINTY 0 --FLOW_UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME SimpleMarkDuplicatesWithMateCigar --READ_NAME_REGEX <optimized capture of last three ':' separated fields as numeric values> --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:17:23 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 13:17:23 MarkDuplicatesWithMateCigar Found 2 optical duplicate clusters. INFO 2025-04-24 13:17:23 MarkDuplicatesWithMateCigar Processed 11 records INFO 2025-04-24 13:17:23 MarkDuplicatesWithMateCigar Marking 8 records as duplicates. [Thu Apr 24 13:17:23 EDT 2025] picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 [Thu Apr 24 13:17:23 EDT 2025] SimpleMarkDuplicatesWithMateCigar --INPUT /tmp/SimpleMarkDuplicatesWithMateCigarTester.tmp15720900273527519838/input.sam --OUTPUT /tmp/SimpleMarkDuplicatesWithMateCigarTester.tmp15720900273527519838/output.sam --METRICS_FILE /tmp/SimpleMarkDuplicatesWithMateCigarTester.tmp15720900273527519838/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_RECORDS_IN_RAM 1000 --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --TAGGING_POLICY DontTag --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_END_IN_UNPAIRED_READS false --FLOW_USE_UNPAIRED_CLIPPED_END false --FLOW_UNPAIRED_END_UNCERTAINTY 0 --FLOW_UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME SimpleMarkDuplicatesWithMateCigar --READ_NAME_REGEX <optimized capture of last three ':' separated fields as numeric values> --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:17:23 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 13:17:23 MarkDuplicatesWithMateCigar Found 2 optical duplicate clusters. INFO 2025-04-24 13:17:23 MarkDuplicatesWithMateCigar Processed 11 records INFO 2025-04-24 13:17:23 MarkDuplicatesWithMateCigar Marking 8 records as duplicates. [Thu Apr 24 13:17:23 EDT 2025] picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 [Thu Apr 24 13:17:23 EDT 2025] SimpleMarkDuplicatesWithMateCigar --INPUT /tmp/SimpleMarkDuplicatesWithMateCigarTester.tmp12728773505777184812/input.sam --OUTPUT /tmp/SimpleMarkDuplicatesWithMateCigarTester.tmp12728773505777184812/output.sam --METRICS_FILE /tmp/SimpleMarkDuplicatesWithMateCigarTester.tmp12728773505777184812/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_RECORDS_IN_RAM 1000 --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --TAGGING_POLICY DontTag --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_END_IN_UNPAIRED_READS false --FLOW_USE_UNPAIRED_CLIPPED_END false --FLOW_UNPAIRED_END_UNCERTAINTY 0 --FLOW_UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME SimpleMarkDuplicatesWithMateCigar --READ_NAME_REGEX <optimized capture of last three ':' separated fields as numeric values> --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:17:23 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 13:17:23 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. INFO 2025-04-24 13:17:23 MarkDuplicatesWithMateCigar Processed 2 records INFO 2025-04-24 13:17:23 MarkDuplicatesWithMateCigar Marking 0 records as duplicates. [Thu Apr 24 13:17:23 EDT 2025] picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 [Thu Apr 24 13:17:23 EDT 2025] SimpleMarkDuplicatesWithMateCigar --INPUT /tmp/SimpleMarkDuplicatesWithMateCigarTester.tmp16212669271660280460/input.sam --OUTPUT /tmp/SimpleMarkDuplicatesWithMateCigarTester.tmp16212669271660280460/output.sam --METRICS_FILE /tmp/SimpleMarkDuplicatesWithMateCigarTester.tmp16212669271660280460/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_RECORDS_IN_RAM 1000 --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --TAGGING_POLICY DontTag --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_END_IN_UNPAIRED_READS false --FLOW_USE_UNPAIRED_CLIPPED_END false --FLOW_UNPAIRED_END_UNCERTAINTY 0 --FLOW_UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME SimpleMarkDuplicatesWithMateCigar --READ_NAME_REGEX <optimized capture of last three ':' separated fields as numeric values> --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:17:23 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 13:17:23 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. INFO 2025-04-24 13:17:23 MarkDuplicatesWithMateCigar Processed 3 records INFO 2025-04-24 13:17:23 MarkDuplicatesWithMateCigar Marking 1 records as duplicates. [Thu Apr 24 13:17:23 EDT 2025] picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 [Thu Apr 24 13:17:23 EDT 2025] SimpleMarkDuplicatesWithMateCigar --INPUT /tmp/SimpleMarkDuplicatesWithMateCigarTester.tmp107004245685557913/input.sam --OUTPUT /tmp/SimpleMarkDuplicatesWithMateCigarTester.tmp107004245685557913/output.sam --METRICS_FILE /tmp/SimpleMarkDuplicatesWithMateCigarTester.tmp107004245685557913/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_RECORDS_IN_RAM 1000 --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --TAGGING_POLICY DontTag --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_END_IN_UNPAIRED_READS false --FLOW_USE_UNPAIRED_CLIPPED_END false --FLOW_UNPAIRED_END_UNCERTAINTY 0 --FLOW_UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME SimpleMarkDuplicatesWithMateCigar --READ_NAME_REGEX <optimized capture of last three ':' separated fields as numeric values> --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:17:23 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 13:17:23 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. INFO 2025-04-24 13:17:23 MarkDuplicatesWithMateCigar Processed 3 records INFO 2025-04-24 13:17:23 MarkDuplicatesWithMateCigar Marking 1 records as duplicates. [Thu Apr 24 13:17:23 EDT 2025] picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 [Thu Apr 24 13:17:23 EDT 2025] SimpleMarkDuplicatesWithMateCigar --INPUT /tmp/SimpleMarkDuplicatesWithMateCigarTester.tmp12365401304495795491/input.sam --OUTPUT /tmp/SimpleMarkDuplicatesWithMateCigarTester.tmp12365401304495795491/output.sam --METRICS_FILE /tmp/SimpleMarkDuplicatesWithMateCigarTester.tmp12365401304495795491/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_RECORDS_IN_RAM 1000 --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --TAGGING_POLICY DontTag --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_END_IN_UNPAIRED_READS false --FLOW_USE_UNPAIRED_CLIPPED_END false --FLOW_UNPAIRED_END_UNCERTAINTY 0 --FLOW_UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME SimpleMarkDuplicatesWithMateCigar --READ_NAME_REGEX <optimized capture of last three ':' separated fields as numeric values> --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:17:23 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 13:17:23 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ1. Cause: String 'READ1' did not start with a parsable number. INFO 2025-04-24 13:17:23 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. INFO 2025-04-24 13:17:23 MarkDuplicatesWithMateCigar Processed 5 records INFO 2025-04-24 13:17:23 MarkDuplicatesWithMateCigar Marking 2 records as duplicates. [Thu Apr 24 13:17:23 EDT 2025] picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 [Thu Apr 24 13:17:23 EDT 2025] SimpleMarkDuplicatesWithMateCigar --INPUT /tmp/SimpleMarkDuplicatesWithMateCigarTester.tmp4571134711391256983/input.sam --OUTPUT /tmp/SimpleMarkDuplicatesWithMateCigarTester.tmp4571134711391256983/output.sam --METRICS_FILE /tmp/SimpleMarkDuplicatesWithMateCigarTester.tmp4571134711391256983/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_RECORDS_IN_RAM 1000 --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --TAGGING_POLICY DontTag --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_END_IN_UNPAIRED_READS false --FLOW_USE_UNPAIRED_CLIPPED_END false --FLOW_UNPAIRED_END_UNCERTAINTY 0 --FLOW_UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME SimpleMarkDuplicatesWithMateCigar --READ_NAME_REGEX <optimized capture of last three ':' separated fields as numeric values> --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:17:23 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 13:17:23 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ1. Cause: String 'READ1' did not start with a parsable number. INFO 2025-04-24 13:17:23 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. INFO 2025-04-24 13:17:23 MarkDuplicatesWithMateCigar Processed 5 records INFO 2025-04-24 13:17:23 MarkDuplicatesWithMateCigar Marking 2 records as duplicates. [Thu Apr 24 13:17:23 EDT 2025] picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 [Thu Apr 24 13:17:23 EDT 2025] SimpleMarkDuplicatesWithMateCigar --INPUT /tmp/SimpleMarkDuplicatesWithMateCigarTester.tmp14509092417614051641/input.sam --OUTPUT /tmp/SimpleMarkDuplicatesWithMateCigarTester.tmp14509092417614051641/output.sam --METRICS_FILE /tmp/SimpleMarkDuplicatesWithMateCigarTester.tmp14509092417614051641/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_RECORDS_IN_RAM 1000 --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --TAGGING_POLICY DontTag --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_END_IN_UNPAIRED_READS false --FLOW_USE_UNPAIRED_CLIPPED_END false --FLOW_UNPAIRED_END_UNCERTAINTY 0 --FLOW_UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME SimpleMarkDuplicatesWithMateCigar --READ_NAME_REGEX <optimized capture of last three ':' separated fields as numeric values> --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:17:23 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 13:17:23 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ1. Cause: String 'READ1' did not start with a parsable number. INFO 2025-04-24 13:17:23 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. INFO 2025-04-24 13:17:23 MarkDuplicatesWithMateCigar Processed 4 records INFO 2025-04-24 13:17:23 MarkDuplicatesWithMateCigar Marking 0 records as duplicates. [Thu Apr 24 13:17:23 EDT 2025] picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 [Thu Apr 24 13:17:23 EDT 2025] SimpleMarkDuplicatesWithMateCigar --INPUT /tmp/SimpleMarkDuplicatesWithMateCigarTester.tmp3182909267181219208/input.sam --OUTPUT /tmp/SimpleMarkDuplicatesWithMateCigarTester.tmp3182909267181219208/output.sam --METRICS_FILE /tmp/SimpleMarkDuplicatesWithMateCigarTester.tmp3182909267181219208/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_RECORDS_IN_RAM 1000 --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --TAGGING_POLICY DontTag --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_END_IN_UNPAIRED_READS false --FLOW_USE_UNPAIRED_CLIPPED_END false --FLOW_UNPAIRED_END_UNCERTAINTY 0 --FLOW_UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME SimpleMarkDuplicatesWithMateCigar --READ_NAME_REGEX <optimized capture of last three ':' separated fields as numeric values> --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:17:23 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 13:17:23 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ1. Cause: String 'READ1' did not start with a parsable number. INFO 2025-04-24 13:17:23 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. INFO 2025-04-24 13:17:23 MarkDuplicatesWithMateCigar Processed 4 records INFO 2025-04-24 13:17:23 MarkDuplicatesWithMateCigar Marking 1 records as duplicates. [Thu Apr 24 13:17:23 EDT 2025] picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 [Thu Apr 24 13:17:23 EDT 2025] SimpleMarkDuplicatesWithMateCigar --INPUT /tmp/SimpleMarkDuplicatesWithMateCigarTester.tmp10977823974477506202/input.sam --OUTPUT /tmp/SimpleMarkDuplicatesWithMateCigarTester.tmp10977823974477506202/output.sam --METRICS_FILE /tmp/SimpleMarkDuplicatesWithMateCigarTester.tmp10977823974477506202/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_RECORDS_IN_RAM 1000 --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --TAGGING_POLICY DontTag --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_END_IN_UNPAIRED_READS false --FLOW_USE_UNPAIRED_CLIPPED_END false --FLOW_UNPAIRED_END_UNCERTAINTY 0 --FLOW_UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME SimpleMarkDuplicatesWithMateCigar --READ_NAME_REGEX <optimized capture of last three ':' separated fields as numeric values> --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:17:23 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 13:17:23 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ1. Cause: String 'READ1' did not start with a parsable number. INFO 2025-04-24 13:17:23 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. INFO 2025-04-24 13:17:23 MarkDuplicatesWithMateCigar Processed 4 records INFO 2025-04-24 13:17:23 MarkDuplicatesWithMateCigar Marking 1 records as duplicates. [Thu Apr 24 13:17:23 EDT 2025] picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 [Thu Apr 24 13:17:23 EDT 2025] SimpleMarkDuplicatesWithMateCigar --INPUT /tmp/SimpleMarkDuplicatesWithMateCigarTester.tmp5456753952621303996/input.sam --OUTPUT /tmp/SimpleMarkDuplicatesWithMateCigarTester.tmp5456753952621303996/output.sam --METRICS_FILE /tmp/SimpleMarkDuplicatesWithMateCigarTester.tmp5456753952621303996/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_RECORDS_IN_RAM 1000 --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --TAGGING_POLICY DontTag --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_END_IN_UNPAIRED_READS false --FLOW_USE_UNPAIRED_CLIPPED_END false --FLOW_UNPAIRED_END_UNCERTAINTY 0 --FLOW_UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME SimpleMarkDuplicatesWithMateCigar --READ_NAME_REGEX <optimized capture of last three ':' separated fields as numeric values> --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:17:23 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 13:17:23 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ1. Cause: String 'READ1' did not start with a parsable number. INFO 2025-04-24 13:17:23 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. INFO 2025-04-24 13:17:23 MarkDuplicatesWithMateCigar Processed 4 records INFO 2025-04-24 13:17:23 MarkDuplicatesWithMateCigar Marking 0 records as duplicates. [Thu Apr 24 13:17:23 EDT 2025] picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 [Thu Apr 24 13:17:23 EDT 2025] SimpleMarkDuplicatesWithMateCigar --INPUT /tmp/SimpleMarkDuplicatesWithMateCigarTester.tmp17691227140333977541/input.sam --OUTPUT /tmp/SimpleMarkDuplicatesWithMateCigarTester.tmp17691227140333977541/output.sam --METRICS_FILE /tmp/SimpleMarkDuplicatesWithMateCigarTester.tmp17691227140333977541/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_RECORDS_IN_RAM 1000 --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --TAGGING_POLICY DontTag --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_END_IN_UNPAIRED_READS false --FLOW_USE_UNPAIRED_CLIPPED_END false --FLOW_UNPAIRED_END_UNCERTAINTY 0 --FLOW_UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME SimpleMarkDuplicatesWithMateCigar --READ_NAME_REGEX <optimized capture of last three ':' separated fields as numeric values> --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:17:23 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 13:17:23 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. INFO 2025-04-24 13:17:23 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. INFO 2025-04-24 13:17:23 MarkDuplicatesWithMateCigar Processed 2 records INFO 2025-04-24 13:17:23 MarkDuplicatesWithMateCigar Marking 0 records as duplicates. [Thu Apr 24 13:17:23 EDT 2025] picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 [Thu Apr 24 13:17:23 EDT 2025] SimpleMarkDuplicatesWithMateCigar --INPUT /tmp/SimpleMarkDuplicatesWithMateCigarTester.tmp13378327955592334403/input.sam --OUTPUT /tmp/SimpleMarkDuplicatesWithMateCigarTester.tmp13378327955592334403/output.sam --METRICS_FILE /tmp/SimpleMarkDuplicatesWithMateCigarTester.tmp13378327955592334403/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_RECORDS_IN_RAM 1000 --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --TAGGING_POLICY DontTag --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_END_IN_UNPAIRED_READS false --FLOW_USE_UNPAIRED_CLIPPED_END false --FLOW_UNPAIRED_END_UNCERTAINTY 0 --FLOW_UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME SimpleMarkDuplicatesWithMateCigar --READ_NAME_REGEX <optimized capture of last three ':' separated fields as numeric values> --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:17:23 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 13:17:23 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. INFO 2025-04-24 13:17:23 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. INFO 2025-04-24 13:17:23 MarkDuplicatesWithMateCigar Processed 2 records INFO 2025-04-24 13:17:23 MarkDuplicatesWithMateCigar Marking 0 records as duplicates. [Thu Apr 24 13:17:23 EDT 2025] picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 [Thu Apr 24 13:17:23 EDT 2025] SimpleMarkDuplicatesWithMateCigar --INPUT /tmp/SimpleMarkDuplicatesWithMateCigarTester.tmp15862742914354975145/input.sam --OUTPUT /tmp/SimpleMarkDuplicatesWithMateCigarTester.tmp15862742914354975145/output.sam --METRICS_FILE /tmp/SimpleMarkDuplicatesWithMateCigarTester.tmp15862742914354975145/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_RECORDS_IN_RAM 1000 --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --TAGGING_POLICY DontTag --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_END_IN_UNPAIRED_READS false --FLOW_USE_UNPAIRED_CLIPPED_END false --FLOW_UNPAIRED_END_UNCERTAINTY 0 --FLOW_UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME SimpleMarkDuplicatesWithMateCigar --READ_NAME_REGEX <optimized capture of last three ':' separated fields as numeric values> --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:17:23 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 13:17:23 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. INFO 2025-04-24 13:17:23 MarkDuplicatesWithMateCigar Processed 2 records INFO 2025-04-24 13:17:23 MarkDuplicatesWithMateCigar Marking 0 records as duplicates. [Thu Apr 24 13:17:23 EDT 2025] picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 [Thu Apr 24 13:17:23 EDT 2025] SimpleMarkDuplicatesWithMateCigar --INPUT /tmp/SimpleMarkDuplicatesWithMateCigarTester.tmp136394275152640649/input.sam --OUTPUT /tmp/SimpleMarkDuplicatesWithMateCigarTester.tmp136394275152640649/output.sam --METRICS_FILE /tmp/SimpleMarkDuplicatesWithMateCigarTester.tmp136394275152640649/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_RECORDS_IN_RAM 1000 --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --TAGGING_POLICY DontTag --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_END_IN_UNPAIRED_READS false --FLOW_USE_UNPAIRED_CLIPPED_END false --FLOW_UNPAIRED_END_UNCERTAINTY 0 --FLOW_UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME SimpleMarkDuplicatesWithMateCigar --READ_NAME_REGEX <optimized capture of last three ':' separated fields as numeric values> --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:17:23 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 13:17:23 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. INFO 2025-04-24 13:17:23 MarkDuplicatesWithMateCigar Processed 2 records INFO 2025-04-24 13:17:23 MarkDuplicatesWithMateCigar Marking 0 records as duplicates. [Thu Apr 24 13:17:23 EDT 2025] picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 [Thu Apr 24 13:17:23 EDT 2025] SimpleMarkDuplicatesWithMateCigar --INPUT /tmp/SimpleMarkDuplicatesWithMateCigarTester.tmp1913725026906907155/input.sam --OUTPUT /tmp/SimpleMarkDuplicatesWithMateCigarTester.tmp1913725026906907155/output.sam --METRICS_FILE /tmp/SimpleMarkDuplicatesWithMateCigarTester.tmp1913725026906907155/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_RECORDS_IN_RAM 1000 --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --TAGGING_POLICY DontTag --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_END_IN_UNPAIRED_READS false --FLOW_USE_UNPAIRED_CLIPPED_END false --FLOW_UNPAIRED_END_UNCERTAINTY 0 --FLOW_UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME SimpleMarkDuplicatesWithMateCigar --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:17:23 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 13:17:23 MarkDuplicatesWithMateCigar Skipped optical duplicate cluster discovery; library size estimation may be inaccurate! INFO 2025-04-24 13:17:23 MarkDuplicatesWithMateCigar Processed 4 records INFO 2025-04-24 13:17:23 MarkDuplicatesWithMateCigar Marking 2 records as duplicates. [Thu Apr 24 13:17:23 EDT 2025] picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 [Thu Apr 24 13:17:23 EDT 2025] SimpleMarkDuplicatesWithMateCigar --INPUT /tmp/SimpleMarkDuplicatesWithMateCigarTester.tmp17744272069115270316/input.sam --OUTPUT /tmp/SimpleMarkDuplicatesWithMateCigarTester.tmp17744272069115270316/output.sam --METRICS_FILE /tmp/SimpleMarkDuplicatesWithMateCigarTester.tmp17744272069115270316/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_RECORDS_IN_RAM 1000 --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --TAGGING_POLICY DontTag --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_END_IN_UNPAIRED_READS false --FLOW_USE_UNPAIRED_CLIPPED_END false --FLOW_UNPAIRED_END_UNCERTAINTY 0 --FLOW_UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME SimpleMarkDuplicatesWithMateCigar --READ_NAME_REGEX <optimized capture of last three ':' separated fields as numeric values> --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:17:23 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 13:17:23 MarkDuplicatesWithMateCigar Found 1 optical duplicate clusters. INFO 2025-04-24 13:17:23 MarkDuplicatesWithMateCigar Processed 4 records INFO 2025-04-24 13:17:23 MarkDuplicatesWithMateCigar Marking 2 records as duplicates. [Thu Apr 24 13:17:23 EDT 2025] picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 [Thu Apr 24 13:17:23 EDT 2025] SimpleMarkDuplicatesWithMateCigar --INPUT /tmp/SimpleMarkDuplicatesWithMateCigarTester.tmp10112607225601068991/input.sam --OUTPUT /tmp/SimpleMarkDuplicatesWithMateCigarTester.tmp10112607225601068991/output.sam --METRICS_FILE /tmp/SimpleMarkDuplicatesWithMateCigarTester.tmp10112607225601068991/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_RECORDS_IN_RAM 1000 --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --TAGGING_POLICY DontTag --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_END_IN_UNPAIRED_READS false --FLOW_USE_UNPAIRED_CLIPPED_END false --FLOW_UNPAIRED_END_UNCERTAINTY 0 --FLOW_UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME SimpleMarkDuplicatesWithMateCigar --READ_NAME_REGEX <optimized capture of last three ':' separated fields as numeric values> --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:17:23 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 13:17:23 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. INFO 2025-04-24 13:17:23 MarkDuplicatesWithMateCigar Processed 4 records INFO 2025-04-24 13:17:23 MarkDuplicatesWithMateCigar Marking 2 records as duplicates. [Thu Apr 24 13:17:23 EDT 2025] picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 [Thu Apr 24 13:17:23 EDT 2025] SimpleMarkDuplicatesWithMateCigar --INPUT /tmp/SimpleMarkDuplicatesWithMateCigarTester.tmp2529905357617552320/input.sam --OUTPUT /tmp/SimpleMarkDuplicatesWithMateCigarTester.tmp2529905357617552320/output.sam --METRICS_FILE /tmp/SimpleMarkDuplicatesWithMateCigarTester.tmp2529905357617552320/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_RECORDS_IN_RAM 1000 --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --TAGGING_POLICY DontTag --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_END_IN_UNPAIRED_READS false --FLOW_USE_UNPAIRED_CLIPPED_END false --FLOW_UNPAIRED_END_UNCERTAINTY 0 --FLOW_UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME SimpleMarkDuplicatesWithMateCigar --READ_NAME_REGEX <optimized capture of last three ':' separated fields as numeric values> --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:17:23 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 13:17:23 MarkDuplicatesWithMateCigar Found 1 optical duplicate clusters. INFO 2025-04-24 13:17:23 MarkDuplicatesWithMateCigar Processed 4 records INFO 2025-04-24 13:17:23 MarkDuplicatesWithMateCigar Marking 2 records as duplicates. [Thu Apr 24 13:17:23 EDT 2025] picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 [Thu Apr 24 13:17:23 EDT 2025] SimpleMarkDuplicatesWithMateCigar --INPUT /tmp/SimpleMarkDuplicatesWithMateCigarTester.tmp1045747162806102248/input.sam --OUTPUT /tmp/SimpleMarkDuplicatesWithMateCigarTester.tmp1045747162806102248/output.sam --METRICS_FILE /tmp/SimpleMarkDuplicatesWithMateCigarTester.tmp1045747162806102248/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_RECORDS_IN_RAM 1000 --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --TAGGING_POLICY DontTag --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_END_IN_UNPAIRED_READS false --FLOW_USE_UNPAIRED_CLIPPED_END false --FLOW_UNPAIRED_END_UNCERTAINTY 0 --FLOW_UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME SimpleMarkDuplicatesWithMateCigar --READ_NAME_REGEX <optimized capture of last three ':' separated fields as numeric values> --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:17:23 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 13:17:23 MarkDuplicatesWithMateCigar Found 1 optical duplicate clusters. INFO 2025-04-24 13:17:23 MarkDuplicatesWithMateCigar Processed 4 records INFO 2025-04-24 13:17:23 MarkDuplicatesWithMateCigar Marking 2 records as duplicates. [Thu Apr 24 13:17:23 EDT 2025] picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 [Thu Apr 24 13:17:23 EDT 2025] SimpleMarkDuplicatesWithMateCigar --INPUT /tmp/SimpleMarkDuplicatesWithMateCigarTester.tmp8102402608105581933/input.sam --OUTPUT /tmp/SimpleMarkDuplicatesWithMateCigarTester.tmp8102402608105581933/output.sam --METRICS_FILE /tmp/SimpleMarkDuplicatesWithMateCigarTester.tmp8102402608105581933/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_RECORDS_IN_RAM 1000 --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --TAGGING_POLICY DontTag --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_END_IN_UNPAIRED_READS false --FLOW_USE_UNPAIRED_CLIPPED_END false --FLOW_UNPAIRED_END_UNCERTAINTY 0 --FLOW_UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME SimpleMarkDuplicatesWithMateCigar --READ_NAME_REGEX <optimized capture of last three ':' separated fields as numeric values> --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:17:23 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 13:17:23 MarkDuplicatesWithMateCigar Found 1 optical duplicate clusters. INFO 2025-04-24 13:17:23 MarkDuplicatesWithMateCigar Processed 6 records INFO 2025-04-24 13:17:23 MarkDuplicatesWithMateCigar Marking 4 records as duplicates. [Thu Apr 24 13:17:23 EDT 2025] picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 [Thu Apr 24 13:17:23 EDT 2025] SimpleMarkDuplicatesWithMateCigar --INPUT /tmp/SimpleMarkDuplicatesWithMateCigarTester.tmp13566478016061996264/input.sam --OUTPUT /tmp/SimpleMarkDuplicatesWithMateCigarTester.tmp13566478016061996264/output.sam --METRICS_FILE /tmp/SimpleMarkDuplicatesWithMateCigarTester.tmp13566478016061996264/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_RECORDS_IN_RAM 1000 --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --TAGGING_POLICY DontTag --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_END_IN_UNPAIRED_READS false --FLOW_USE_UNPAIRED_CLIPPED_END false --FLOW_UNPAIRED_END_UNCERTAINTY 0 --FLOW_UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME SimpleMarkDuplicatesWithMateCigar --READ_NAME_REGEX <optimized capture of last three ':' separated fields as numeric values> --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:17:23 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 13:17:23 MarkDuplicatesWithMateCigar Found 1 optical duplicate clusters. INFO 2025-04-24 13:17:23 MarkDuplicatesWithMateCigar Processed 4 records INFO 2025-04-24 13:17:23 MarkDuplicatesWithMateCigar Marking 2 records as duplicates. [Thu Apr 24 13:17:23 EDT 2025] picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 [Thu Apr 24 13:17:23 EDT 2025] SimpleMarkDuplicatesWithMateCigar --INPUT /tmp/SimpleMarkDuplicatesWithMateCigarTester.tmp10621018258416310533/input.sam --OUTPUT /tmp/SimpleMarkDuplicatesWithMateCigarTester.tmp10621018258416310533/output.sam --METRICS_FILE /tmp/SimpleMarkDuplicatesWithMateCigarTester.tmp10621018258416310533/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_RECORDS_IN_RAM 1000 --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --TAGGING_POLICY DontTag --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_END_IN_UNPAIRED_READS false --FLOW_USE_UNPAIRED_CLIPPED_END false --FLOW_UNPAIRED_END_UNCERTAINTY 0 --FLOW_UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME SimpleMarkDuplicatesWithMateCigar --READ_NAME_REGEX <optimized capture of last three ':' separated fields as numeric values> --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:17:23 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 13:17:23 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. INFO 2025-04-24 13:17:23 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. INFO 2025-04-24 13:17:23 MarkDuplicatesWithMateCigar Processed 2 records INFO 2025-04-24 13:17:23 MarkDuplicatesWithMateCigar Marking 0 records as duplicates. [Thu Apr 24 13:17:23 EDT 2025] picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 [Thu Apr 24 13:17:23 EDT 2025] SimpleMarkDuplicatesWithMateCigar --INPUT /tmp/SimpleMarkDuplicatesWithMateCigarTester.tmp3409989514030236624/input.sam --OUTPUT /tmp/SimpleMarkDuplicatesWithMateCigarTester.tmp3409989514030236624/output.sam --METRICS_FILE /tmp/SimpleMarkDuplicatesWithMateCigarTester.tmp3409989514030236624/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_RECORDS_IN_RAM 1000 --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --TAGGING_POLICY DontTag --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_END_IN_UNPAIRED_READS false --FLOW_USE_UNPAIRED_CLIPPED_END false --FLOW_UNPAIRED_END_UNCERTAINTY 0 --FLOW_UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME SimpleMarkDuplicatesWithMateCigar --READ_NAME_REGEX <optimized capture of last three ':' separated fields as numeric values> --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:17:23 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 13:17:23 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. INFO 2025-04-24 13:17:23 MarkDuplicatesWithMateCigar Processed 1 records INFO 2025-04-24 13:17:23 MarkDuplicatesWithMateCigar Marking 0 records as duplicates. [Thu Apr 24 13:17:23 EDT 2025] picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 [Thu Apr 24 13:17:23 EDT 2025] SimpleMarkDuplicatesWithMateCigar --INPUT /tmp/SimpleMarkDuplicatesWithMateCigarTester.tmp16418939400969713857/input.sam --OUTPUT /tmp/SimpleMarkDuplicatesWithMateCigarTester.tmp16418939400969713857/output.sam --METRICS_FILE /tmp/SimpleMarkDuplicatesWithMateCigarTester.tmp16418939400969713857/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_RECORDS_IN_RAM 1000 --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --TAGGING_POLICY DontTag --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_END_IN_UNPAIRED_READS false --FLOW_USE_UNPAIRED_CLIPPED_END false --FLOW_UNPAIRED_END_UNCERTAINTY 0 --FLOW_UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME SimpleMarkDuplicatesWithMateCigar --READ_NAME_REGEX <optimized capture of last three ':' separated fields as numeric values> --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:17:23 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 13:17:23 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ1. Cause: String 'READ1' did not start with a parsable number. INFO 2025-04-24 13:17:23 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. INFO 2025-04-24 13:17:23 MarkDuplicatesWithMateCigar Processed 3 records INFO 2025-04-24 13:17:23 MarkDuplicatesWithMateCigar Marking 1 records as duplicates. [Thu Apr 24 13:17:23 EDT 2025] picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 [Thu Apr 24 13:17:23 EDT 2025] SimpleMarkDuplicatesWithMateCigar --INPUT /tmp/SimpleMarkDuplicatesWithMateCigarTester.tmp8207933292496076627/input.sam --OUTPUT /tmp/SimpleMarkDuplicatesWithMateCigarTester.tmp8207933292496076627/output.sam --METRICS_FILE /tmp/SimpleMarkDuplicatesWithMateCigarTester.tmp8207933292496076627/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_RECORDS_IN_RAM 1000 --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --TAGGING_POLICY DontTag --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_END_IN_UNPAIRED_READS false --FLOW_USE_UNPAIRED_CLIPPED_END false --FLOW_UNPAIRED_END_UNCERTAINTY 0 --FLOW_UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME SimpleMarkDuplicatesWithMateCigar --READ_NAME_REGEX <optimized capture of last three ':' separated fields as numeric values> --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:17:23 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 13:17:23 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ1. Cause: String 'READ1' did not start with a parsable number. INFO 2025-04-24 13:17:23 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. INFO 2025-04-24 13:17:23 MarkDuplicatesWithMateCigar Processed 5 records INFO 2025-04-24 13:17:23 MarkDuplicatesWithMateCigar Marking 3 records as duplicates. [Thu Apr 24 13:17:23 EDT 2025] picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 [Thu Apr 24 13:17:23 EDT 2025] SimpleMarkDuplicatesWithMateCigar --INPUT /tmp/SimpleMarkDuplicatesWithMateCigarTester.tmp8410981504939093916/input.sam --OUTPUT /tmp/SimpleMarkDuplicatesWithMateCigarTester.tmp8410981504939093916/output.sam --METRICS_FILE /tmp/SimpleMarkDuplicatesWithMateCigarTester.tmp8410981504939093916/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_RECORDS_IN_RAM 1000 --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --TAGGING_POLICY DontTag --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_END_IN_UNPAIRED_READS false --FLOW_USE_UNPAIRED_CLIPPED_END false --FLOW_UNPAIRED_END_UNCERTAINTY 0 --FLOW_UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME SimpleMarkDuplicatesWithMateCigar --READ_NAME_REGEX <optimized capture of last three ':' separated fields as numeric values> --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:17:23 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 13:17:23 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. INFO 2025-04-24 13:17:23 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. INFO 2025-04-24 13:17:23 MarkDuplicatesWithMateCigar Processed 2 records INFO 2025-04-24 13:17:23 MarkDuplicatesWithMateCigar Marking 0 records as duplicates. [Thu Apr 24 13:17:23 EDT 2025] picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 [Thu Apr 24 13:17:23 EDT 2025] SimpleMarkDuplicatesWithMateCigar --INPUT /tmp/SimpleMarkDuplicatesWithMateCigarTester.tmp18185984117903276112/input.sam --OUTPUT /tmp/SimpleMarkDuplicatesWithMateCigarTester.tmp18185984117903276112/output.sam --METRICS_FILE /tmp/SimpleMarkDuplicatesWithMateCigarTester.tmp18185984117903276112/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_RECORDS_IN_RAM 1000 --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --TAGGING_POLICY DontTag --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_END_IN_UNPAIRED_READS false --FLOW_USE_UNPAIRED_CLIPPED_END false --FLOW_UNPAIRED_END_UNCERTAINTY 0 --FLOW_UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME SimpleMarkDuplicatesWithMateCigar --READ_NAME_REGEX <optimized capture of last three ':' separated fields as numeric values> --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:17:23 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 13:17:23 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. INFO 2025-04-24 13:17:23 MarkDuplicatesWithMateCigar Processed 1 records INFO 2025-04-24 13:17:23 MarkDuplicatesWithMateCigar Marking 0 records as duplicates. [Thu Apr 24 13:17:23 EDT 2025] picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 [Thu Apr 24 13:17:23 EDT 2025] SimpleMarkDuplicatesWithMateCigar --INPUT /tmp/SimpleMarkDuplicatesWithMateCigarTester.tmp8053203690934944057/input.sam --OUTPUT /tmp/SimpleMarkDuplicatesWithMateCigarTester.tmp8053203690934944057/output.sam --METRICS_FILE /tmp/SimpleMarkDuplicatesWithMateCigarTester.tmp8053203690934944057/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_RECORDS_IN_RAM 1000 --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --TAGGING_POLICY DontTag --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_END_IN_UNPAIRED_READS false --FLOW_USE_UNPAIRED_CLIPPED_END false --FLOW_UNPAIRED_END_UNCERTAINTY 0 --FLOW_UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME SimpleMarkDuplicatesWithMateCigar --READ_NAME_REGEX <optimized capture of last three ':' separated fields as numeric values> --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:17:23 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 13:17:23 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. INFO 2025-04-24 13:17:23 MarkDuplicatesWithMateCigar Processed 2 records INFO 2025-04-24 13:17:23 MarkDuplicatesWithMateCigar Marking 0 records as duplicates. [Thu Apr 24 13:17:23 EDT 2025] picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 [Thu Apr 24 13:17:23 EDT 2025] SimpleMarkDuplicatesWithMateCigar --INPUT /tmp/SimpleMarkDuplicatesWithMateCigarTester.tmp14780571327595250123/input.sam --OUTPUT /tmp/SimpleMarkDuplicatesWithMateCigarTester.tmp14780571327595250123/output.sam --METRICS_FILE /tmp/SimpleMarkDuplicatesWithMateCigarTester.tmp14780571327595250123/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_RECORDS_IN_RAM 1000 --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --TAGGING_POLICY DontTag --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_END_IN_UNPAIRED_READS false --FLOW_USE_UNPAIRED_CLIPPED_END false --FLOW_UNPAIRED_END_UNCERTAINTY 0 --FLOW_UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME SimpleMarkDuplicatesWithMateCigar --READ_NAME_REGEX <optimized capture of last three ':' separated fields as numeric values> --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:17:23 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 13:17:23 MarkDuplicatesWithMateCigar Found 1 optical duplicate clusters. INFO 2025-04-24 13:17:23 MarkDuplicatesWithMateCigar Processed 4 records INFO 2025-04-24 13:17:23 MarkDuplicatesWithMateCigar Marking 2 records as duplicates. [Thu Apr 24 13:17:23 EDT 2025] picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 [Thu Apr 24 13:17:23 EDT 2025] SimpleMarkDuplicatesWithMateCigar --INPUT /tmp/SimpleMarkDuplicatesWithMateCigarTester.tmp11885358749965713870/input.sam --OUTPUT /tmp/SimpleMarkDuplicatesWithMateCigarTester.tmp11885358749965713870/output.sam --METRICS_FILE /tmp/SimpleMarkDuplicatesWithMateCigarTester.tmp11885358749965713870/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_RECORDS_IN_RAM 1000 --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --TAGGING_POLICY DontTag --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_END_IN_UNPAIRED_READS false --FLOW_USE_UNPAIRED_CLIPPED_END false --FLOW_UNPAIRED_END_UNCERTAINTY 0 --FLOW_UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME SimpleMarkDuplicatesWithMateCigar --READ_NAME_REGEX <optimized capture of last three ':' separated fields as numeric values> --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:17:23 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 13:17:23 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. INFO 2025-04-24 13:17:23 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. INFO 2025-04-24 13:17:23 MarkDuplicatesWithMateCigar Processed 18 records INFO 2025-04-24 13:17:23 MarkDuplicatesWithMateCigar Marking 12 records as duplicates. [Thu Apr 24 13:17:23 EDT 2025] picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 [Thu Apr 24 13:17:23 EDT 2025] SimpleMarkDuplicatesWithMateCigar --INPUT /tmp/SimpleMarkDuplicatesWithMateCigarTester.tmp7452140177489876016/input.sam --OUTPUT /tmp/SimpleMarkDuplicatesWithMateCigarTester.tmp7452140177489876016/output.sam --METRICS_FILE /tmp/SimpleMarkDuplicatesWithMateCigarTester.tmp7452140177489876016/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_RECORDS_IN_RAM 1000 --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --TAGGING_POLICY DontTag --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_END_IN_UNPAIRED_READS false --FLOW_USE_UNPAIRED_CLIPPED_END false --FLOW_UNPAIRED_END_UNCERTAINTY 0 --FLOW_UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME SimpleMarkDuplicatesWithMateCigar --READ_NAME_REGEX <optimized capture of last three ':' separated fields as numeric values> --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:17:23 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 13:17:23 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. INFO 2025-04-24 13:17:23 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. INFO 2025-04-24 13:17:23 MarkDuplicatesWithMateCigar Processed 6 records INFO 2025-04-24 13:17:23 MarkDuplicatesWithMateCigar Marking 4 records as duplicates. [Thu Apr 24 13:17:23 EDT 2025] picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 [Thu Apr 24 13:17:23 EDT 2025] SimpleMarkDuplicatesWithMateCigar --INPUT /tmp/SimpleMarkDuplicatesWithMateCigarTester.tmp4747527117047555528/input.sam --OUTPUT /tmp/SimpleMarkDuplicatesWithMateCigarTester.tmp4747527117047555528/output.sam --METRICS_FILE /tmp/SimpleMarkDuplicatesWithMateCigarTester.tmp4747527117047555528/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_RECORDS_IN_RAM 1000 --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --TAGGING_POLICY DontTag --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_END_IN_UNPAIRED_READS false --FLOW_USE_UNPAIRED_CLIPPED_END false --FLOW_UNPAIRED_END_UNCERTAINTY 0 --FLOW_UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME SimpleMarkDuplicatesWithMateCigar --READ_NAME_REGEX <optimized capture of last three ':' separated fields as numeric values> --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:17:23 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 13:17:23 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. INFO 2025-04-24 13:17:23 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. INFO 2025-04-24 13:17:23 MarkDuplicatesWithMateCigar Processed 6 records INFO 2025-04-24 13:17:23 MarkDuplicatesWithMateCigar Marking 2 records as duplicates. [Thu Apr 24 13:17:23 EDT 2025] picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 [Thu Apr 24 13:17:23 EDT 2025] SimpleMarkDuplicatesWithMateCigar --INPUT /tmp/SimpleMarkDuplicatesWithMateCigarTester.tmp7996299643960717326/input.sam --OUTPUT /tmp/SimpleMarkDuplicatesWithMateCigarTester.tmp7996299643960717326/output.sam --METRICS_FILE /tmp/SimpleMarkDuplicatesWithMateCigarTester.tmp7996299643960717326/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_RECORDS_IN_RAM 1000 --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --TAGGING_POLICY DontTag --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_END_IN_UNPAIRED_READS false --FLOW_USE_UNPAIRED_CLIPPED_END false --FLOW_UNPAIRED_END_UNCERTAINTY 0 --FLOW_UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME SimpleMarkDuplicatesWithMateCigar --READ_NAME_REGEX <optimized capture of last three ':' separated fields as numeric values> --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:17:23 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 13:17:23 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. INFO 2025-04-24 13:17:23 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. INFO 2025-04-24 13:17:23 MarkDuplicatesWithMateCigar Processed 12 records INFO 2025-04-24 13:17:23 MarkDuplicatesWithMateCigar Marking 8 records as duplicates. [Thu Apr 24 13:17:23 EDT 2025] picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 [Thu Apr 24 13:17:23 EDT 2025] SimpleMarkDuplicatesWithMateCigar --INPUT /tmp/SimpleMarkDuplicatesWithMateCigarTester.tmp13362453957917287454/input.sam --OUTPUT /tmp/SimpleMarkDuplicatesWithMateCigarTester.tmp13362453957917287454/output.sam --METRICS_FILE /tmp/SimpleMarkDuplicatesWithMateCigarTester.tmp13362453957917287454/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_RECORDS_IN_RAM 1000 --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --TAGGING_POLICY DontTag --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_END_IN_UNPAIRED_READS false --FLOW_USE_UNPAIRED_CLIPPED_END false --FLOW_UNPAIRED_END_UNCERTAINTY 0 --FLOW_UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME SimpleMarkDuplicatesWithMateCigar --READ_NAME_REGEX <optimized capture of last three ':' separated fields as numeric values> --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:17:23 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 13:17:23 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. INFO 2025-04-24 13:17:23 MarkDuplicatesWithMateCigar Processed 4 records INFO 2025-04-24 13:17:23 MarkDuplicatesWithMateCigar Marking 2 records as duplicates. [Thu Apr 24 13:17:23 EDT 2025] picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 [Thu Apr 24 13:17:23 EDT 2025] SimpleMarkDuplicatesWithMateCigar --INPUT /tmp/SimpleMarkDuplicatesWithMateCigarTester.tmp13270652093436133355/input.sam --OUTPUT /tmp/SimpleMarkDuplicatesWithMateCigarTester.tmp13270652093436133355/output.sam --METRICS_FILE /tmp/SimpleMarkDuplicatesWithMateCigarTester.tmp13270652093436133355/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_RECORDS_IN_RAM 1000 --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --TAGGING_POLICY DontTag --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_END_IN_UNPAIRED_READS false --FLOW_USE_UNPAIRED_CLIPPED_END false --FLOW_UNPAIRED_END_UNCERTAINTY 0 --FLOW_UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME SimpleMarkDuplicatesWithMateCigar --READ_NAME_REGEX <optimized capture of last three ':' separated fields as numeric values> --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:17:23 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 13:17:23 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. INFO 2025-04-24 13:17:23 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. INFO 2025-04-24 13:17:23 MarkDuplicatesWithMateCigar Processed 8 records INFO 2025-04-24 13:17:23 MarkDuplicatesWithMateCigar Marking 4 records as duplicates. [Thu Apr 24 13:17:23 EDT 2025] picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 [Thu Apr 24 13:17:23 EDT 2025] SimpleMarkDuplicatesWithMateCigar --INPUT /tmp/SimpleMarkDuplicatesWithMateCigarTester.tmp2704921051992324025/input.sam --OUTPUT /tmp/SimpleMarkDuplicatesWithMateCigarTester.tmp2704921051992324025/output.sam --METRICS_FILE /tmp/SimpleMarkDuplicatesWithMateCigarTester.tmp2704921051992324025/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_RECORDS_IN_RAM 1000 --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --TAGGING_POLICY DontTag --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_END_IN_UNPAIRED_READS false --FLOW_USE_UNPAIRED_CLIPPED_END false --FLOW_UNPAIRED_END_UNCERTAINTY 0 --FLOW_UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME SimpleMarkDuplicatesWithMateCigar --READ_NAME_REGEX <optimized capture of last three ':' separated fields as numeric values> --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:17:23 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 13:17:23 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. INFO 2025-04-24 13:17:23 MarkDuplicatesWithMateCigar Processed 2 records INFO 2025-04-24 13:17:23 MarkDuplicatesWithMateCigar Marking 1 records as duplicates. [Thu Apr 24 13:17:23 EDT 2025] picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 [Thu Apr 24 13:17:23 EDT 2025] SimpleMarkDuplicatesWithMateCigar --INPUT /tmp/SimpleMarkDuplicatesWithMateCigarTester.tmp2174193093033795943/input.sam --OUTPUT /tmp/SimpleMarkDuplicatesWithMateCigarTester.tmp2174193093033795943/output.sam --METRICS_FILE /tmp/SimpleMarkDuplicatesWithMateCigarTester.tmp2174193093033795943/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_RECORDS_IN_RAM 1000 --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --TAGGING_POLICY DontTag --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_END_IN_UNPAIRED_READS false --FLOW_USE_UNPAIRED_CLIPPED_END false --FLOW_UNPAIRED_END_UNCERTAINTY 0 --FLOW_UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME SimpleMarkDuplicatesWithMateCigar --READ_NAME_REGEX <optimized capture of last three ':' separated fields as numeric values> --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:17:23 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 13:17:23 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. INFO 2025-04-24 13:17:23 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. INFO 2025-04-24 13:17:23 MarkDuplicatesWithMateCigar Processed 4 records INFO 2025-04-24 13:17:23 MarkDuplicatesWithMateCigar Marking 2 records as duplicates. [Thu Apr 24 13:17:23 EDT 2025] picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 [Thu Apr 24 13:17:23 EDT 2025] SimpleMarkDuplicatesWithMateCigar --INPUT /tmp/SimpleMarkDuplicatesWithMateCigarTester.tmp14994204324448550425/input.sam --OUTPUT /tmp/SimpleMarkDuplicatesWithMateCigarTester.tmp14994204324448550425/output.sam --METRICS_FILE /tmp/SimpleMarkDuplicatesWithMateCigarTester.tmp14994204324448550425/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_RECORDS_IN_RAM 1000 --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --TAGGING_POLICY DontTag --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_END_IN_UNPAIRED_READS false --FLOW_USE_UNPAIRED_CLIPPED_END false --FLOW_UNPAIRED_END_UNCERTAINTY 0 --FLOW_UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME SimpleMarkDuplicatesWithMateCigar --READ_NAME_REGEX <optimized capture of last three ':' separated fields as numeric values> --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:17:23 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 13:17:23 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. INFO 2025-04-24 13:17:23 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. INFO 2025-04-24 13:17:23 MarkDuplicatesWithMateCigar Processed 4 records INFO 2025-04-24 13:17:23 MarkDuplicatesWithMateCigar Marking 2 records as duplicates. [Thu Apr 24 13:17:23 EDT 2025] picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 [Thu Apr 24 13:17:23 EDT 2025] SimpleMarkDuplicatesWithMateCigar --INPUT /tmp/SimpleMarkDuplicatesWithMateCigarTester.tmp7008147791811421425/input.sam --OUTPUT /tmp/SimpleMarkDuplicatesWithMateCigarTester.tmp7008147791811421425/output.sam --METRICS_FILE /tmp/SimpleMarkDuplicatesWithMateCigarTester.tmp7008147791811421425/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_RECORDS_IN_RAM 1000 --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --TAGGING_POLICY DontTag --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_END_IN_UNPAIRED_READS false --FLOW_USE_UNPAIRED_CLIPPED_END false --FLOW_UNPAIRED_END_UNCERTAINTY 0 --FLOW_UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME SimpleMarkDuplicatesWithMateCigar --READ_NAME_REGEX <optimized capture of last three ':' separated fields as numeric values> --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:17:23 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 13:17:23 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. INFO 2025-04-24 13:17:23 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. INFO 2025-04-24 13:17:23 MarkDuplicatesWithMateCigar Processed 4 records INFO 2025-04-24 13:17:23 MarkDuplicatesWithMateCigar Marking 2 records as duplicates. [Thu Apr 24 13:17:23 EDT 2025] picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 [Thu Apr 24 13:17:23 EDT 2025] SimpleMarkDuplicatesWithMateCigar --INPUT /tmp/SimpleMarkDuplicatesWithMateCigarTester.tmp9374139770494962555/input.sam --OUTPUT /tmp/SimpleMarkDuplicatesWithMateCigarTester.tmp9374139770494962555/output.sam --METRICS_FILE /tmp/SimpleMarkDuplicatesWithMateCigarTester.tmp9374139770494962555/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_RECORDS_IN_RAM 1000 --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --TAGGING_POLICY DontTag --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_END_IN_UNPAIRED_READS false --FLOW_USE_UNPAIRED_CLIPPED_END false --FLOW_UNPAIRED_END_UNCERTAINTY 0 --FLOW_UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME SimpleMarkDuplicatesWithMateCigar --READ_NAME_REGEX <optimized capture of last three ':' separated fields as numeric values> --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:17:23 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 13:17:23 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. INFO 2025-04-24 13:17:23 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. INFO 2025-04-24 13:17:23 MarkDuplicatesWithMateCigar Processed 4 records INFO 2025-04-24 13:17:23 MarkDuplicatesWithMateCigar Marking 2 records as duplicates. [Thu Apr 24 13:17:23 EDT 2025] picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 [Thu Apr 24 13:17:23 EDT 2025] SimpleMarkDuplicatesWithMateCigar --INPUT /tmp/SimpleMarkDuplicatesWithMateCigarTester.tmp16300672852530404615/input.sam --OUTPUT /tmp/SimpleMarkDuplicatesWithMateCigarTester.tmp16300672852530404615/output.sam --METRICS_FILE /tmp/SimpleMarkDuplicatesWithMateCigarTester.tmp16300672852530404615/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_RECORDS_IN_RAM 1000 --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --TAGGING_POLICY DontTag --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_END_IN_UNPAIRED_READS false --FLOW_USE_UNPAIRED_CLIPPED_END false --FLOW_UNPAIRED_END_UNCERTAINTY 0 --FLOW_UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME SimpleMarkDuplicatesWithMateCigar --READ_NAME_REGEX <optimized capture of last three ':' separated fields as numeric values> --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:17:23 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 13:17:23 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. INFO 2025-04-24 13:17:23 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. INFO 2025-04-24 13:17:23 MarkDuplicatesWithMateCigar Processed 5 records INFO 2025-04-24 13:17:23 MarkDuplicatesWithMateCigar Marking 2 records as duplicates. [Thu Apr 24 13:17:23 EDT 2025] picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 [Thu Apr 24 13:17:23 EDT 2025] SimpleMarkDuplicatesWithMateCigar --INPUT /tmp/SimpleMarkDuplicatesWithMateCigarTester.tmp154909232492326265/input.sam --OUTPUT /tmp/SimpleMarkDuplicatesWithMateCigarTester.tmp154909232492326265/output.sam --METRICS_FILE /tmp/SimpleMarkDuplicatesWithMateCigarTester.tmp154909232492326265/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_RECORDS_IN_RAM 1000 --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --TAGGING_POLICY DontTag --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_END_IN_UNPAIRED_READS false --FLOW_USE_UNPAIRED_CLIPPED_END false --FLOW_UNPAIRED_END_UNCERTAINTY 0 --FLOW_UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME SimpleMarkDuplicatesWithMateCigar --READ_NAME_REGEX <optimized capture of last three ':' separated fields as numeric values> --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:17:23 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 13:17:23 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. INFO 2025-04-24 13:17:23 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. INFO 2025-04-24 13:17:23 MarkDuplicatesWithMateCigar Processed 5 records INFO 2025-04-24 13:17:23 MarkDuplicatesWithMateCigar Marking 2 records as duplicates. [Thu Apr 24 13:17:23 EDT 2025] picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 [Thu Apr 24 13:17:23 EDT 2025] SimpleMarkDuplicatesWithMateCigar --INPUT /tmp/SimpleMarkDuplicatesWithMateCigarTester.tmp2573637326168797521/input.sam --OUTPUT /tmp/SimpleMarkDuplicatesWithMateCigarTester.tmp2573637326168797521/output.sam --METRICS_FILE /tmp/SimpleMarkDuplicatesWithMateCigarTester.tmp2573637326168797521/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_RECORDS_IN_RAM 1000 --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --TAGGING_POLICY DontTag --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_END_IN_UNPAIRED_READS false --FLOW_USE_UNPAIRED_CLIPPED_END false --FLOW_UNPAIRED_END_UNCERTAINTY 0 --FLOW_UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME SimpleMarkDuplicatesWithMateCigar --READ_NAME_REGEX <optimized capture of last three ':' separated fields as numeric values> --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:17:23 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 13:17:23 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. INFO 2025-04-24 13:17:23 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. INFO 2025-04-24 13:17:23 MarkDuplicatesWithMateCigar Processed 6 records INFO 2025-04-24 13:17:23 MarkDuplicatesWithMateCigar Marking 2 records as duplicates. [Thu Apr 24 13:17:23 EDT 2025] picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 [Thu Apr 24 13:17:23 EDT 2025] SimpleMarkDuplicatesWithMateCigar --INPUT /tmp/SimpleMarkDuplicatesWithMateCigarTester.tmp13393083610981757846/input.sam --OUTPUT /tmp/SimpleMarkDuplicatesWithMateCigarTester.tmp13393083610981757846/output.sam --METRICS_FILE /tmp/SimpleMarkDuplicatesWithMateCigarTester.tmp13393083610981757846/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_RECORDS_IN_RAM 1000 --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --TAGGING_POLICY DontTag --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_END_IN_UNPAIRED_READS false --FLOW_USE_UNPAIRED_CLIPPED_END false --FLOW_UNPAIRED_END_UNCERTAINTY 0 --FLOW_UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME SimpleMarkDuplicatesWithMateCigar --READ_NAME_REGEX <optimized capture of last three ':' separated fields as numeric values> --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:17:23 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 13:17:23 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. INFO 2025-04-24 13:17:23 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. INFO 2025-04-24 13:17:23 MarkDuplicatesWithMateCigar Processed 4 records INFO 2025-04-24 13:17:23 MarkDuplicatesWithMateCigar Marking 0 records as duplicates. [Thu Apr 24 13:17:23 EDT 2025] picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 [Thu Apr 24 13:17:23 EDT 2025] SimpleMarkDuplicatesWithMateCigar --INPUT /tmp/SimpleMarkDuplicatesWithMateCigarTester.tmp4592402596816950789/input.sam --OUTPUT /tmp/SimpleMarkDuplicatesWithMateCigarTester.tmp4592402596816950789/output.sam --METRICS_FILE /tmp/SimpleMarkDuplicatesWithMateCigarTester.tmp4592402596816950789/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_RECORDS_IN_RAM 1000 --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --TAGGING_POLICY DontTag --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_END_IN_UNPAIRED_READS false --FLOW_USE_UNPAIRED_CLIPPED_END false --FLOW_UNPAIRED_END_UNCERTAINTY 0 --FLOW_UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME SimpleMarkDuplicatesWithMateCigar --READ_NAME_REGEX <optimized capture of last three ':' separated fields as numeric values> --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:17:23 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 13:17:23 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ1. Cause: String 'READ1' did not start with a parsable number. INFO 2025-04-24 13:17:23 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. INFO 2025-04-24 13:17:23 MarkDuplicatesWithMateCigar Processed 4 records INFO 2025-04-24 13:17:23 MarkDuplicatesWithMateCigar Marking 2 records as duplicates. [Thu Apr 24 13:17:23 EDT 2025] picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 [Thu Apr 24 13:17:23 EDT 2025] SimpleMarkDuplicatesWithMateCigar --INPUT /tmp/SimpleMarkDuplicatesWithMateCigarTester.tmp8891744319613006131/input.sam --OUTPUT /tmp/SimpleMarkDuplicatesWithMateCigarTester.tmp8891744319613006131/output.sam --METRICS_FILE /tmp/SimpleMarkDuplicatesWithMateCigarTester.tmp8891744319613006131/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_RECORDS_IN_RAM 1000 --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --TAGGING_POLICY DontTag --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_END_IN_UNPAIRED_READS false --FLOW_USE_UNPAIRED_CLIPPED_END false --FLOW_UNPAIRED_END_UNCERTAINTY 0 --FLOW_UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME SimpleMarkDuplicatesWithMateCigar --READ_NAME_REGEX <optimized capture of last three ':' separated fields as numeric values> --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:17:23 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 13:17:23 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. INFO 2025-04-24 13:17:23 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. INFO 2025-04-24 13:17:23 MarkDuplicatesWithMateCigar Processed 4 records INFO 2025-04-24 13:17:23 MarkDuplicatesWithMateCigar Marking 2 records as duplicates. [Thu Apr 24 13:17:23 EDT 2025] picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 [Thu Apr 24 13:17:23 EDT 2025] SimpleMarkDuplicatesWithMateCigar --INPUT /tmp/SimpleMarkDuplicatesWithMateCigarTester.tmp15775763725625236699/input.sam --OUTPUT /tmp/SimpleMarkDuplicatesWithMateCigarTester.tmp15775763725625236699/output.sam --METRICS_FILE /tmp/SimpleMarkDuplicatesWithMateCigarTester.tmp15775763725625236699/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_RECORDS_IN_RAM 1000 --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --TAGGING_POLICY DontTag --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_END_IN_UNPAIRED_READS false --FLOW_USE_UNPAIRED_CLIPPED_END false --FLOW_UNPAIRED_END_UNCERTAINTY 0 --FLOW_UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME SimpleMarkDuplicatesWithMateCigar --READ_NAME_REGEX <optimized capture of last three ':' separated fields as numeric values> --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:17:23 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 13:17:23 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ0. Cause: String 'READ0' did not start with a parsable number. INFO 2025-04-24 13:17:23 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. INFO 2025-04-24 13:17:23 MarkDuplicatesWithMateCigar Processed 4 records INFO 2025-04-24 13:17:23 MarkDuplicatesWithMateCigar Marking 2 records as duplicates. [Thu Apr 24 13:17:23 EDT 2025] picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 [Thu Apr 24 13:17:23 EDT 2025] SimpleMarkDuplicatesWithMateCigar --INPUT /tmp/SimpleMarkDuplicatesWithMateCigarTester.tmp15355403693877761561/input.sam --OUTPUT /tmp/SimpleMarkDuplicatesWithMateCigarTester.tmp15355403693877761561/output.sam --METRICS_FILE /tmp/SimpleMarkDuplicatesWithMateCigarTester.tmp15355403693877761561/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_RECORDS_IN_RAM 1000 --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --TAGGING_POLICY DontTag --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_END_IN_UNPAIRED_READS false --FLOW_USE_UNPAIRED_CLIPPED_END false --FLOW_UNPAIRED_END_UNCERTAINTY 0 --FLOW_UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME SimpleMarkDuplicatesWithMateCigar --READ_NAME_REGEX <optimized capture of last three ':' separated fields as numeric values> --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:17:23 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 13:17:23 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ1. Cause: String 'READ1' did not start with a parsable number. INFO 2025-04-24 13:17:23 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. INFO 2025-04-24 13:17:23 MarkDuplicatesWithMateCigar Processed 4 records INFO 2025-04-24 13:17:23 MarkDuplicatesWithMateCigar Marking 2 records as duplicates. [Thu Apr 24 13:17:23 EDT 2025] picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 [Thu Apr 24 13:17:23 EDT 2025] SimpleMarkDuplicatesWithMateCigar --INPUT /tmp/SimpleMarkDuplicatesWithMateCigarTester.tmp6054085958505251416/input.sam --OUTPUT /tmp/SimpleMarkDuplicatesWithMateCigarTester.tmp6054085958505251416/output.sam --METRICS_FILE /tmp/SimpleMarkDuplicatesWithMateCigarTester.tmp6054085958505251416/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_RECORDS_IN_RAM 1000 --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --TAGGING_POLICY DontTag --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_END_IN_UNPAIRED_READS false --FLOW_USE_UNPAIRED_CLIPPED_END false --FLOW_UNPAIRED_END_UNCERTAINTY 0 --FLOW_UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME SimpleMarkDuplicatesWithMateCigar --READ_NAME_REGEX <optimized capture of last three ':' separated fields as numeric values> --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:17:23 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 13:17:23 MarkDuplicatesWithMateCigar Found 1 optical duplicate clusters. INFO 2025-04-24 13:17:23 MarkDuplicatesWithMateCigar Processed 5 records INFO 2025-04-24 13:17:23 MarkDuplicatesWithMateCigar Marking 2 records as duplicates. [Thu Apr 24 13:17:23 EDT 2025] picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 [Thu Apr 24 13:17:23 EDT 2025] SimpleMarkDuplicatesWithMateCigar --INPUT /tmp/SimpleMarkDuplicatesWithMateCigarTester.tmp11678775145390647309/input.sam --OUTPUT /tmp/SimpleMarkDuplicatesWithMateCigarTester.tmp11678775145390647309/output.sam --METRICS_FILE /tmp/SimpleMarkDuplicatesWithMateCigarTester.tmp11678775145390647309/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_RECORDS_IN_RAM 1000 --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --TAGGING_POLICY DontTag --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_END_IN_UNPAIRED_READS false --FLOW_USE_UNPAIRED_CLIPPED_END false --FLOW_UNPAIRED_END_UNCERTAINTY 0 --FLOW_UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME SimpleMarkDuplicatesWithMateCigar --READ_NAME_REGEX <optimized capture of last three ':' separated fields as numeric values> --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:17:23 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 13:17:23 MarkDuplicatesWithMateCigar Found 1 optical duplicate clusters. INFO 2025-04-24 13:17:23 MarkDuplicatesWithMateCigar Processed 5 records INFO 2025-04-24 13:17:23 MarkDuplicatesWithMateCigar Marking 2 records as duplicates. [Thu Apr 24 13:17:23 EDT 2025] picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 [Thu Apr 24 13:17:23 EDT 2025] SimpleMarkDuplicatesWithMateCigar --INPUT /tmp/SimpleMarkDuplicatesWithMateCigarTester.tmp18133399294085817782/input.sam --OUTPUT /tmp/SimpleMarkDuplicatesWithMateCigarTester.tmp18133399294085817782/output.sam --METRICS_FILE /tmp/SimpleMarkDuplicatesWithMateCigarTester.tmp18133399294085817782/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_RECORDS_IN_RAM 1000 --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --TAGGING_POLICY DontTag --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_END_IN_UNPAIRED_READS false --FLOW_USE_UNPAIRED_CLIPPED_END false --FLOW_UNPAIRED_END_UNCERTAINTY 0 --FLOW_UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME SimpleMarkDuplicatesWithMateCigar --READ_NAME_REGEX <optimized capture of last three ':' separated fields as numeric values> --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:17:23 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 13:17:23 MarkDuplicatesWithMateCigar Found 1 optical duplicate clusters. INFO 2025-04-24 13:17:23 MarkDuplicatesWithMateCigar Processed 5 records INFO 2025-04-24 13:17:23 MarkDuplicatesWithMateCigar Marking 2 records as duplicates. [Thu Apr 24 13:17:23 EDT 2025] picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 [Thu Apr 24 13:17:23 EDT 2025] SimpleMarkDuplicatesWithMateCigar --INPUT /tmp/SimpleMarkDuplicatesWithMateCigarTester.tmp12761710764821694100/input.sam --OUTPUT /tmp/SimpleMarkDuplicatesWithMateCigarTester.tmp12761710764821694100/output.sam --METRICS_FILE /tmp/SimpleMarkDuplicatesWithMateCigarTester.tmp12761710764821694100/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_RECORDS_IN_RAM 1000 --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --TAGGING_POLICY DontTag --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_END_IN_UNPAIRED_READS false --FLOW_USE_UNPAIRED_CLIPPED_END false --FLOW_UNPAIRED_END_UNCERTAINTY 0 --FLOW_UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME SimpleMarkDuplicatesWithMateCigar --READ_NAME_REGEX <optimized capture of last three ':' separated fields as numeric values> --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:17:23 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 13:17:23 MarkDuplicatesWithMateCigar Found 1 optical duplicate clusters. INFO 2025-04-24 13:17:23 MarkDuplicatesWithMateCigar Processed 5 records INFO 2025-04-24 13:17:23 MarkDuplicatesWithMateCigar Marking 2 records as duplicates. [Thu Apr 24 13:17:23 EDT 2025] picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 [Thu Apr 24 13:17:23 EDT 2025] SimpleMarkDuplicatesWithMateCigar --INPUT /tmp/SimpleMarkDuplicatesWithMateCigarTester.tmp9301113650458179496/input.sam --OUTPUT /tmp/SimpleMarkDuplicatesWithMateCigarTester.tmp9301113650458179496/output.sam --METRICS_FILE /tmp/SimpleMarkDuplicatesWithMateCigarTester.tmp9301113650458179496/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_RECORDS_IN_RAM 1000 --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --TAGGING_POLICY DontTag --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_END_IN_UNPAIRED_READS false --FLOW_USE_UNPAIRED_CLIPPED_END false --FLOW_UNPAIRED_END_UNCERTAINTY 0 --FLOW_UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME SimpleMarkDuplicatesWithMateCigar --READ_NAME_REGEX <optimized capture of last three ':' separated fields as numeric values> --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:17:23 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 13:17:23 MarkDuplicatesWithMateCigar Found 1 optical duplicate clusters. INFO 2025-04-24 13:17:23 MarkDuplicatesWithMateCigar Processed 5 records INFO 2025-04-24 13:17:23 MarkDuplicatesWithMateCigar Marking 2 records as duplicates. [Thu Apr 24 13:17:23 EDT 2025] picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 [Thu Apr 24 13:17:23 EDT 2025] SimpleMarkDuplicatesWithMateCigar --INPUT /tmp/SimpleMarkDuplicatesWithMateCigarTester.tmp5030354569701565043/input.sam --OUTPUT /tmp/SimpleMarkDuplicatesWithMateCigarTester.tmp5030354569701565043/output.sam --METRICS_FILE /tmp/SimpleMarkDuplicatesWithMateCigarTester.tmp5030354569701565043/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_RECORDS_IN_RAM 1000 --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --TAGGING_POLICY DontTag --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_END_IN_UNPAIRED_READS false --FLOW_USE_UNPAIRED_CLIPPED_END false --FLOW_UNPAIRED_END_UNCERTAINTY 0 --FLOW_UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME SimpleMarkDuplicatesWithMateCigar --READ_NAME_REGEX <optimized capture of last three ':' separated fields as numeric values> --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:17:23 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 13:17:23 MarkDuplicatesWithMateCigar Found 1 optical duplicate clusters. INFO 2025-04-24 13:17:23 MarkDuplicatesWithMateCigar Processed 5 records INFO 2025-04-24 13:17:23 MarkDuplicatesWithMateCigar Marking 2 records as duplicates. [Thu Apr 24 13:17:23 EDT 2025] picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 [Thu Apr 24 13:17:23 EDT 2025] SimpleMarkDuplicatesWithMateCigar --INPUT /tmp/SimpleMarkDuplicatesWithMateCigarTester.tmp15617601358361074300/input.sam --OUTPUT /tmp/SimpleMarkDuplicatesWithMateCigarTester.tmp15617601358361074300/output.sam --METRICS_FILE /tmp/SimpleMarkDuplicatesWithMateCigarTester.tmp15617601358361074300/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_RECORDS_IN_RAM 1000 --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --TAGGING_POLICY DontTag --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_END_IN_UNPAIRED_READS false --FLOW_USE_UNPAIRED_CLIPPED_END false --FLOW_UNPAIRED_END_UNCERTAINTY 0 --FLOW_UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME SimpleMarkDuplicatesWithMateCigar --READ_NAME_REGEX <optimized capture of last three ':' separated fields as numeric values> --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:17:23 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 13:17:23 MarkDuplicatesWithMateCigar Found 1 optical duplicate clusters. INFO 2025-04-24 13:17:23 MarkDuplicatesWithMateCigar Processed 5 records INFO 2025-04-24 13:17:23 MarkDuplicatesWithMateCigar Marking 2 records as duplicates. [Thu Apr 24 13:17:23 EDT 2025] picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 [Thu Apr 24 13:17:23 EDT 2025] SimpleMarkDuplicatesWithMateCigar --INPUT /tmp/SimpleMarkDuplicatesWithMateCigarTester.tmp2661635395496000316/input.sam --OUTPUT /tmp/SimpleMarkDuplicatesWithMateCigarTester.tmp2661635395496000316/output.sam --METRICS_FILE /tmp/SimpleMarkDuplicatesWithMateCigarTester.tmp2661635395496000316/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_RECORDS_IN_RAM 1000 --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --TAGGING_POLICY DontTag --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_END_IN_UNPAIRED_READS false --FLOW_USE_UNPAIRED_CLIPPED_END false --FLOW_UNPAIRED_END_UNCERTAINTY 0 --FLOW_UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME SimpleMarkDuplicatesWithMateCigar --READ_NAME_REGEX <optimized capture of last three ':' separated fields as numeric values> --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:17:23 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 13:17:23 MarkDuplicatesWithMateCigar Found 1 optical duplicate clusters. INFO 2025-04-24 13:17:23 MarkDuplicatesWithMateCigar Processed 5 records INFO 2025-04-24 13:17:23 MarkDuplicatesWithMateCigar Marking 2 records as duplicates. [Thu Apr 24 13:17:23 EDT 2025] picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 [Thu Apr 24 13:17:23 EDT 2025] SimpleMarkDuplicatesWithMateCigar --INPUT /tmp/SimpleMarkDuplicatesWithMateCigarTester.tmp8081191527302027340/input.sam --OUTPUT /tmp/SimpleMarkDuplicatesWithMateCigarTester.tmp8081191527302027340/output.sam --METRICS_FILE /tmp/SimpleMarkDuplicatesWithMateCigarTester.tmp8081191527302027340/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_RECORDS_IN_RAM 1000 --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --TAGGING_POLICY DontTag --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_END_IN_UNPAIRED_READS false --FLOW_USE_UNPAIRED_CLIPPED_END false --FLOW_UNPAIRED_END_UNCERTAINTY 0 --FLOW_UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME SimpleMarkDuplicatesWithMateCigar --READ_NAME_REGEX <optimized capture of last three ':' separated fields as numeric values> --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:17:23 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 13:17:23 MarkDuplicatesWithMateCigar Found 1 optical duplicate clusters. INFO 2025-04-24 13:17:23 MarkDuplicatesWithMateCigar Processed 5 records INFO 2025-04-24 13:17:23 MarkDuplicatesWithMateCigar Marking 2 records as duplicates. [Thu Apr 24 13:17:23 EDT 2025] picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 [Thu Apr 24 13:17:23 EDT 2025] SimpleMarkDuplicatesWithMateCigar --INPUT /tmp/SimpleMarkDuplicatesWithMateCigarTester.tmp10937202354175024181/input.sam --OUTPUT /tmp/SimpleMarkDuplicatesWithMateCigarTester.tmp10937202354175024181/output.sam --METRICS_FILE /tmp/SimpleMarkDuplicatesWithMateCigarTester.tmp10937202354175024181/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_RECORDS_IN_RAM 1000 --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --TAGGING_POLICY DontTag --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_END_IN_UNPAIRED_READS false --FLOW_USE_UNPAIRED_CLIPPED_END false --FLOW_UNPAIRED_END_UNCERTAINTY 0 --FLOW_UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME SimpleMarkDuplicatesWithMateCigar --READ_NAME_REGEX <optimized capture of last three ':' separated fields as numeric values> --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:17:23 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 13:17:24 MarkDuplicatesWithMateCigar Found 1 optical duplicate clusters. INFO 2025-04-24 13:17:24 MarkDuplicatesWithMateCigar Processed 5 records INFO 2025-04-24 13:17:24 MarkDuplicatesWithMateCigar Marking 2 records as duplicates. [Thu Apr 24 13:17:24 EDT 2025] picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 [Thu Apr 24 13:17:24 EDT 2025] SimpleMarkDuplicatesWithMateCigar --INPUT /tmp/SimpleMarkDuplicatesWithMateCigarTester.tmp15063012734846889608/input.sam --OUTPUT /tmp/SimpleMarkDuplicatesWithMateCigarTester.tmp15063012734846889608/output.sam --METRICS_FILE /tmp/SimpleMarkDuplicatesWithMateCigarTester.tmp15063012734846889608/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_RECORDS_IN_RAM 1000 --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --TAGGING_POLICY DontTag --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_END_IN_UNPAIRED_READS false --FLOW_USE_UNPAIRED_CLIPPED_END false --FLOW_UNPAIRED_END_UNCERTAINTY 0 --FLOW_UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME SimpleMarkDuplicatesWithMateCigar --READ_NAME_REGEX <optimized capture of last three ':' separated fields as numeric values> --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:17:24 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 13:17:24 MarkDuplicatesWithMateCigar Found 1 optical duplicate clusters. INFO 2025-04-24 13:17:24 MarkDuplicatesWithMateCigar Processed 5 records INFO 2025-04-24 13:17:24 MarkDuplicatesWithMateCigar Marking 2 records as duplicates. [Thu Apr 24 13:17:24 EDT 2025] picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 [Thu Apr 24 13:17:24 EDT 2025] SimpleMarkDuplicatesWithMateCigar --INPUT /tmp/SimpleMarkDuplicatesWithMateCigarTester.tmp17590861807825646915/input.sam --OUTPUT /tmp/SimpleMarkDuplicatesWithMateCigarTester.tmp17590861807825646915/output.sam --METRICS_FILE /tmp/SimpleMarkDuplicatesWithMateCigarTester.tmp17590861807825646915/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_RECORDS_IN_RAM 1000 --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --TAGGING_POLICY DontTag --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_END_IN_UNPAIRED_READS false --FLOW_USE_UNPAIRED_CLIPPED_END false --FLOW_UNPAIRED_END_UNCERTAINTY 0 --FLOW_UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME SimpleMarkDuplicatesWithMateCigar --READ_NAME_REGEX <optimized capture of last three ':' separated fields as numeric values> --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:17:24 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 13:17:24 MarkDuplicatesWithMateCigar Found 1 optical duplicate clusters. INFO 2025-04-24 13:17:24 MarkDuplicatesWithMateCigar Processed 5 records INFO 2025-04-24 13:17:24 MarkDuplicatesWithMateCigar Marking 2 records as duplicates. [Thu Apr 24 13:17:24 EDT 2025] picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 [Thu Apr 24 13:17:24 EDT 2025] SimpleMarkDuplicatesWithMateCigar --INPUT /tmp/SimpleMarkDuplicatesWithMateCigarTester.tmp6511371395591599499/input.sam --OUTPUT /tmp/SimpleMarkDuplicatesWithMateCigarTester.tmp6511371395591599499/output.sam --METRICS_FILE /tmp/SimpleMarkDuplicatesWithMateCigarTester.tmp6511371395591599499/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_RECORDS_IN_RAM 1000 --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --TAGGING_POLICY DontTag --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_END_IN_UNPAIRED_READS false --FLOW_USE_UNPAIRED_CLIPPED_END false --FLOW_UNPAIRED_END_UNCERTAINTY 0 --FLOW_UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME SimpleMarkDuplicatesWithMateCigar --READ_NAME_REGEX <optimized capture of last three ':' separated fields as numeric values> --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:17:24 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 13:17:24 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. INFO 2025-04-24 13:17:24 MarkDuplicatesWithMateCigar Processed 2 records INFO 2025-04-24 13:17:24 MarkDuplicatesWithMateCigar Marking 0 records as duplicates. [Thu Apr 24 13:17:24 EDT 2025] picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 [Thu Apr 24 13:17:24 EDT 2025] SimpleMarkDuplicatesWithMateCigar --INPUT /tmp/SimpleMarkDuplicatesWithMateCigarTester.tmp1980322341828501021/input.sam --OUTPUT /tmp/SimpleMarkDuplicatesWithMateCigarTester.tmp1980322341828501021/output.sam --METRICS_FILE /tmp/SimpleMarkDuplicatesWithMateCigarTester.tmp1980322341828501021/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_RECORDS_IN_RAM 1000 --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --TAGGING_POLICY DontTag --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_END_IN_UNPAIRED_READS false --FLOW_USE_UNPAIRED_CLIPPED_END false --FLOW_UNPAIRED_END_UNCERTAINTY 0 --FLOW_UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME SimpleMarkDuplicatesWithMateCigar --READ_NAME_REGEX <optimized capture of last three ':' separated fields as numeric values> --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:17:24 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 13:17:24 EDT 2025] picard.sam.markduplicates.SimpleMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp