Class picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigarTest
|
100%
successful |
Tests
| Test | Duration | Result |
|---|---|---|
| testBadUmis[0]([AAAA, A], [AAAA, A], [false, false], 4) | 0.007s | passed |
| testBadUmis[1]([T, GG], [T, GG], [false, false], 1) | 0.007s | passed |
| testBadUmis[2]([TTGA, TTAT, null], [TTGA, TTAT, null], [false, false, false], 4) | 0.006s | passed |
| testBulkFragmentsNoDuplicates[0](.sam) | 0.595s | passed |
| testBulkFragmentsNoDuplicates[1](.bam) | 0.628s | passed |
| testBulkFragmentsNoDuplicates[2](.cram) | 0.934s | passed |
| testBulkFragmentsWithDuplicates[0](.sam) | 0.782s | passed |
| testBulkFragmentsWithDuplicates[1](.bam) | 0.819s | passed |
| testBulkFragmentsWithDuplicates[2](.cram) | 1.485s | passed |
| testBulkPairsNoDuplicates[0](.sam) | 0.906s | passed |
| testBulkPairsNoDuplicates[1](.bam) | 0.947s | passed |
| testBulkPairsNoDuplicates[2](.cram) | 1.612s | passed |
| testBulkPairsWithDuplicates[0](.sam) | 0.495s | passed |
| testBulkPairsWithDuplicates[1](.bam) | 0.509s | passed |
| testBulkPairsWithDuplicates[2](.cram) | 0.846s | passed |
| testDifferentChromosomesInOppositeOrder | 0.011s | passed |
| testDuplexUmi[0](true, 0, [AAA-GGG, GGG-AAA], [AAA-GGG, GGG-AAA], [false, true], [1, 4], [4, 1], [false, true], [true, false], LIBRARY A MEAN_UMI_LENGTH 6 OBSERVED_UNIQUE_UMIS 1 INFERRED_UNIQUE_UMIS 1 OBSERVED_BASE_ERRORS 0 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 2 OBSERVED_UMI_ENTROPY 0 INFERRED_UMI_ENTROPY 0 UMI_BASE_QUALITIES -1 PCT_UMI_WITH_N 0 ) | 0.009s | passed |
| testDuplexUmi[1](false, 0, [AAA-GGG, GGG-AAA], [AAA-GGG, GGG-AAA], [false, false], [1, 4], [4, 1], [false, true], [true, false], LIBRARY A MEAN_UMI_LENGTH 6 OBSERVED_UNIQUE_UMIS 2 INFERRED_UNIQUE_UMIS 2 OBSERVED_BASE_ERRORS 0 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 4 OBSERVED_UMI_ENTROPY 0.5 INFERRED_UMI_ENTROPY 0.5 UMI_BASE_QUALITIES -1 PCT_UMI_WITH_N 0 ) | 0.008s | passed |
| testDuplexUmi[2](true, 1, [AAA-GGG, GGG-ATA], [AAA-GGG, GGG-AAA], [false, true], [1, 4], [4, 1], [false, true], [true, false], LIBRARY A MEAN_UMI_LENGTH 6 OBSERVED_UNIQUE_UMIS 2 INFERRED_UNIQUE_UMIS 1 OBSERVED_BASE_ERRORS 2 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 2 OBSERVED_UMI_ENTROPY 0.5 INFERRED_UMI_ENTROPY 0 UMI_BASE_QUALITIES 11 PCT_UMI_WITH_N 0 ) | 0.007s | passed |
| testEmptyUmis[0]([null, null, null], [null, null, null], [false, true, true], 4) | 0.007s | passed |
| testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[0](true, true, true) | 0.009s | passed |
| testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[1](true, false, true) | 0.008s | passed |
| testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[2](false, true, true) | 0.008s | passed |
| testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[3](true, true, false) | 0.007s | passed |
| testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[4](true, false, false) | 0.007s | passed |
| testManyOpticalDuplicateClusterOneEndSamePositionOneCluster[5](false, true, false) | 0.008s | passed |
| testMappedFragmentAndMappedPairFirstOfPairNonPrimary | 0.007s | passed |
| testMappedFragmentAndMatePairFirstUnmapped | 0.007s | passed |
| testMappedFragmentAndMatePairSecondUnmapped | 0.007s | passed |
| testMappedPairAndMappedFragmentAndMatePairFirstUnmapped | 0.007s | passed |
| testMappedPairAndMappedFragmentAndMatePairSecondUnmapped | 0.008s | passed |
| testMappedPairAndMatePairFirstOppositeStrandSecondUnmapped | 0.007s | passed |
| testMappedPairAndMatePairFirstUnmapped | 0.007s | passed |
| testMappedPairAndMatePairSecondUnmapped | 0.008s | passed |
| testMappedPairWithFirstEndSamePositionAndOther | 0.007s | passed |
| testMappedPairWithSamePosition | 0.007s | passed |
| testMappedPairWithSamePositionSameCigar | 0.007s | passed |
| testMatePairFirstUnmapped | 0.007s | passed |
| testMatePairSecondUnmapped | 0.007s | passed |
| testMultipleLibraryUmiMetrics[0]([A, B, A, B, A], [AAAA, AAAA, ATTA, AAAA, AAAT], [AAAA, AAAA, ATTA, AAAA, AAAA], [false, false, false, true, true], 1, [LIBRARY A MEAN_UMI_LENGTH 4 OBSERVED_UNIQUE_UMIS 3 INFERRED_UNIQUE_UMIS 2 OBSERVED_BASE_ERRORS 2 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 4 OBSERVED_UMI_ENTROPY 0.792481 INFERRED_UMI_ENTROPY 0.459148 UMI_BASE_QUALITIES 11 PCT_UMI_WITH_N 0 , LIBRARY B MEAN_UMI_LENGTH 4 OBSERVED_UNIQUE_UMIS 1 INFERRED_UNIQUE_UMIS 1 OBSERVED_BASE_ERRORS 0 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 2 OBSERVED_UMI_ENTROPY 0 INFERRED_UMI_ENTROPY 0 UMI_BASE_QUALITIES -1 PCT_UMI_WITH_N 0 ]) | 0.014s | passed |
| testMultipleLibraryUmiMetrics[1]([A, B, C, C, C], [AAA, AAA, TTA, AAA, AAT], [AAA, AAA, TTA, AAA, AAA], [false, false, false, false, true], 1, [LIBRARY A MEAN_UMI_LENGTH 3 OBSERVED_UNIQUE_UMIS 1 INFERRED_UNIQUE_UMIS 1 OBSERVED_BASE_ERRORS 0 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 2 OBSERVED_UMI_ENTROPY 0 INFERRED_UMI_ENTROPY 0 UMI_BASE_QUALITIES -1 PCT_UMI_WITH_N 0 , LIBRARY B MEAN_UMI_LENGTH 3 OBSERVED_UNIQUE_UMIS 1 INFERRED_UNIQUE_UMIS 1 OBSERVED_BASE_ERRORS 0 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 2 OBSERVED_UMI_ENTROPY 0 INFERRED_UMI_ENTROPY 0 UMI_BASE_QUALITIES -1 PCT_UMI_WITH_N 0 , LIBRARY C MEAN_UMI_LENGTH 3 OBSERVED_UNIQUE_UMIS 3 INFERRED_UNIQUE_UMIS 2 OBSERVED_BASE_ERRORS 2 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 4 OBSERVED_UMI_ENTROPY 0.792481 INFERRED_UMI_ENTROPY 0.459148 UMI_BASE_QUALITIES 10 PCT_UMI_WITH_N 0 ]) | 0.021s | passed |
| testOpticalDuplicateBehaviorNullRegex | 0.007s | passed |
| testOpticalDuplicateClusterOneEndSamePositionOneCluster | 0.007s | passed |
| testOpticalDuplicateClusterSamePositionNoOpticalDuplicatesWithinPixelDistance | 0.008s | passed |
| testOpticalDuplicateClusterSamePositionOneOpticalDuplicatesWithinPixelDistance | 0.007s | passed |
| testOpticalDuplicateClustersAddingSecondEndFirstSameCoordinate | 0.008s | passed |
| testOpticalDuplicateFinding | 0.008s | passed |
| testPathologicalOrderingAtTheSamePosition | 0.007s | passed |
| testSecondEndIsBeforeFirstInCoordinate | 0.008s | passed |
| testSingleMappedFragment | 0.007s | passed |
| testSingleMappedFragmentAndSingleMappedPair | 0.007s | passed |
| testSingleMappedFragmentAndTwoMappedPairs | 0.008s | passed |
| testSingleMappedPair | 0.007s | passed |
| testSingleUnmappedFragment | 0.007s | passed |
| testSingleUnmappedPair | 0.007s | passed |
| testStackOverFlowPairSetSwap | 0.009s | passed |
| testThreeGroupsOnDifferentChromosomesOfThreeMappedPairs | 0.008s | passed |
| testThreeMappedPairs | 0.008s | passed |
| testThreeMappedPairsWithMatchingSecondMate | 0.008s | passed |
| testTwoGroupsOnDifferentChromosomesOfThreeMappedPairs | 0.008s | passed |
| testTwoGroupsOnDifferentChromosomesOfTwoFragments | 0.007s | passed |
| testTwoGroupsOnDifferentChromosomesOfTwoMappedPairs | 0.008s | passed |
| testTwoMappedFragments | 0.008s | passed |
| testTwoMappedPairWithSamePosition | 0.007s | passed |
| testTwoMappedPairWithSamePositionDifferentStrands | 0.008s | passed |
| testTwoMappedPairWithSamePositionDifferentStrands2 | 0.008s | passed |
| testTwoMappedPairs | 0.007s | passed |
| testTwoMappedPairsAndMappedSecondaryFragment | 0.008s | passed |
| testTwoMappedPairsAndTerminalUnmappedFragment | 0.007s | passed |
| testTwoMappedPairsAndTerminalUnmappedPair | 0.008s | passed |
| testTwoMappedPairsMatesSoftClipped | 0.007s | passed |
| testTwoMappedPairsWithOppositeOrientations | 0.008s | passed |
| testTwoMappedPairsWithOppositeOrientationsNumberTwo | 0.007s | passed |
| testTwoMappedPairsWithSoftClipping | 0.007s | passed |
| testTwoMappedPairsWithSoftClippingBoth | 0.008s | passed |
| testTwoMappedPairsWithSoftClippingFirstOfPairOnlyNoMateCigar | 0.006s | passed |
| testTwoMappedPairsWithSupplementaryReadsAfterCanonical[0](true, true, true) | 0.007s | passed |
| testTwoMappedPairsWithSupplementaryReadsAfterCanonical[1](true, false, true) | 0.007s | passed |
| testTwoMappedPairsWithSupplementaryReadsAfterCanonical[2](false, true, true) | 0.007s | passed |
| testTwoMappedPairsWithSupplementaryReadsAfterCanonical[3](true, true, false) | 0.006s | passed |
| testTwoMappedPairsWithSupplementaryReadsAfterCanonical[4](true, false, false) | 0.007s | passed |
| testTwoMappedPairsWithSupplementaryReadsAfterCanonical[5](false, true, false) | 0.007s | passed |
| testTwoMappedPairsWithSupplementaryReads[0](true, true, true) | 0.007s | passed |
| testTwoMappedPairsWithSupplementaryReads[1](true, false, true) | 0.008s | passed |
| testTwoMappedPairsWithSupplementaryReads[2](false, true, true) | 0.007s | passed |
| testTwoMappedPairsWithSupplementaryReads[3](true, true, false) | 0.007s | passed |
| testTwoMappedPairsWithSupplementaryReads[4](true, false, false) | 0.008s | passed |
| testTwoMappedPairsWithSupplementaryReads[5](false, true, false) | 0.007s | passed |
| testTwoUnmappedFragments | 0.008s | passed |
| testUmiMetrics[0]([AAAA, AAAA, ATTA, AAAA, AAAT], [AAAA, AAAA, ATTA, AAAA, AAAA], [false, true, false, true, true], 1, LIBRARY A MEAN_UMI_LENGTH 4 OBSERVED_UNIQUE_UMIS 3 INFERRED_UNIQUE_UMIS 2 OBSERVED_BASE_ERRORS 2 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 4 OBSERVED_UMI_ENTROPY 0.685475 INFERRED_UMI_ENTROPY 0.360964 UMI_BASE_QUALITIES 13 PCT_UMI_WITH_N 0 ) | 0.008s | passed |
| testUmiMetrics[1]([AAAA, AAAA, ATTA, AAAA, AAAT], [AAAA, AAAA, AAAA, AAAA, AAAA], [false, true, true, true, true], 2, LIBRARY A MEAN_UMI_LENGTH 4 OBSERVED_UNIQUE_UMIS 3 INFERRED_UNIQUE_UMIS 1 OBSERVED_BASE_ERRORS 6 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 2 OBSERVED_UMI_ENTROPY 0.685475 INFERRED_UMI_ENTROPY 0 UMI_BASE_QUALITIES 8 PCT_UMI_WITH_N 0 ) | 0.008s | passed |
| testUmiMetrics[2]([AAAA, AAAA, AANA, ANNA, ATTA, AAAA, ANAT], [AAAA, AAAA, AAAA, AAAA, AAAA, AAAA, AAAA], [false, true, true, true, true, true, true], 2, LIBRARY A MEAN_UMI_LENGTH 4 OBSERVED_UNIQUE_UMIS 2 INFERRED_UNIQUE_UMIS 1 OBSERVED_BASE_ERRORS 4 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 2 OBSERVED_UMI_ENTROPY 0.405639 INFERRED_UMI_ENTROPY 0 UMI_BASE_QUALITIES 9 PCT_UMI_WITH_N 0.428571 ) | 0.007s | passed |
| testUmiMetrics[3]([AA, AT, AC, AG, TA, TT, TC, TG, CA, CT, CC, CG, GA, GT, GC, GG], [AA, AT, AC, AG, TA, TT, TC, TG, CA, CT, CC, CG, GA, GT, GC, GG], [false, false, false, false, false, false, false, false, false, false, false, false, false, false, false, false], 0, LIBRARY A MEAN_UMI_LENGTH 2 OBSERVED_UNIQUE_UMIS 16 INFERRED_UNIQUE_UMIS 16 OBSERVED_BASE_ERRORS 0 DUPLICATE_SETS_IGNORING_UMI 2 DUPLICATE_SETS_WITH_UMI 32 OBSERVED_UMI_ENTROPY 2 INFERRED_UMI_ENTROPY 2 UMI_BASE_QUALITIES -1 PCT_UMI_WITH_N 0 ) | 0.008s | passed |
| testUmi[0]([AAAA, AAAA, ATTA, AAAA, AAAT], [AAAA, AAAA, ATTA, AAAA, AAAA], [false, true, false, true, true], 1) | 0.008s | passed |
| testUmi[1]([AAAA, AAAA, ATTA, AAAA, AAAT], [AAAA, AAAA, AAAA, AAAA, AAAA], [false, true, true, true, true], 2) | 0.007s | passed |
| testUmi[2]([AAAA, AAAA, AAAT, AAGT, ACGT, TCGT, CCCC], [AAAA, AAAA, AAAA, AAAA, AAAA, AAAA, CCCC], [false, true, true, true, true, true, false], 1) | 0.008s | passed |
| testUmi[3]([A, A, T, G, G, C, C, A], [A, A, A, A, A, A, A, A], [false, true, true, true, true, true, true, true], 1) | 0.008s | passed |
| testUmi[4]([A, A, T, G, G, C, C, A], [A, A, T, G, G, C, C, A], [false, true, false, false, true, false, true, true], 0) | 0.008s | passed |
| testUmi[5]([TTGACATCCA, ATGCCATCGA, AAGTCACCGT], [TTGACATCCA, TTGACATCCA, TTGACATCCA], [false, true, true], 4) | 0.008s | passed |
| testUmi[6]([AAAN, AANN], [AAAN, AAAN], [false, true], 1) | 0.008s | passed |
| testUmi[7]([AAAN, AAAN, AAAA, AAAA, AAAN], [AAAA, AAAA, AAAA, AAAA, AAAA], [false, true, true, true, true], 1) | 0.007s | passed |
| testUmi[8]([AAAN, AAAN, AANN, AANN, AANN], [AAAN, AAAN, AAAN, AAAN, AAAN], [false, true, true, true, true, true], 1) | 0.007s | passed |
Standard error
[Thu Apr 24 13:17:24 EDT 2025] UmiAwareMarkDuplicatesWithMateCigar --UMI_METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.tmp9475413390548939516/umi_metrics.txt --ALLOW_MISSING_UMIS true --INPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.tmp9475413390548939516/input.sam --OUTPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.tmp9475413390548939516/output.sam --METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.tmp9475413390548939516/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_EDIT_DISTANCE_TO_JOIN 1 --UMI_TAG_NAME RX --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 UmiAwareMarkDuplicatesWithMateCigar --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 --MAX_RECORDS_IN_RAM 1000 --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 10000 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.UmiAwareMarkDuplicatesWithMateCigar done. Elapsed time: 0.01 minutes. Runtime.totalMemory()=1073741824 [Thu Apr 24 13:17:24 EDT 2025] UmiAwareMarkDuplicatesWithMateCigar --UMI_METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.tmp18419614547439015101/umi_metrics.txt --ALLOW_MISSING_UMIS true --INPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.tmp18419614547439015101/input.bam --OUTPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.tmp18419614547439015101/output.sam --METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.tmp18419614547439015101/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_EDIT_DISTANCE_TO_JOIN 1 --UMI_TAG_NAME RX --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 UmiAwareMarkDuplicatesWithMateCigar --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 --MAX_RECORDS_IN_RAM 1000 --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 13:17:25 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. INFO 2025-04-24 13:17:25 MarkDuplicatesWithMateCigar Processed 10000 records INFO 2025-04-24 13:17:25 MarkDuplicatesWithMateCigar Marking 0 records as duplicates. [Thu Apr 24 13:17:25 EDT 2025] picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigar done. Elapsed time: 0.01 minutes. Runtime.totalMemory()=1073741824 [Thu Apr 24 13:17:25 EDT 2025] UmiAwareMarkDuplicatesWithMateCigar --UMI_METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.tmp11186477234717680364/umi_metrics.txt --ALLOW_MISSING_UMIS true --INPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.tmp11186477234717680364/input.cram --OUTPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.tmp11186477234717680364/output.sam --METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.tmp11186477234717680364/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --REFERENCE_SEQUENCE /tmp/SamFileTester15432866970796677852/input.fasta --MAX_EDIT_DISTANCE_TO_JOIN 1 --UMI_TAG_NAME RX --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 UmiAwareMarkDuplicatesWithMateCigar --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 --MAX_RECORDS_IN_RAM 1000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:17:25 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null INFO 2025-04-24 13:17:26 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. INFO 2025-04-24 13:17:26 MarkDuplicatesWithMateCigar Processed 10000 records INFO 2025-04-24 13:17:26 MarkDuplicatesWithMateCigar Marking 0 records as duplicates. [Thu Apr 24 13:17:26 EDT 2025] picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigar done. Elapsed time: 0.01 minutes. Runtime.totalMemory()=1073741824 [Thu Apr 24 13:17:26 EDT 2025] UmiAwareMarkDuplicatesWithMateCigar --UMI_METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.tmp10974961986583151254/umi_metrics.txt --ALLOW_MISSING_UMIS true --INPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.tmp10974961986583151254/input.sam --OUTPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.tmp10974961986583151254/output.sam --METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.tmp10974961986583151254/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_EDIT_DISTANCE_TO_JOIN 1 --UMI_TAG_NAME RX --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 UmiAwareMarkDuplicatesWithMateCigar --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 --MAX_RECORDS_IN_RAM 1000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:17:26 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null INFO 2025-04-24 13:17:26 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. INFO 2025-04-24 13:17:26 MarkDuplicatesWithMateCigar Processed 21000 records INFO 2025-04-24 13:17:26 MarkDuplicatesWithMateCigar Marking 20000 records as duplicates. [Thu Apr 24 13:17:26 EDT 2025] picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigar done. Elapsed time: 0.01 minutes. Runtime.totalMemory()=1073741824 [Thu Apr 24 13:17:27 EDT 2025] UmiAwareMarkDuplicatesWithMateCigar --UMI_METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.tmp810714891282071602/umi_metrics.txt --ALLOW_MISSING_UMIS true --INPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.tmp810714891282071602/input.bam --OUTPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.tmp810714891282071602/output.sam --METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.tmp810714891282071602/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_EDIT_DISTANCE_TO_JOIN 1 --UMI_TAG_NAME RX --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 UmiAwareMarkDuplicatesWithMateCigar --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 --MAX_RECORDS_IN_RAM 1000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:17:27 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null INFO 2025-04-24 13:17:27 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. INFO 2025-04-24 13:17:27 MarkDuplicatesWithMateCigar Processed 21000 records INFO 2025-04-24 13:17:27 MarkDuplicatesWithMateCigar Marking 20000 records as duplicates. [Thu Apr 24 13:17:27 EDT 2025] picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigar done. Elapsed time: 0.01 minutes. Runtime.totalMemory()=1073741824 [Thu Apr 24 13:17:28 EDT 2025] UmiAwareMarkDuplicatesWithMateCigar --UMI_METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.tmp2120581419984382978/umi_metrics.txt --ALLOW_MISSING_UMIS true --INPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.tmp2120581419984382978/input.cram --OUTPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.tmp2120581419984382978/output.sam --METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.tmp2120581419984382978/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --REFERENCE_SEQUENCE /tmp/SamFileTester10561603399934940209/input.fasta --MAX_EDIT_DISTANCE_TO_JOIN 1 --UMI_TAG_NAME RX --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 UmiAwareMarkDuplicatesWithMateCigar --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 --MAX_RECORDS_IN_RAM 1000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:17:28 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null INFO 2025-04-24 13:17:29 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. INFO 2025-04-24 13:17:29 MarkDuplicatesWithMateCigar Processed 21000 records INFO 2025-04-24 13:17:29 MarkDuplicatesWithMateCigar Marking 20000 records as duplicates. [Thu Apr 24 13:17:29 EDT 2025] picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigar done. Elapsed time: 0.01 minutes. Runtime.totalMemory()=1073741824 [Thu Apr 24 13:17:29 EDT 2025] UmiAwareMarkDuplicatesWithMateCigar --UMI_METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.tmp3962400160230184633/umi_metrics.txt --ALLOW_MISSING_UMIS true --INPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.tmp3962400160230184633/input.sam --OUTPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.tmp3962400160230184633/output.sam --METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.tmp3962400160230184633/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_EDIT_DISTANCE_TO_JOIN 1 --UMI_TAG_NAME RX --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 UmiAwareMarkDuplicatesWithMateCigar --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 --MAX_RECORDS_IN_RAM 1000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:17:29 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 13:17:29 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 13:17:30 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. INFO 2025-04-24 13:17:30 MarkDuplicatesWithMateCigar Processed 20200 records INFO 2025-04-24 13:17:30 MarkDuplicatesWithMateCigar Marking 0 records as duplicates. [Thu Apr 24 13:17:30 EDT 2025] picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigar done. Elapsed time: 0.01 minutes. Runtime.totalMemory()=1073741824 [Thu Apr 24 13:17:30 EDT 2025] UmiAwareMarkDuplicatesWithMateCigar --UMI_METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.tmp16659311538774533973/umi_metrics.txt --ALLOW_MISSING_UMIS true --INPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.tmp16659311538774533973/input.bam --OUTPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.tmp16659311538774533973/output.sam --METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.tmp16659311538774533973/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_EDIT_DISTANCE_TO_JOIN 1 --UMI_TAG_NAME RX --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 UmiAwareMarkDuplicatesWithMateCigar --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 --MAX_RECORDS_IN_RAM 1000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:17:30 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null WARNING 2025-04-24 13:17:30 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 13:17:31 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. INFO 2025-04-24 13:17:31 MarkDuplicatesWithMateCigar Processed 20200 records INFO 2025-04-24 13:17:31 MarkDuplicatesWithMateCigar Marking 0 records as duplicates. [Thu Apr 24 13:17:31 EDT 2025] picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigar done. Elapsed time: 0.01 minutes. Runtime.totalMemory()=1073741824 [Thu Apr 24 13:17:31 EDT 2025] UmiAwareMarkDuplicatesWithMateCigar --UMI_METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.tmp3525395393067445246/umi_metrics.txt --ALLOW_MISSING_UMIS true --INPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.tmp3525395393067445246/input.cram --OUTPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.tmp3525395393067445246/output.sam --METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.tmp3525395393067445246/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --REFERENCE_SEQUENCE /tmp/SamFileTester17488093961456352473/input.fasta --MAX_EDIT_DISTANCE_TO_JOIN 1 --UMI_TAG_NAME RX --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 UmiAwareMarkDuplicatesWithMateCigar --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 --MAX_RECORDS_IN_RAM 1000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:17:31 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null WARNING 2025-04-24 13:17:32 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 13:17:32 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. INFO 2025-04-24 13:17:32 MarkDuplicatesWithMateCigar Processed 20200 records INFO 2025-04-24 13:17:32 MarkDuplicatesWithMateCigar Marking 0 records as duplicates. [Thu Apr 24 13:17:32 EDT 2025] picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigar done. Elapsed time: 0.01 minutes. Runtime.totalMemory()=1073741824 [Thu Apr 24 13:17:32 EDT 2025] UmiAwareMarkDuplicatesWithMateCigar --UMI_METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.tmp17281485056694506409/umi_metrics.txt --ALLOW_MISSING_UMIS true --INPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.tmp17281485056694506409/input.sam --OUTPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.tmp17281485056694506409/output.sam --METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.tmp17281485056694506409/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_EDIT_DISTANCE_TO_JOIN 1 --UMI_TAG_NAME RX --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 UmiAwareMarkDuplicatesWithMateCigar --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 --MAX_RECORDS_IN_RAM 1000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:17:32 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null WARNING 2025-04-24 13:17:32 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 13:17:33 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. INFO 2025-04-24 13:17:33 MarkDuplicatesWithMateCigar Processed 6820 records INFO 2025-04-24 13:17:33 MarkDuplicatesWithMateCigar Marking 6200 records as duplicates. [Thu Apr 24 13:17:33 EDT 2025] picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigar done. Elapsed time: 0.01 minutes. Runtime.totalMemory()=1073741824 [Thu Apr 24 13:17:33 EDT 2025] UmiAwareMarkDuplicatesWithMateCigar --UMI_METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.tmp5566200897608696667/umi_metrics.txt --ALLOW_MISSING_UMIS true --INPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.tmp5566200897608696667/input.bam --OUTPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.tmp5566200897608696667/output.sam --METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.tmp5566200897608696667/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_EDIT_DISTANCE_TO_JOIN 1 --UMI_TAG_NAME RX --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 UmiAwareMarkDuplicatesWithMateCigar --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 --MAX_RECORDS_IN_RAM 1000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:17:33 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null WARNING 2025-04-24 13:17:33 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 13:17:33 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. INFO 2025-04-24 13:17:33 MarkDuplicatesWithMateCigar Processed 6820 records INFO 2025-04-24 13:17:33 MarkDuplicatesWithMateCigar Marking 6200 records as duplicates. [Thu Apr 24 13:17:33 EDT 2025] picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigar done. Elapsed time: 0.01 minutes. Runtime.totalMemory()=1073741824 [Thu Apr 24 13:17:34 EDT 2025] UmiAwareMarkDuplicatesWithMateCigar --UMI_METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.tmp5249703600945901007/umi_metrics.txt --ALLOW_MISSING_UMIS true --INPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.tmp5249703600945901007/input.cram --OUTPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.tmp5249703600945901007/output.sam --METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.tmp5249703600945901007/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --REFERENCE_SEQUENCE /tmp/SamFileTester6758144852018358964/input.fasta --MAX_EDIT_DISTANCE_TO_JOIN 1 --UMI_TAG_NAME RX --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 UmiAwareMarkDuplicatesWithMateCigar --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 --MAX_RECORDS_IN_RAM 1000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:17:34 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 13:17:34 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 13:17:34 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. INFO 2025-04-24 13:17:34 MarkDuplicatesWithMateCigar Processed 6820 records INFO 2025-04-24 13:17:34 MarkDuplicatesWithMateCigar Marking 6200 records as duplicates. [Thu Apr 24 13:17:34 EDT 2025] picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigar done. Elapsed time: 0.01 minutes. Runtime.totalMemory()=1073741824 [Thu Apr 24 13:17:34 EDT 2025] UmiAwareMarkDuplicatesWithMateCigar --UMI_METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.tmp8327055648150368170/umi_metrics.txt --ALLOW_MISSING_UMIS true --INPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.tmp8327055648150368170/input.sam --OUTPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.tmp8327055648150368170/output.sam --METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.tmp8327055648150368170/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_EDIT_DISTANCE_TO_JOIN 1 --UMI_TAG_NAME RX --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 UmiAwareMarkDuplicatesWithMateCigar --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 --MAX_RECORDS_IN_RAM 1000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:17:34 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 13:17:34 MarkDuplicatesWithMateCigar Found 1 optical duplicate clusters. INFO 2025-04-24 13:17:34 MarkDuplicatesWithMateCigar Processed 4 records INFO 2025-04-24 13:17:34 MarkDuplicatesWithMateCigar Marking 2 records as duplicates. [Thu Apr 24 13:17:34 EDT 2025] picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 [Thu Apr 24 13:17:34 EDT 2025] UmiAwareMarkDuplicatesWithMateCigar --UMI_METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.tmp5116766781513746021/umi_metrics.txt --ALLOW_MISSING_UMIS true --INPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.tmp5116766781513746021/input.sam --OUTPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.tmp5116766781513746021/output.sam --METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.tmp5116766781513746021/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_EDIT_DISTANCE_TO_JOIN 1 --UMI_TAG_NAME RX --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 UmiAwareMarkDuplicatesWithMateCigar --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 --MAX_RECORDS_IN_RAM 1000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:17:34 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 13:17:34 MarkDuplicatesWithMateCigar Found 2 optical duplicate clusters. INFO 2025-04-24 13:17:34 MarkDuplicatesWithMateCigar Processed 11 records INFO 2025-04-24 13:17:34 MarkDuplicatesWithMateCigar Marking 8 records as duplicates. [Thu Apr 24 13:17:34 EDT 2025] picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 [Thu Apr 24 13:17:34 EDT 2025] UmiAwareMarkDuplicatesWithMateCigar --UMI_METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.tmp11676178466003552409/umi_metrics.txt --ALLOW_MISSING_UMIS true --INPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.tmp11676178466003552409/input.sam --OUTPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.tmp11676178466003552409/output.sam --METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.tmp11676178466003552409/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_EDIT_DISTANCE_TO_JOIN 1 --UMI_TAG_NAME RX --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 UmiAwareMarkDuplicatesWithMateCigar --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 --MAX_RECORDS_IN_RAM 1000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:17:34 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 13:17:34 MarkDuplicatesWithMateCigar Found 2 optical duplicate clusters. INFO 2025-04-24 13:17:34 MarkDuplicatesWithMateCigar Processed 11 records INFO 2025-04-24 13:17:34 MarkDuplicatesWithMateCigar Marking 8 records as duplicates. [Thu Apr 24 13:17:34 EDT 2025] picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 [Thu Apr 24 13:17:34 EDT 2025] UmiAwareMarkDuplicatesWithMateCigar --UMI_METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.tmp6772130489922901890/umi_metrics.txt --ALLOW_MISSING_UMIS true --INPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.tmp6772130489922901890/input.sam --OUTPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.tmp6772130489922901890/output.sam --METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.tmp6772130489922901890/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_EDIT_DISTANCE_TO_JOIN 1 --UMI_TAG_NAME RX --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 UmiAwareMarkDuplicatesWithMateCigar --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 --MAX_RECORDS_IN_RAM 1000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:17:34 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 13:17:34 MarkDuplicatesWithMateCigar Found 2 optical duplicate clusters. INFO 2025-04-24 13:17:34 MarkDuplicatesWithMateCigar Processed 11 records INFO 2025-04-24 13:17:34 MarkDuplicatesWithMateCigar Marking 8 records as duplicates. [Thu Apr 24 13:17:34 EDT 2025] picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 [Thu Apr 24 13:17:34 EDT 2025] UmiAwareMarkDuplicatesWithMateCigar --UMI_METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.tmp4871688773817727125/umi_metrics.txt --ALLOW_MISSING_UMIS true --INPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.tmp4871688773817727125/input.sam --OUTPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.tmp4871688773817727125/output.sam --METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.tmp4871688773817727125/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_EDIT_DISTANCE_TO_JOIN 1 --UMI_TAG_NAME RX --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 UmiAwareMarkDuplicatesWithMateCigar --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 --MAX_RECORDS_IN_RAM 1000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:17:34 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 13:17:34 MarkDuplicatesWithMateCigar Found 2 optical duplicate clusters. INFO 2025-04-24 13:17:34 MarkDuplicatesWithMateCigar Processed 11 records INFO 2025-04-24 13:17:34 MarkDuplicatesWithMateCigar Marking 8 records as duplicates. [Thu Apr 24 13:17:34 EDT 2025] picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 [Thu Apr 24 13:17:34 EDT 2025] UmiAwareMarkDuplicatesWithMateCigar --UMI_METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.tmp1631814181150781169/umi_metrics.txt --ALLOW_MISSING_UMIS true --INPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.tmp1631814181150781169/input.sam --OUTPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.tmp1631814181150781169/output.sam --METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.tmp1631814181150781169/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_EDIT_DISTANCE_TO_JOIN 1 --UMI_TAG_NAME RX --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 UmiAwareMarkDuplicatesWithMateCigar --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 --MAX_RECORDS_IN_RAM 1000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:17:34 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 13:17:34 MarkDuplicatesWithMateCigar Found 2 optical duplicate clusters. INFO 2025-04-24 13:17:34 MarkDuplicatesWithMateCigar Processed 11 records INFO 2025-04-24 13:17:34 MarkDuplicatesWithMateCigar Marking 8 records as duplicates. [Thu Apr 24 13:17:34 EDT 2025] picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 [Thu Apr 24 13:17:34 EDT 2025] UmiAwareMarkDuplicatesWithMateCigar --UMI_METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.tmp501707131507732444/umi_metrics.txt --ALLOW_MISSING_UMIS true --INPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.tmp501707131507732444/input.sam --OUTPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.tmp501707131507732444/output.sam --METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.tmp501707131507732444/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_EDIT_DISTANCE_TO_JOIN 1 --UMI_TAG_NAME RX --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 UmiAwareMarkDuplicatesWithMateCigar --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 --MAX_RECORDS_IN_RAM 1000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:17:34 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 13:17:34 MarkDuplicatesWithMateCigar Found 2 optical duplicate clusters. INFO 2025-04-24 13:17:34 MarkDuplicatesWithMateCigar Processed 11 records INFO 2025-04-24 13:17:34 MarkDuplicatesWithMateCigar Marking 8 records as duplicates. [Thu Apr 24 13:17:34 EDT 2025] picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 [Thu Apr 24 13:17:34 EDT 2025] UmiAwareMarkDuplicatesWithMateCigar --UMI_METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.tmp7697133025623746385/umi_metrics.txt --ALLOW_MISSING_UMIS true --INPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.tmp7697133025623746385/input.sam --OUTPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.tmp7697133025623746385/output.sam --METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.tmp7697133025623746385/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_EDIT_DISTANCE_TO_JOIN 1 --UMI_TAG_NAME RX --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 UmiAwareMarkDuplicatesWithMateCigar --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 --MAX_RECORDS_IN_RAM 1000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:17:34 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 13:17:34 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. INFO 2025-04-24 13:17:34 MarkDuplicatesWithMateCigar Processed 2 records INFO 2025-04-24 13:17:34 MarkDuplicatesWithMateCigar Marking 0 records as duplicates. [Thu Apr 24 13:17:34 EDT 2025] picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 [Thu Apr 24 13:17:34 EDT 2025] UmiAwareMarkDuplicatesWithMateCigar --UMI_METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.tmp3195040944541493152/umi_metrics.txt --ALLOW_MISSING_UMIS true --INPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.tmp3195040944541493152/input.sam --OUTPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.tmp3195040944541493152/output.sam --METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.tmp3195040944541493152/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_EDIT_DISTANCE_TO_JOIN 1 --UMI_TAG_NAME RX --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 UmiAwareMarkDuplicatesWithMateCigar --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 --MAX_RECORDS_IN_RAM 1000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:17:34 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 13:17:34 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. INFO 2025-04-24 13:17:34 MarkDuplicatesWithMateCigar Processed 3 records INFO 2025-04-24 13:17:34 MarkDuplicatesWithMateCigar Marking 1 records as duplicates. [Thu Apr 24 13:17:34 EDT 2025] picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 [Thu Apr 24 13:17:34 EDT 2025] UmiAwareMarkDuplicatesWithMateCigar --UMI_METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.tmp7025444259669784638/umi_metrics.txt --ALLOW_MISSING_UMIS true --INPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.tmp7025444259669784638/input.sam --OUTPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.tmp7025444259669784638/output.sam --METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.tmp7025444259669784638/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_EDIT_DISTANCE_TO_JOIN 1 --UMI_TAG_NAME RX --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 UmiAwareMarkDuplicatesWithMateCigar --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 --MAX_RECORDS_IN_RAM 1000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:17:34 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 13:17:34 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. INFO 2025-04-24 13:17:34 MarkDuplicatesWithMateCigar Processed 3 records INFO 2025-04-24 13:17:34 MarkDuplicatesWithMateCigar Marking 1 records as duplicates. [Thu Apr 24 13:17:34 EDT 2025] picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 [Thu Apr 24 13:17:34 EDT 2025] UmiAwareMarkDuplicatesWithMateCigar --UMI_METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.tmp6614024252986213656/umi_metrics.txt --ALLOW_MISSING_UMIS true --INPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.tmp6614024252986213656/input.sam --OUTPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.tmp6614024252986213656/output.sam --METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.tmp6614024252986213656/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_EDIT_DISTANCE_TO_JOIN 1 --UMI_TAG_NAME RX --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 UmiAwareMarkDuplicatesWithMateCigar --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 --MAX_RECORDS_IN_RAM 1000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:17:34 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 13:17:34 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 13:17:34 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. INFO 2025-04-24 13:17:34 MarkDuplicatesWithMateCigar Processed 5 records INFO 2025-04-24 13:17:34 MarkDuplicatesWithMateCigar Marking 2 records as duplicates. [Thu Apr 24 13:17:34 EDT 2025] picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 [Thu Apr 24 13:17:34 EDT 2025] UmiAwareMarkDuplicatesWithMateCigar --UMI_METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.tmp9503691270655539701/umi_metrics.txt --ALLOW_MISSING_UMIS true --INPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.tmp9503691270655539701/input.sam --OUTPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.tmp9503691270655539701/output.sam --METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.tmp9503691270655539701/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_EDIT_DISTANCE_TO_JOIN 1 --UMI_TAG_NAME RX --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 UmiAwareMarkDuplicatesWithMateCigar --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 --MAX_RECORDS_IN_RAM 1000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:17:34 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 13:17:34 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 13:17:34 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. INFO 2025-04-24 13:17:34 MarkDuplicatesWithMateCigar Processed 5 records INFO 2025-04-24 13:17:34 MarkDuplicatesWithMateCigar Marking 2 records as duplicates. [Thu Apr 24 13:17:34 EDT 2025] picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 [Thu Apr 24 13:17:34 EDT 2025] UmiAwareMarkDuplicatesWithMateCigar --UMI_METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.tmp12559638157589589610/umi_metrics.txt --ALLOW_MISSING_UMIS true --INPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.tmp12559638157589589610/input.sam --OUTPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.tmp12559638157589589610/output.sam --METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.tmp12559638157589589610/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_EDIT_DISTANCE_TO_JOIN 1 --UMI_TAG_NAME RX --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 UmiAwareMarkDuplicatesWithMateCigar --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 --MAX_RECORDS_IN_RAM 1000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:17:34 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 13:17:34 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 13:17:34 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. INFO 2025-04-24 13:17:34 MarkDuplicatesWithMateCigar Processed 4 records INFO 2025-04-24 13:17:34 MarkDuplicatesWithMateCigar Marking 0 records as duplicates. [Thu Apr 24 13:17:34 EDT 2025] picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 [Thu Apr 24 13:17:34 EDT 2025] UmiAwareMarkDuplicatesWithMateCigar --UMI_METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.tmp7106783258240677786/umi_metrics.txt --ALLOW_MISSING_UMIS true --INPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.tmp7106783258240677786/input.sam --OUTPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.tmp7106783258240677786/output.sam --METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.tmp7106783258240677786/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_EDIT_DISTANCE_TO_JOIN 1 --UMI_TAG_NAME RX --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 UmiAwareMarkDuplicatesWithMateCigar --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 --MAX_RECORDS_IN_RAM 1000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:17:34 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 13:17:34 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 13:17:34 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. INFO 2025-04-24 13:17:34 MarkDuplicatesWithMateCigar Processed 4 records INFO 2025-04-24 13:17:34 MarkDuplicatesWithMateCigar Marking 1 records as duplicates. [Thu Apr 24 13:17:34 EDT 2025] picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 [Thu Apr 24 13:17:34 EDT 2025] UmiAwareMarkDuplicatesWithMateCigar --UMI_METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.tmp11106558637353463741/umi_metrics.txt --ALLOW_MISSING_UMIS true --INPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.tmp11106558637353463741/input.sam --OUTPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.tmp11106558637353463741/output.sam --METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.tmp11106558637353463741/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_EDIT_DISTANCE_TO_JOIN 1 --UMI_TAG_NAME RX --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 UmiAwareMarkDuplicatesWithMateCigar --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 --MAX_RECORDS_IN_RAM 1000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:17:34 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 13:17:34 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 13:17:34 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. INFO 2025-04-24 13:17:34 MarkDuplicatesWithMateCigar Processed 4 records INFO 2025-04-24 13:17:34 MarkDuplicatesWithMateCigar Marking 1 records as duplicates. [Thu Apr 24 13:17:34 EDT 2025] picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 [Thu Apr 24 13:17:34 EDT 2025] UmiAwareMarkDuplicatesWithMateCigar --UMI_METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.tmp13425609388363447155/umi_metrics.txt --ALLOW_MISSING_UMIS true --INPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.tmp13425609388363447155/input.sam --OUTPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.tmp13425609388363447155/output.sam --METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.tmp13425609388363447155/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_EDIT_DISTANCE_TO_JOIN 1 --UMI_TAG_NAME RX --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 UmiAwareMarkDuplicatesWithMateCigar --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 --MAX_RECORDS_IN_RAM 1000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:17:34 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 13:17:34 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 13:17:34 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. INFO 2025-04-24 13:17:34 MarkDuplicatesWithMateCigar Processed 4 records INFO 2025-04-24 13:17:34 MarkDuplicatesWithMateCigar Marking 0 records as duplicates. [Thu Apr 24 13:17:34 EDT 2025] picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 [Thu Apr 24 13:17:34 EDT 2025] UmiAwareMarkDuplicatesWithMateCigar --UMI_METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.tmp6947769323930851697/umi_metrics.txt --ALLOW_MISSING_UMIS true --INPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.tmp6947769323930851697/input.sam --OUTPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.tmp6947769323930851697/output.sam --METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.tmp6947769323930851697/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_EDIT_DISTANCE_TO_JOIN 1 --UMI_TAG_NAME RX --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 UmiAwareMarkDuplicatesWithMateCigar --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 --MAX_RECORDS_IN_RAM 1000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:17:34 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 13:17:34 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 13:17:34 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. INFO 2025-04-24 13:17:34 MarkDuplicatesWithMateCigar Processed 2 records INFO 2025-04-24 13:17:34 MarkDuplicatesWithMateCigar Marking 0 records as duplicates. [Thu Apr 24 13:17:34 EDT 2025] picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 [Thu Apr 24 13:17:34 EDT 2025] UmiAwareMarkDuplicatesWithMateCigar --UMI_METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.tmp14227111434304567982/umi_metrics.txt --ALLOW_MISSING_UMIS true --INPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.tmp14227111434304567982/input.sam --OUTPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.tmp14227111434304567982/output.sam --METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.tmp14227111434304567982/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_EDIT_DISTANCE_TO_JOIN 1 --UMI_TAG_NAME RX --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 UmiAwareMarkDuplicatesWithMateCigar --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 --MAX_RECORDS_IN_RAM 1000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:17:34 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 13:17:34 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 13:17:34 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. INFO 2025-04-24 13:17:34 MarkDuplicatesWithMateCigar Processed 2 records INFO 2025-04-24 13:17:34 MarkDuplicatesWithMateCigar Marking 0 records as duplicates. [Thu Apr 24 13:17:34 EDT 2025] picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 [Thu Apr 24 13:17:34 EDT 2025] UmiAwareMarkDuplicatesWithMateCigar --UMI_METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.tmp2718197105821457058/umi_metrics.txt --ALLOW_MISSING_UMIS true --INPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.tmp2718197105821457058/input.sam --OUTPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.tmp2718197105821457058/output.sam --METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.tmp2718197105821457058/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_EDIT_DISTANCE_TO_JOIN 1 --UMI_TAG_NAME RX --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 UmiAwareMarkDuplicatesWithMateCigar --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 --MAX_RECORDS_IN_RAM 1000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:17:34 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 13:17:34 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. INFO 2025-04-24 13:17:34 MarkDuplicatesWithMateCigar Processed 2 records INFO 2025-04-24 13:17:34 MarkDuplicatesWithMateCigar Marking 0 records as duplicates. [Thu Apr 24 13:17:34 EDT 2025] picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 [Thu Apr 24 13:17:34 EDT 2025] UmiAwareMarkDuplicatesWithMateCigar --UMI_METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.tmp15207303149506714223/umi_metrics.txt --ALLOW_MISSING_UMIS true --INPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.tmp15207303149506714223/input.sam --OUTPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.tmp15207303149506714223/output.sam --METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.tmp15207303149506714223/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_EDIT_DISTANCE_TO_JOIN 1 --UMI_TAG_NAME RX --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 UmiAwareMarkDuplicatesWithMateCigar --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 --MAX_RECORDS_IN_RAM 1000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:17:34 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 13:17:34 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. INFO 2025-04-24 13:17:34 MarkDuplicatesWithMateCigar Processed 2 records INFO 2025-04-24 13:17:34 MarkDuplicatesWithMateCigar Marking 0 records as duplicates. [Thu Apr 24 13:17:34 EDT 2025] picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 [Thu Apr 24 13:17:34 EDT 2025] UmiAwareMarkDuplicatesWithMateCigar --UMI_METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.tmp816251367936562862/umi_metrics.txt --ALLOW_MISSING_UMIS true --INPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.tmp816251367936562862/input.sam --OUTPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.tmp816251367936562862/output.sam --METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.tmp816251367936562862/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_EDIT_DISTANCE_TO_JOIN 1 --UMI_TAG_NAME RX --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 UmiAwareMarkDuplicatesWithMateCigar --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 1000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:17:34 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 13:17:34 MarkDuplicatesWithMateCigar Skipped optical duplicate cluster discovery; library size estimation may be inaccurate! INFO 2025-04-24 13:17:34 MarkDuplicatesWithMateCigar Processed 4 records INFO 2025-04-24 13:17:34 MarkDuplicatesWithMateCigar Marking 2 records as duplicates. [Thu Apr 24 13:17:34 EDT 2025] picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 [Thu Apr 24 13:17:34 EDT 2025] UmiAwareMarkDuplicatesWithMateCigar --UMI_METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.tmp16423253343414907914/umi_metrics.txt --ALLOW_MISSING_UMIS true --INPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.tmp16423253343414907914/input.sam --OUTPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.tmp16423253343414907914/output.sam --METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.tmp16423253343414907914/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_EDIT_DISTANCE_TO_JOIN 1 --UMI_TAG_NAME RX --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 UmiAwareMarkDuplicatesWithMateCigar --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 --MAX_RECORDS_IN_RAM 1000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:17:34 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 13:17:34 MarkDuplicatesWithMateCigar Found 1 optical duplicate clusters. INFO 2025-04-24 13:17:34 MarkDuplicatesWithMateCigar Processed 4 records INFO 2025-04-24 13:17:34 MarkDuplicatesWithMateCigar Marking 2 records as duplicates. [Thu Apr 24 13:17:34 EDT 2025] picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 [Thu Apr 24 13:17:34 EDT 2025] UmiAwareMarkDuplicatesWithMateCigar --UMI_METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.tmp2288595409543658106/umi_metrics.txt --ALLOW_MISSING_UMIS true --INPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.tmp2288595409543658106/input.sam --OUTPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.tmp2288595409543658106/output.sam --METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.tmp2288595409543658106/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_EDIT_DISTANCE_TO_JOIN 1 --UMI_TAG_NAME RX --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 UmiAwareMarkDuplicatesWithMateCigar --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 --MAX_RECORDS_IN_RAM 1000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:17:34 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 13:17:34 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. INFO 2025-04-24 13:17:34 MarkDuplicatesWithMateCigar Processed 4 records INFO 2025-04-24 13:17:34 MarkDuplicatesWithMateCigar Marking 2 records as duplicates. [Thu Apr 24 13:17:34 EDT 2025] picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 [Thu Apr 24 13:17:34 EDT 2025] UmiAwareMarkDuplicatesWithMateCigar --UMI_METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.tmp5016346410050153340/umi_metrics.txt --ALLOW_MISSING_UMIS true --INPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.tmp5016346410050153340/input.sam --OUTPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.tmp5016346410050153340/output.sam --METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.tmp5016346410050153340/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_EDIT_DISTANCE_TO_JOIN 1 --UMI_TAG_NAME RX --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 UmiAwareMarkDuplicatesWithMateCigar --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 --MAX_RECORDS_IN_RAM 1000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:17:34 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 13:17:34 MarkDuplicatesWithMateCigar Found 1 optical duplicate clusters. INFO 2025-04-24 13:17:34 MarkDuplicatesWithMateCigar Processed 4 records INFO 2025-04-24 13:17:34 MarkDuplicatesWithMateCigar Marking 2 records as duplicates. [Thu Apr 24 13:17:34 EDT 2025] picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 [Thu Apr 24 13:17:34 EDT 2025] UmiAwareMarkDuplicatesWithMateCigar --UMI_METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.tmp3946661433274738760/umi_metrics.txt --ALLOW_MISSING_UMIS true --INPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.tmp3946661433274738760/input.sam --OUTPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.tmp3946661433274738760/output.sam --METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.tmp3946661433274738760/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_EDIT_DISTANCE_TO_JOIN 1 --UMI_TAG_NAME RX --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 UmiAwareMarkDuplicatesWithMateCigar --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 --MAX_RECORDS_IN_RAM 1000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:17:34 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 13:17:34 MarkDuplicatesWithMateCigar Found 1 optical duplicate clusters. INFO 2025-04-24 13:17:34 MarkDuplicatesWithMateCigar Processed 4 records INFO 2025-04-24 13:17:34 MarkDuplicatesWithMateCigar Marking 2 records as duplicates. [Thu Apr 24 13:17:34 EDT 2025] picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 [Thu Apr 24 13:17:34 EDT 2025] UmiAwareMarkDuplicatesWithMateCigar --UMI_METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.tmp12958300350005166017/umi_metrics.txt --ALLOW_MISSING_UMIS true --INPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.tmp12958300350005166017/input.sam --OUTPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.tmp12958300350005166017/output.sam --METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.tmp12958300350005166017/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_EDIT_DISTANCE_TO_JOIN 1 --UMI_TAG_NAME RX --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 UmiAwareMarkDuplicatesWithMateCigar --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 --MAX_RECORDS_IN_RAM 1000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:17:34 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 13:17:34 MarkDuplicatesWithMateCigar Found 1 optical duplicate clusters. INFO 2025-04-24 13:17:34 MarkDuplicatesWithMateCigar Processed 6 records INFO 2025-04-24 13:17:34 MarkDuplicatesWithMateCigar Marking 4 records as duplicates. [Thu Apr 24 13:17:34 EDT 2025] picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 [Thu Apr 24 13:17:34 EDT 2025] UmiAwareMarkDuplicatesWithMateCigar --UMI_METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.tmp2591308620861375844/umi_metrics.txt --ALLOW_MISSING_UMIS true --INPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.tmp2591308620861375844/input.sam --OUTPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.tmp2591308620861375844/output.sam --METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.tmp2591308620861375844/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_EDIT_DISTANCE_TO_JOIN 1 --UMI_TAG_NAME RX --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 UmiAwareMarkDuplicatesWithMateCigar --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 --MAX_RECORDS_IN_RAM 1000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:17:34 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 13:17:34 MarkDuplicatesWithMateCigar Found 1 optical duplicate clusters. INFO 2025-04-24 13:17:34 MarkDuplicatesWithMateCigar Processed 4 records INFO 2025-04-24 13:17:34 MarkDuplicatesWithMateCigar Marking 2 records as duplicates. [Thu Apr 24 13:17:34 EDT 2025] picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 [Thu Apr 24 13:17:34 EDT 2025] UmiAwareMarkDuplicatesWithMateCigar --UMI_METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.tmp12840341018406177849/umi_metrics.txt --ALLOW_MISSING_UMIS true --INPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.tmp12840341018406177849/input.sam --OUTPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.tmp12840341018406177849/output.sam --METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.tmp12840341018406177849/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_EDIT_DISTANCE_TO_JOIN 1 --UMI_TAG_NAME RX --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 UmiAwareMarkDuplicatesWithMateCigar --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 --MAX_RECORDS_IN_RAM 1000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:17:34 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 13:17:34 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 13:17:34 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. INFO 2025-04-24 13:17:34 MarkDuplicatesWithMateCigar Processed 2 records INFO 2025-04-24 13:17:34 MarkDuplicatesWithMateCigar Marking 0 records as duplicates. [Thu Apr 24 13:17:34 EDT 2025] picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 [Thu Apr 24 13:17:34 EDT 2025] UmiAwareMarkDuplicatesWithMateCigar --UMI_METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.tmp16211882073124960099/umi_metrics.txt --ALLOW_MISSING_UMIS true --INPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.tmp16211882073124960099/input.sam --OUTPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.tmp16211882073124960099/output.sam --METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.tmp16211882073124960099/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_EDIT_DISTANCE_TO_JOIN 1 --UMI_TAG_NAME RX --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 UmiAwareMarkDuplicatesWithMateCigar --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 --MAX_RECORDS_IN_RAM 1000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:17:34 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 13:17:34 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. INFO 2025-04-24 13:17:34 MarkDuplicatesWithMateCigar Processed 1 records INFO 2025-04-24 13:17:34 MarkDuplicatesWithMateCigar Marking 0 records as duplicates. [Thu Apr 24 13:17:34 EDT 2025] picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 [Thu Apr 24 13:17:34 EDT 2025] UmiAwareMarkDuplicatesWithMateCigar --UMI_METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.tmp15391810026209013260/umi_metrics.txt --ALLOW_MISSING_UMIS true --INPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.tmp15391810026209013260/input.sam --OUTPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.tmp15391810026209013260/output.sam --METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.tmp15391810026209013260/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_EDIT_DISTANCE_TO_JOIN 1 --UMI_TAG_NAME RX --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 UmiAwareMarkDuplicatesWithMateCigar --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 --MAX_RECORDS_IN_RAM 1000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:17:34 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 13:17:34 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 13:17:34 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. INFO 2025-04-24 13:17:34 MarkDuplicatesWithMateCigar Processed 3 records INFO 2025-04-24 13:17:34 MarkDuplicatesWithMateCigar Marking 1 records as duplicates. [Thu Apr 24 13:17:34 EDT 2025] picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 [Thu Apr 24 13:17:34 EDT 2025] UmiAwareMarkDuplicatesWithMateCigar --UMI_METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.tmp11039246842300839958/umi_metrics.txt --ALLOW_MISSING_UMIS true --INPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.tmp11039246842300839958/input.sam --OUTPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.tmp11039246842300839958/output.sam --METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.tmp11039246842300839958/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_EDIT_DISTANCE_TO_JOIN 1 --UMI_TAG_NAME RX --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 UmiAwareMarkDuplicatesWithMateCigar --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 --MAX_RECORDS_IN_RAM 1000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:17:34 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 13:17:34 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 13:17:34 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. INFO 2025-04-24 13:17:34 MarkDuplicatesWithMateCigar Processed 5 records INFO 2025-04-24 13:17:34 MarkDuplicatesWithMateCigar Marking 3 records as duplicates. [Thu Apr 24 13:17:34 EDT 2025] picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 [Thu Apr 24 13:17:34 EDT 2025] UmiAwareMarkDuplicatesWithMateCigar --UMI_METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.tmp11343985231626407193/umi_metrics.txt --ALLOW_MISSING_UMIS true --INPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.tmp11343985231626407193/input.sam --OUTPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.tmp11343985231626407193/output.sam --METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.tmp11343985231626407193/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_EDIT_DISTANCE_TO_JOIN 1 --UMI_TAG_NAME RX --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 UmiAwareMarkDuplicatesWithMateCigar --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 --MAX_RECORDS_IN_RAM 1000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:17:34 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 13:17:34 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 13:17:34 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. INFO 2025-04-24 13:17:34 MarkDuplicatesWithMateCigar Processed 2 records INFO 2025-04-24 13:17:34 MarkDuplicatesWithMateCigar Marking 0 records as duplicates. [Thu Apr 24 13:17:34 EDT 2025] picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 [Thu Apr 24 13:17:34 EDT 2025] UmiAwareMarkDuplicatesWithMateCigar --UMI_METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.tmp8814663437017788709/umi_metrics.txt --ALLOW_MISSING_UMIS true --INPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.tmp8814663437017788709/input.sam --OUTPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.tmp8814663437017788709/output.sam --METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.tmp8814663437017788709/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_EDIT_DISTANCE_TO_JOIN 1 --UMI_TAG_NAME RX --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 UmiAwareMarkDuplicatesWithMateCigar --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 --MAX_RECORDS_IN_RAM 1000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:17:34 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 13:17:34 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. INFO 2025-04-24 13:17:34 MarkDuplicatesWithMateCigar Processed 1 records INFO 2025-04-24 13:17:34 MarkDuplicatesWithMateCigar Marking 0 records as duplicates. [Thu Apr 24 13:17:34 EDT 2025] picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 [Thu Apr 24 13:17:34 EDT 2025] UmiAwareMarkDuplicatesWithMateCigar --UMI_METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.tmp15115304493472387379/umi_metrics.txt --ALLOW_MISSING_UMIS true --INPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.tmp15115304493472387379/input.sam --OUTPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.tmp15115304493472387379/output.sam --METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.tmp15115304493472387379/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_EDIT_DISTANCE_TO_JOIN 1 --UMI_TAG_NAME RX --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 UmiAwareMarkDuplicatesWithMateCigar --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 --MAX_RECORDS_IN_RAM 1000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:17:34 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 13:17:34 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. INFO 2025-04-24 13:17:34 MarkDuplicatesWithMateCigar Processed 2 records INFO 2025-04-24 13:17:34 MarkDuplicatesWithMateCigar Marking 0 records as duplicates. [Thu Apr 24 13:17:34 EDT 2025] picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 [Thu Apr 24 13:17:34 EDT 2025] UmiAwareMarkDuplicatesWithMateCigar --UMI_METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.tmp1966125718703300476/umi_metrics.txt --ALLOW_MISSING_UMIS true --INPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.tmp1966125718703300476/input.sam --OUTPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.tmp1966125718703300476/output.sam --METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.tmp1966125718703300476/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_EDIT_DISTANCE_TO_JOIN 1 --UMI_TAG_NAME RX --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 UmiAwareMarkDuplicatesWithMateCigar --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 --MAX_RECORDS_IN_RAM 1000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:17:34 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 13:17:34 MarkDuplicatesWithMateCigar Found 1 optical duplicate clusters. INFO 2025-04-24 13:17:34 MarkDuplicatesWithMateCigar Processed 4 records INFO 2025-04-24 13:17:34 MarkDuplicatesWithMateCigar Marking 2 records as duplicates. [Thu Apr 24 13:17:34 EDT 2025] picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 [Thu Apr 24 13:17:34 EDT 2025] UmiAwareMarkDuplicatesWithMateCigar --UMI_METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.tmp7370965536675258915/umi_metrics.txt --ALLOW_MISSING_UMIS true --INPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.tmp7370965536675258915/input.sam --OUTPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.tmp7370965536675258915/output.sam --METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.tmp7370965536675258915/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_EDIT_DISTANCE_TO_JOIN 1 --UMI_TAG_NAME RX --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 UmiAwareMarkDuplicatesWithMateCigar --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 --MAX_RECORDS_IN_RAM 1000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:17:34 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 13:17:34 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 13:17:34 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. INFO 2025-04-24 13:17:34 MarkDuplicatesWithMateCigar Processed 18 records INFO 2025-04-24 13:17:34 MarkDuplicatesWithMateCigar Marking 12 records as duplicates. [Thu Apr 24 13:17:34 EDT 2025] picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 [Thu Apr 24 13:17:34 EDT 2025] UmiAwareMarkDuplicatesWithMateCigar --UMI_METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.tmp5165630292776037772/umi_metrics.txt --ALLOW_MISSING_UMIS true --INPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.tmp5165630292776037772/input.sam --OUTPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.tmp5165630292776037772/output.sam --METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.tmp5165630292776037772/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_EDIT_DISTANCE_TO_JOIN 1 --UMI_TAG_NAME RX --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 UmiAwareMarkDuplicatesWithMateCigar --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 --MAX_RECORDS_IN_RAM 1000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:17:34 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 13:17:34 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 13:17:34 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. INFO 2025-04-24 13:17:34 MarkDuplicatesWithMateCigar Processed 6 records INFO 2025-04-24 13:17:34 MarkDuplicatesWithMateCigar Marking 4 records as duplicates. [Thu Apr 24 13:17:34 EDT 2025] picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 [Thu Apr 24 13:17:34 EDT 2025] UmiAwareMarkDuplicatesWithMateCigar --UMI_METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.tmp12523004356895397867/umi_metrics.txt --ALLOW_MISSING_UMIS true --INPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.tmp12523004356895397867/input.sam --OUTPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.tmp12523004356895397867/output.sam --METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.tmp12523004356895397867/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_EDIT_DISTANCE_TO_JOIN 1 --UMI_TAG_NAME RX --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 UmiAwareMarkDuplicatesWithMateCigar --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 --MAX_RECORDS_IN_RAM 1000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:17:34 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 13:17:34 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 13:17:34 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. INFO 2025-04-24 13:17:34 MarkDuplicatesWithMateCigar Processed 6 records INFO 2025-04-24 13:17:34 MarkDuplicatesWithMateCigar Marking 2 records as duplicates. [Thu Apr 24 13:17:34 EDT 2025] picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 [Thu Apr 24 13:17:34 EDT 2025] UmiAwareMarkDuplicatesWithMateCigar --UMI_METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.tmp200063442359880199/umi_metrics.txt --ALLOW_MISSING_UMIS true --INPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.tmp200063442359880199/input.sam --OUTPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.tmp200063442359880199/output.sam --METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.tmp200063442359880199/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_EDIT_DISTANCE_TO_JOIN 1 --UMI_TAG_NAME RX --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 UmiAwareMarkDuplicatesWithMateCigar --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 --MAX_RECORDS_IN_RAM 1000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:17:34 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 13:17:34 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 13:17:34 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. INFO 2025-04-24 13:17:34 MarkDuplicatesWithMateCigar Processed 12 records INFO 2025-04-24 13:17:34 MarkDuplicatesWithMateCigar Marking 8 records as duplicates. [Thu Apr 24 13:17:34 EDT 2025] picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 [Thu Apr 24 13:17:34 EDT 2025] UmiAwareMarkDuplicatesWithMateCigar --UMI_METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.tmp15136076641887479777/umi_metrics.txt --ALLOW_MISSING_UMIS true --INPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.tmp15136076641887479777/input.sam --OUTPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.tmp15136076641887479777/output.sam --METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.tmp15136076641887479777/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_EDIT_DISTANCE_TO_JOIN 1 --UMI_TAG_NAME RX --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 UmiAwareMarkDuplicatesWithMateCigar --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 --MAX_RECORDS_IN_RAM 1000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:17:34 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 13:17:34 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. INFO 2025-04-24 13:17:34 MarkDuplicatesWithMateCigar Processed 4 records INFO 2025-04-24 13:17:34 MarkDuplicatesWithMateCigar Marking 2 records as duplicates. [Thu Apr 24 13:17:34 EDT 2025] picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 [Thu Apr 24 13:17:34 EDT 2025] UmiAwareMarkDuplicatesWithMateCigar --UMI_METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.tmp13722054508140644486/umi_metrics.txt --ALLOW_MISSING_UMIS true --INPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.tmp13722054508140644486/input.sam --OUTPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.tmp13722054508140644486/output.sam --METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.tmp13722054508140644486/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_EDIT_DISTANCE_TO_JOIN 1 --UMI_TAG_NAME RX --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 UmiAwareMarkDuplicatesWithMateCigar --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 --MAX_RECORDS_IN_RAM 1000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:17:34 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 13:17:34 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 13:17:34 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. INFO 2025-04-24 13:17:34 MarkDuplicatesWithMateCigar Processed 8 records INFO 2025-04-24 13:17:34 MarkDuplicatesWithMateCigar Marking 4 records as duplicates. [Thu Apr 24 13:17:34 EDT 2025] picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 [Thu Apr 24 13:17:34 EDT 2025] UmiAwareMarkDuplicatesWithMateCigar --UMI_METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.tmp12058974406156389623/umi_metrics.txt --ALLOW_MISSING_UMIS true --INPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.tmp12058974406156389623/input.sam --OUTPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.tmp12058974406156389623/output.sam --METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.tmp12058974406156389623/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_EDIT_DISTANCE_TO_JOIN 1 --UMI_TAG_NAME RX --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 UmiAwareMarkDuplicatesWithMateCigar --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 --MAX_RECORDS_IN_RAM 1000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:17:34 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 13:17:34 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. INFO 2025-04-24 13:17:34 MarkDuplicatesWithMateCigar Processed 2 records INFO 2025-04-24 13:17:34 MarkDuplicatesWithMateCigar Marking 1 records as duplicates. [Thu Apr 24 13:17:34 EDT 2025] picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 [Thu Apr 24 13:17:34 EDT 2025] UmiAwareMarkDuplicatesWithMateCigar --UMI_METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.tmp14420982056848136372/umi_metrics.txt --ALLOW_MISSING_UMIS true --INPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.tmp14420982056848136372/input.sam --OUTPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.tmp14420982056848136372/output.sam --METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.tmp14420982056848136372/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_EDIT_DISTANCE_TO_JOIN 1 --UMI_TAG_NAME RX --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 UmiAwareMarkDuplicatesWithMateCigar --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 --MAX_RECORDS_IN_RAM 1000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:17:34 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 13:17:34 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 13:17:34 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. INFO 2025-04-24 13:17:34 MarkDuplicatesWithMateCigar Processed 4 records INFO 2025-04-24 13:17:34 MarkDuplicatesWithMateCigar Marking 2 records as duplicates. [Thu Apr 24 13:17:34 EDT 2025] picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 [Thu Apr 24 13:17:34 EDT 2025] UmiAwareMarkDuplicatesWithMateCigar --UMI_METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.tmp9150201841921263833/umi_metrics.txt --ALLOW_MISSING_UMIS true --INPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.tmp9150201841921263833/input.sam --OUTPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.tmp9150201841921263833/output.sam --METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.tmp9150201841921263833/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_EDIT_DISTANCE_TO_JOIN 1 --UMI_TAG_NAME RX --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 UmiAwareMarkDuplicatesWithMateCigar --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 --MAX_RECORDS_IN_RAM 1000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:17:34 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 13:17:34 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 13:17:34 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. INFO 2025-04-24 13:17:34 MarkDuplicatesWithMateCigar Processed 4 records INFO 2025-04-24 13:17:34 MarkDuplicatesWithMateCigar Marking 2 records as duplicates. [Thu Apr 24 13:17:34 EDT 2025] picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 [Thu Apr 24 13:17:34 EDT 2025] UmiAwareMarkDuplicatesWithMateCigar --UMI_METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.tmp15729986937883501330/umi_metrics.txt --ALLOW_MISSING_UMIS true --INPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.tmp15729986937883501330/input.sam --OUTPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.tmp15729986937883501330/output.sam --METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.tmp15729986937883501330/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_EDIT_DISTANCE_TO_JOIN 1 --UMI_TAG_NAME RX --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 UmiAwareMarkDuplicatesWithMateCigar --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 --MAX_RECORDS_IN_RAM 1000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:17:34 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 13:17:34 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 13:17:34 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. INFO 2025-04-24 13:17:34 MarkDuplicatesWithMateCigar Processed 4 records INFO 2025-04-24 13:17:34 MarkDuplicatesWithMateCigar Marking 2 records as duplicates. [Thu Apr 24 13:17:34 EDT 2025] picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 [Thu Apr 24 13:17:34 EDT 2025] UmiAwareMarkDuplicatesWithMateCigar --UMI_METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.tmp10492152223154656823/umi_metrics.txt --ALLOW_MISSING_UMIS true --INPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.tmp10492152223154656823/input.sam --OUTPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.tmp10492152223154656823/output.sam --METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.tmp10492152223154656823/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_EDIT_DISTANCE_TO_JOIN 1 --UMI_TAG_NAME RX --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 UmiAwareMarkDuplicatesWithMateCigar --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 --MAX_RECORDS_IN_RAM 1000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:17:34 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 13:17:34 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 13:17:34 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. INFO 2025-04-24 13:17:34 MarkDuplicatesWithMateCigar Processed 4 records INFO 2025-04-24 13:17:34 MarkDuplicatesWithMateCigar Marking 2 records as duplicates. [Thu Apr 24 13:17:34 EDT 2025] picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 [Thu Apr 24 13:17:34 EDT 2025] UmiAwareMarkDuplicatesWithMateCigar --UMI_METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.tmp8174364439912651426/umi_metrics.txt --ALLOW_MISSING_UMIS true --INPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.tmp8174364439912651426/input.sam --OUTPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.tmp8174364439912651426/output.sam --METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.tmp8174364439912651426/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_EDIT_DISTANCE_TO_JOIN 1 --UMI_TAG_NAME RX --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 UmiAwareMarkDuplicatesWithMateCigar --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 --MAX_RECORDS_IN_RAM 1000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:17:34 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 13:17:34 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 13:17:34 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. INFO 2025-04-24 13:17:34 MarkDuplicatesWithMateCigar Processed 5 records INFO 2025-04-24 13:17:34 MarkDuplicatesWithMateCigar Marking 2 records as duplicates. [Thu Apr 24 13:17:34 EDT 2025] picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 [Thu Apr 24 13:17:34 EDT 2025] UmiAwareMarkDuplicatesWithMateCigar --UMI_METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.tmp8268129286244112447/umi_metrics.txt --ALLOW_MISSING_UMIS true --INPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.tmp8268129286244112447/input.sam --OUTPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.tmp8268129286244112447/output.sam --METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.tmp8268129286244112447/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_EDIT_DISTANCE_TO_JOIN 1 --UMI_TAG_NAME RX --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 UmiAwareMarkDuplicatesWithMateCigar --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 --MAX_RECORDS_IN_RAM 1000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:17:34 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 13:17:34 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 13:17:34 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. INFO 2025-04-24 13:17:34 MarkDuplicatesWithMateCigar Processed 5 records INFO 2025-04-24 13:17:34 MarkDuplicatesWithMateCigar Marking 2 records as duplicates. [Thu Apr 24 13:17:34 EDT 2025] picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 [Thu Apr 24 13:17:34 EDT 2025] UmiAwareMarkDuplicatesWithMateCigar --UMI_METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.tmp1379330001327669446/umi_metrics.txt --ALLOW_MISSING_UMIS true --INPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.tmp1379330001327669446/input.sam --OUTPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.tmp1379330001327669446/output.sam --METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.tmp1379330001327669446/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_EDIT_DISTANCE_TO_JOIN 1 --UMI_TAG_NAME RX --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 UmiAwareMarkDuplicatesWithMateCigar --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 --MAX_RECORDS_IN_RAM 1000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:17:34 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 13:17:34 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 13:17:34 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. INFO 2025-04-24 13:17:34 MarkDuplicatesWithMateCigar Processed 6 records INFO 2025-04-24 13:17:34 MarkDuplicatesWithMateCigar Marking 2 records as duplicates. [Thu Apr 24 13:17:34 EDT 2025] picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 [Thu Apr 24 13:17:34 EDT 2025] UmiAwareMarkDuplicatesWithMateCigar --UMI_METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.tmp14592535770727743351/umi_metrics.txt --ALLOW_MISSING_UMIS true --INPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.tmp14592535770727743351/input.sam --OUTPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.tmp14592535770727743351/output.sam --METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.tmp14592535770727743351/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_EDIT_DISTANCE_TO_JOIN 1 --UMI_TAG_NAME RX --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 UmiAwareMarkDuplicatesWithMateCigar --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 --MAX_RECORDS_IN_RAM 1000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:17:34 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 13:17:34 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 13:17:34 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. INFO 2025-04-24 13:17:34 MarkDuplicatesWithMateCigar Processed 4 records INFO 2025-04-24 13:17:34 MarkDuplicatesWithMateCigar Marking 0 records as duplicates. [Thu Apr 24 13:17:34 EDT 2025] picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 [Thu Apr 24 13:17:34 EDT 2025] UmiAwareMarkDuplicatesWithMateCigar --UMI_METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.tmp17752149335452560338/umi_metrics.txt --ALLOW_MISSING_UMIS true --INPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.tmp17752149335452560338/input.sam --OUTPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.tmp17752149335452560338/output.sam --METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.tmp17752149335452560338/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_EDIT_DISTANCE_TO_JOIN 1 --UMI_TAG_NAME RX --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 UmiAwareMarkDuplicatesWithMateCigar --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 --MAX_RECORDS_IN_RAM 1000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:17:34 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 13:17:34 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 13:17:34 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. INFO 2025-04-24 13:17:34 MarkDuplicatesWithMateCigar Processed 4 records INFO 2025-04-24 13:17:34 MarkDuplicatesWithMateCigar Marking 2 records as duplicates. [Thu Apr 24 13:17:34 EDT 2025] picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 [Thu Apr 24 13:17:34 EDT 2025] UmiAwareMarkDuplicatesWithMateCigar --UMI_METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.tmp248300339570967860/umi_metrics.txt --ALLOW_MISSING_UMIS true --INPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.tmp248300339570967860/input.sam --OUTPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.tmp248300339570967860/output.sam --METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.tmp248300339570967860/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_EDIT_DISTANCE_TO_JOIN 1 --UMI_TAG_NAME RX --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 UmiAwareMarkDuplicatesWithMateCigar --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 --MAX_RECORDS_IN_RAM 1000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:17:34 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 13:17:34 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 13:17:34 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. INFO 2025-04-24 13:17:34 MarkDuplicatesWithMateCigar Processed 4 records INFO 2025-04-24 13:17:34 MarkDuplicatesWithMateCigar Marking 2 records as duplicates. [Thu Apr 24 13:17:34 EDT 2025] picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 [Thu Apr 24 13:17:34 EDT 2025] UmiAwareMarkDuplicatesWithMateCigar --UMI_METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.tmp6532147766950470845/umi_metrics.txt --ALLOW_MISSING_UMIS true --INPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.tmp6532147766950470845/input.sam --OUTPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.tmp6532147766950470845/output.sam --METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.tmp6532147766950470845/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_EDIT_DISTANCE_TO_JOIN 1 --UMI_TAG_NAME RX --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 UmiAwareMarkDuplicatesWithMateCigar --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 --MAX_RECORDS_IN_RAM 1000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:17:34 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 13:17:34 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 13:17:34 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. INFO 2025-04-24 13:17:34 MarkDuplicatesWithMateCigar Processed 4 records INFO 2025-04-24 13:17:34 MarkDuplicatesWithMateCigar Marking 2 records as duplicates. [Thu Apr 24 13:17:34 EDT 2025] picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 [Thu Apr 24 13:17:34 EDT 2025] UmiAwareMarkDuplicatesWithMateCigar --UMI_METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.tmp5753370271340818449/umi_metrics.txt --ALLOW_MISSING_UMIS true --INPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.tmp5753370271340818449/input.sam --OUTPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.tmp5753370271340818449/output.sam --METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.tmp5753370271340818449/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_EDIT_DISTANCE_TO_JOIN 1 --UMI_TAG_NAME RX --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 UmiAwareMarkDuplicatesWithMateCigar --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 --MAX_RECORDS_IN_RAM 1000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:17:34 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 13:17:34 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 13:17:34 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. INFO 2025-04-24 13:17:34 MarkDuplicatesWithMateCigar Processed 4 records INFO 2025-04-24 13:17:34 MarkDuplicatesWithMateCigar Marking 2 records as duplicates. [Thu Apr 24 13:17:34 EDT 2025] picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 [Thu Apr 24 13:17:35 EDT 2025] UmiAwareMarkDuplicatesWithMateCigar --UMI_METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.tmp12060155515576553457/umi_metrics.txt --ALLOW_MISSING_UMIS true --INPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.tmp12060155515576553457/input.sam --OUTPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.tmp12060155515576553457/output.sam --METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.tmp12060155515576553457/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_EDIT_DISTANCE_TO_JOIN 1 --UMI_TAG_NAME RX --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 UmiAwareMarkDuplicatesWithMateCigar --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 --MAX_RECORDS_IN_RAM 1000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:17:35 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 13:17:35 MarkDuplicatesWithMateCigar Found 1 optical duplicate clusters. INFO 2025-04-24 13:17:35 MarkDuplicatesWithMateCigar Processed 5 records INFO 2025-04-24 13:17:35 MarkDuplicatesWithMateCigar Marking 2 records as duplicates. [Thu Apr 24 13:17:35 EDT 2025] picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 [Thu Apr 24 13:17:35 EDT 2025] UmiAwareMarkDuplicatesWithMateCigar --UMI_METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.tmp1867716238649957806/umi_metrics.txt --ALLOW_MISSING_UMIS true --INPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.tmp1867716238649957806/input.sam --OUTPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.tmp1867716238649957806/output.sam --METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.tmp1867716238649957806/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_EDIT_DISTANCE_TO_JOIN 1 --UMI_TAG_NAME RX --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 UmiAwareMarkDuplicatesWithMateCigar --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 --MAX_RECORDS_IN_RAM 1000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:17:35 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 13:17:35 MarkDuplicatesWithMateCigar Found 1 optical duplicate clusters. INFO 2025-04-24 13:17:35 MarkDuplicatesWithMateCigar Processed 5 records INFO 2025-04-24 13:17:35 MarkDuplicatesWithMateCigar Marking 2 records as duplicates. [Thu Apr 24 13:17:35 EDT 2025] picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 [Thu Apr 24 13:17:35 EDT 2025] UmiAwareMarkDuplicatesWithMateCigar --UMI_METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.tmp11556333594785488269/umi_metrics.txt --ALLOW_MISSING_UMIS true --INPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.tmp11556333594785488269/input.sam --OUTPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.tmp11556333594785488269/output.sam --METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.tmp11556333594785488269/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_EDIT_DISTANCE_TO_JOIN 1 --UMI_TAG_NAME RX --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 UmiAwareMarkDuplicatesWithMateCigar --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 --MAX_RECORDS_IN_RAM 1000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:17:35 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 13:17:35 MarkDuplicatesWithMateCigar Found 1 optical duplicate clusters. INFO 2025-04-24 13:17:35 MarkDuplicatesWithMateCigar Processed 5 records INFO 2025-04-24 13:17:35 MarkDuplicatesWithMateCigar Marking 2 records as duplicates. [Thu Apr 24 13:17:35 EDT 2025] picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 [Thu Apr 24 13:17:35 EDT 2025] UmiAwareMarkDuplicatesWithMateCigar --UMI_METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.tmp1012874175250173768/umi_metrics.txt --ALLOW_MISSING_UMIS true --INPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.tmp1012874175250173768/input.sam --OUTPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.tmp1012874175250173768/output.sam --METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.tmp1012874175250173768/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_EDIT_DISTANCE_TO_JOIN 1 --UMI_TAG_NAME RX --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 UmiAwareMarkDuplicatesWithMateCigar --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 --MAX_RECORDS_IN_RAM 1000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:17:35 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 13:17:35 MarkDuplicatesWithMateCigar Found 1 optical duplicate clusters. INFO 2025-04-24 13:17:35 MarkDuplicatesWithMateCigar Processed 5 records INFO 2025-04-24 13:17:35 MarkDuplicatesWithMateCigar Marking 2 records as duplicates. [Thu Apr 24 13:17:35 EDT 2025] picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 [Thu Apr 24 13:17:35 EDT 2025] UmiAwareMarkDuplicatesWithMateCigar --UMI_METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.tmp18174063645029539850/umi_metrics.txt --ALLOW_MISSING_UMIS true --INPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.tmp18174063645029539850/input.sam --OUTPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.tmp18174063645029539850/output.sam --METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.tmp18174063645029539850/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_EDIT_DISTANCE_TO_JOIN 1 --UMI_TAG_NAME RX --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 UmiAwareMarkDuplicatesWithMateCigar --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 --MAX_RECORDS_IN_RAM 1000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:17:35 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 13:17:35 MarkDuplicatesWithMateCigar Found 1 optical duplicate clusters. INFO 2025-04-24 13:17:35 MarkDuplicatesWithMateCigar Processed 5 records INFO 2025-04-24 13:17:35 MarkDuplicatesWithMateCigar Marking 2 records as duplicates. [Thu Apr 24 13:17:35 EDT 2025] picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 [Thu Apr 24 13:17:35 EDT 2025] UmiAwareMarkDuplicatesWithMateCigar --UMI_METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.tmp5941126024206967195/umi_metrics.txt --ALLOW_MISSING_UMIS true --INPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.tmp5941126024206967195/input.sam --OUTPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.tmp5941126024206967195/output.sam --METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.tmp5941126024206967195/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_EDIT_DISTANCE_TO_JOIN 1 --UMI_TAG_NAME RX --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 UmiAwareMarkDuplicatesWithMateCigar --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 --MAX_RECORDS_IN_RAM 1000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:17:35 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 13:17:35 MarkDuplicatesWithMateCigar Found 1 optical duplicate clusters. INFO 2025-04-24 13:17:35 MarkDuplicatesWithMateCigar Processed 5 records INFO 2025-04-24 13:17:35 MarkDuplicatesWithMateCigar Marking 2 records as duplicates. [Thu Apr 24 13:17:35 EDT 2025] picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 [Thu Apr 24 13:17:35 EDT 2025] UmiAwareMarkDuplicatesWithMateCigar --UMI_METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.tmp16280567512368921405/umi_metrics.txt --ALLOW_MISSING_UMIS true --INPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.tmp16280567512368921405/input.sam --OUTPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.tmp16280567512368921405/output.sam --METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.tmp16280567512368921405/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_EDIT_DISTANCE_TO_JOIN 1 --UMI_TAG_NAME RX --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 UmiAwareMarkDuplicatesWithMateCigar --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 --MAX_RECORDS_IN_RAM 1000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:17:35 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 13:17:35 MarkDuplicatesWithMateCigar Found 1 optical duplicate clusters. INFO 2025-04-24 13:17:35 MarkDuplicatesWithMateCigar Processed 5 records INFO 2025-04-24 13:17:35 MarkDuplicatesWithMateCigar Marking 2 records as duplicates. [Thu Apr 24 13:17:35 EDT 2025] picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 [Thu Apr 24 13:17:35 EDT 2025] UmiAwareMarkDuplicatesWithMateCigar --UMI_METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.tmp3193416417669807354/umi_metrics.txt --ALLOW_MISSING_UMIS true --INPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.tmp3193416417669807354/input.sam --OUTPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.tmp3193416417669807354/output.sam --METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.tmp3193416417669807354/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_EDIT_DISTANCE_TO_JOIN 1 --UMI_TAG_NAME RX --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 UmiAwareMarkDuplicatesWithMateCigar --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 --MAX_RECORDS_IN_RAM 1000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:17:35 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 13:17:35 MarkDuplicatesWithMateCigar Found 1 optical duplicate clusters. INFO 2025-04-24 13:17:35 MarkDuplicatesWithMateCigar Processed 5 records INFO 2025-04-24 13:17:35 MarkDuplicatesWithMateCigar Marking 2 records as duplicates. [Thu Apr 24 13:17:35 EDT 2025] picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 [Thu Apr 24 13:17:35 EDT 2025] UmiAwareMarkDuplicatesWithMateCigar --UMI_METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.tmp5089052968367780084/umi_metrics.txt --ALLOW_MISSING_UMIS true --INPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.tmp5089052968367780084/input.sam --OUTPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.tmp5089052968367780084/output.sam --METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.tmp5089052968367780084/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_EDIT_DISTANCE_TO_JOIN 1 --UMI_TAG_NAME RX --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 UmiAwareMarkDuplicatesWithMateCigar --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 --MAX_RECORDS_IN_RAM 1000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:17:35 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 13:17:35 MarkDuplicatesWithMateCigar Found 1 optical duplicate clusters. INFO 2025-04-24 13:17:35 MarkDuplicatesWithMateCigar Processed 5 records INFO 2025-04-24 13:17:35 MarkDuplicatesWithMateCigar Marking 2 records as duplicates. [Thu Apr 24 13:17:35 EDT 2025] picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 [Thu Apr 24 13:17:35 EDT 2025] UmiAwareMarkDuplicatesWithMateCigar --UMI_METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.tmp7168704350111143113/umi_metrics.txt --ALLOW_MISSING_UMIS true --INPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.tmp7168704350111143113/input.sam --OUTPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.tmp7168704350111143113/output.sam --METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.tmp7168704350111143113/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_EDIT_DISTANCE_TO_JOIN 1 --UMI_TAG_NAME RX --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 UmiAwareMarkDuplicatesWithMateCigar --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 --MAX_RECORDS_IN_RAM 1000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:17:35 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 13:17:35 MarkDuplicatesWithMateCigar Found 1 optical duplicate clusters. INFO 2025-04-24 13:17:35 MarkDuplicatesWithMateCigar Processed 5 records INFO 2025-04-24 13:17:35 MarkDuplicatesWithMateCigar Marking 2 records as duplicates. [Thu Apr 24 13:17:35 EDT 2025] picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 [Thu Apr 24 13:17:35 EDT 2025] UmiAwareMarkDuplicatesWithMateCigar --UMI_METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.tmp13636413981288996953/umi_metrics.txt --ALLOW_MISSING_UMIS true --INPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.tmp13636413981288996953/input.sam --OUTPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.tmp13636413981288996953/output.sam --METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.tmp13636413981288996953/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_EDIT_DISTANCE_TO_JOIN 1 --UMI_TAG_NAME RX --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 UmiAwareMarkDuplicatesWithMateCigar --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 --MAX_RECORDS_IN_RAM 1000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:17:35 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 13:17:35 MarkDuplicatesWithMateCigar Found 1 optical duplicate clusters. INFO 2025-04-24 13:17:35 MarkDuplicatesWithMateCigar Processed 5 records INFO 2025-04-24 13:17:35 MarkDuplicatesWithMateCigar Marking 2 records as duplicates. [Thu Apr 24 13:17:35 EDT 2025] picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 [Thu Apr 24 13:17:35 EDT 2025] UmiAwareMarkDuplicatesWithMateCigar --UMI_METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.tmp5574428347342967771/umi_metrics.txt --ALLOW_MISSING_UMIS true --INPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.tmp5574428347342967771/input.sam --OUTPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.tmp5574428347342967771/output.sam --METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.tmp5574428347342967771/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_EDIT_DISTANCE_TO_JOIN 1 --UMI_TAG_NAME RX --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 UmiAwareMarkDuplicatesWithMateCigar --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 --MAX_RECORDS_IN_RAM 1000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:17:35 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 13:17:35 MarkDuplicatesWithMateCigar Found 1 optical duplicate clusters. INFO 2025-04-24 13:17:35 MarkDuplicatesWithMateCigar Processed 5 records INFO 2025-04-24 13:17:35 MarkDuplicatesWithMateCigar Marking 2 records as duplicates. [Thu Apr 24 13:17:35 EDT 2025] picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 [Thu Apr 24 13:17:35 EDT 2025] UmiAwareMarkDuplicatesWithMateCigar --UMI_METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.tmp6569232107349796892/umi_metrics.txt --ALLOW_MISSING_UMIS true --INPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.tmp6569232107349796892/input.sam --OUTPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.tmp6569232107349796892/output.sam --METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.tmp6569232107349796892/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_EDIT_DISTANCE_TO_JOIN 1 --UMI_TAG_NAME RX --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 UmiAwareMarkDuplicatesWithMateCigar --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 --MAX_RECORDS_IN_RAM 1000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:17:35 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 13:17:35 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. INFO 2025-04-24 13:17:35 MarkDuplicatesWithMateCigar Processed 2 records INFO 2025-04-24 13:17:35 MarkDuplicatesWithMateCigar Marking 0 records as duplicates. [Thu Apr 24 13:17:35 EDT 2025] picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 [Thu Apr 24 13:17:35 EDT 2025] UmiAwareMarkDuplicatesWithMateCigar --UMI_METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.tmp14993945322903729024/umi_metrics.txt --ALLOW_MISSING_UMIS true --INPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.tmp14993945322903729024/input.sam --OUTPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.tmp14993945322903729024/output.sam --METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.tmp14993945322903729024/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --MAX_EDIT_DISTANCE_TO_JOIN 1 --UMI_TAG_NAME RX --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 UmiAwareMarkDuplicatesWithMateCigar --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 --MAX_RECORDS_IN_RAM 1000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:17:35 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 13:17:35 EDT 2025] picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp [Thu Apr 24 13:17:35 EDT 2025] UmiAwareMarkDuplicatesWithMateCigar --MAX_EDIT_DISTANCE_TO_JOIN 4 --UMI_METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.tmp15751246441598758122/umi_metrics.txt --INPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.tmp15751246441598758122/input.sam --OUTPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.tmp15751246441598758122/output.sam --METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.tmp15751246441598758122/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --UMI_TAG_NAME RX --ALLOW_MISSING_UMIS false --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 UmiAwareMarkDuplicatesWithMateCigar --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 --MAX_RECORDS_IN_RAM 1000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:17:35 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 13:17:35 EDT 2025] picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp [Thu Apr 24 13:17:35 EDT 2025] UmiAwareMarkDuplicatesWithMateCigar --MAX_EDIT_DISTANCE_TO_JOIN 1 --UMI_METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.tmp4939179796216872958/umi_metrics.txt --INPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.tmp4939179796216872958/input.sam --OUTPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.tmp4939179796216872958/output.sam --METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.tmp4939179796216872958/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --UMI_TAG_NAME RX --ALLOW_MISSING_UMIS false --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 UmiAwareMarkDuplicatesWithMateCigar --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 --MAX_RECORDS_IN_RAM 1000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:17:35 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 13:17:35 EDT 2025] picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp [Thu Apr 24 13:17:35 EDT 2025] UmiAwareMarkDuplicatesWithMateCigar --MAX_EDIT_DISTANCE_TO_JOIN 4 --UMI_METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.tmp17430968248770737874/umi_metrics.txt --INPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.tmp17430968248770737874/input.sam --OUTPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.tmp17430968248770737874/output.sam --METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.tmp17430968248770737874/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --UMI_TAG_NAME RX --ALLOW_MISSING_UMIS false --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 UmiAwareMarkDuplicatesWithMateCigar --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 --MAX_RECORDS_IN_RAM 1000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:17:35 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 13:17:35 EDT 2025] picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp [Thu Apr 24 13:17:35 EDT 2025] UmiAwareMarkDuplicatesWithMateCigar --MAX_EDIT_DISTANCE_TO_JOIN 0 --UMI_METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.tmp4992043663638062099/umi_metrics.txt --DUPLEX_UMI true --INPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.tmp4992043663638062099/input.sam --OUTPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.tmp4992043663638062099/output.sam --METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.tmp4992043663638062099/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --UMI_TAG_NAME RX --ALLOW_MISSING_UMIS false --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 --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 UmiAwareMarkDuplicatesWithMateCigar --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 --MAX_RECORDS_IN_RAM 1000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:17:35 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 13:17:35 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 13:17:35 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. INFO 2025-04-24 13:17:35 MarkDuplicatesWithMateCigar Processed 4 records INFO 2025-04-24 13:17:35 MarkDuplicatesWithMateCigar Marking 2 records as duplicates. [Thu Apr 24 13:17:35 EDT 2025] picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 [Thu Apr 24 13:17:35 EDT 2025] UmiAwareMarkDuplicatesWithMateCigar --MAX_EDIT_DISTANCE_TO_JOIN 0 --UMI_METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.tmp11397617036591907172/umi_metrics.txt --DUPLEX_UMI false --INPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.tmp11397617036591907172/input.sam --OUTPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.tmp11397617036591907172/output.sam --METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.tmp11397617036591907172/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --UMI_TAG_NAME RX --ALLOW_MISSING_UMIS false --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 --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 UmiAwareMarkDuplicatesWithMateCigar --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 --MAX_RECORDS_IN_RAM 1000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:17:35 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 13:17:35 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 13:17:35 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. INFO 2025-04-24 13:17:35 MarkDuplicatesWithMateCigar Processed 4 records INFO 2025-04-24 13:17:35 MarkDuplicatesWithMateCigar Marking 0 records as duplicates. [Thu Apr 24 13:17:35 EDT 2025] picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 [Thu Apr 24 13:17:35 EDT 2025] UmiAwareMarkDuplicatesWithMateCigar --MAX_EDIT_DISTANCE_TO_JOIN 1 --UMI_METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.tmp1419770177054248789/umi_metrics.txt --DUPLEX_UMI true --INPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.tmp1419770177054248789/input.sam --OUTPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.tmp1419770177054248789/output.sam --METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.tmp1419770177054248789/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --UMI_TAG_NAME RX --ALLOW_MISSING_UMIS false --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 --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 UmiAwareMarkDuplicatesWithMateCigar --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 --MAX_RECORDS_IN_RAM 1000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:17:35 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 13:17:35 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 13:17:35 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. INFO 2025-04-24 13:17:35 MarkDuplicatesWithMateCigar Processed 4 records INFO 2025-04-24 13:17:35 MarkDuplicatesWithMateCigar Marking 2 records as duplicates. [Thu Apr 24 13:17:35 EDT 2025] picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 [Thu Apr 24 13:17:35 EDT 2025] UmiAwareMarkDuplicatesWithMateCigar --MAX_EDIT_DISTANCE_TO_JOIN 4 --UMI_METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.tmp16628290060770068555/umi_metrics.txt --ALLOW_MISSING_UMIS true --INPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.tmp16628290060770068555/input.sam --OUTPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.tmp16628290060770068555/output.sam --METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.tmp16628290060770068555/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --UMI_TAG_NAME RX --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 UmiAwareMarkDuplicatesWithMateCigar --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 --MAX_RECORDS_IN_RAM 1000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:17:35 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 13:17:35 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 13:17:35 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. INFO 2025-04-24 13:17:35 MarkDuplicatesWithMateCigar Processed 6 records INFO 2025-04-24 13:17:35 MarkDuplicatesWithMateCigar Marking 4 records as duplicates. [Thu Apr 24 13:17:35 EDT 2025] picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 [Thu Apr 24 13:17:35 EDT 2025] UmiAwareMarkDuplicatesWithMateCigar --MAX_EDIT_DISTANCE_TO_JOIN 1 --UMI_METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.tmp12242374641334815931/umi_metrics.txt --MOLECULAR_IDENTIFIER_TAG MI --INPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.tmp12242374641334815931/input.sam --OUTPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.tmp12242374641334815931/output.sam --METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.tmp12242374641334815931/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --UMI_TAG_NAME RX --ALLOW_MISSING_UMIS false --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 UmiAwareMarkDuplicatesWithMateCigar --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 --MAX_RECORDS_IN_RAM 1000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:17:35 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 13:17:35 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 13:17:35 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. INFO 2025-04-24 13:17:35 MarkDuplicatesWithMateCigar Processed 6 records INFO 2025-04-24 13:17:35 MarkDuplicatesWithMateCigar Marking 2 records as duplicates. [Thu Apr 24 13:17:35 EDT 2025] picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 [Thu Apr 24 13:17:35 EDT 2025] UmiAwareMarkDuplicatesWithMateCigar --MAX_EDIT_DISTANCE_TO_JOIN 1 --UMI_METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.tmp7542287854273339228/umi_metrics.txt --MOLECULAR_IDENTIFIER_TAG MI --INPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.tmp7542287854273339228/input.sam --OUTPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.tmp7542287854273339228/output.sam --METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.tmp7542287854273339228/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --UMI_TAG_NAME RX --ALLOW_MISSING_UMIS false --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 UmiAwareMarkDuplicatesWithMateCigar --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 --MAX_RECORDS_IN_RAM 1000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:17:35 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 13:17:35 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 13:17:35 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. INFO 2025-04-24 13:17:35 MarkDuplicatesWithMateCigar Processed 4 records INFO 2025-04-24 13:17:35 MarkDuplicatesWithMateCigar Marking 2 records as duplicates. [Thu Apr 24 13:17:35 EDT 2025] picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 [Thu Apr 24 13:17:35 EDT 2025] UmiAwareMarkDuplicatesWithMateCigar --MAX_EDIT_DISTANCE_TO_JOIN 1 --UMI_METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.tmp1974442883001993857/umi_metrics.txt --MOLECULAR_IDENTIFIER_TAG MI --INPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.tmp1974442883001993857/input.sam --OUTPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.tmp1974442883001993857/output.sam --METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.tmp1974442883001993857/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --UMI_TAG_NAME RX --ALLOW_MISSING_UMIS false --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 UmiAwareMarkDuplicatesWithMateCigar --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 --MAX_RECORDS_IN_RAM 1000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:17:35 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 13:17:35 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 13:17:35 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. INFO 2025-04-24 13:17:35 MarkDuplicatesWithMateCigar Processed 2 records INFO 2025-04-24 13:17:35 MarkDuplicatesWithMateCigar Marking 0 records as duplicates. [Thu Apr 24 13:17:35 EDT 2025] picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 [Thu Apr 24 13:17:35 EDT 2025] UmiAwareMarkDuplicatesWithMateCigar --MAX_EDIT_DISTANCE_TO_JOIN 1 --UMI_METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.tmp5344117398668852068/umi_metrics.txt --MOLECULAR_IDENTIFIER_TAG MI --INPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.tmp5344117398668852068/input.sam --OUTPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.tmp5344117398668852068/output.sam --METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.tmp5344117398668852068/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --UMI_TAG_NAME RX --ALLOW_MISSING_UMIS false --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 UmiAwareMarkDuplicatesWithMateCigar --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 --MAX_RECORDS_IN_RAM 1000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:17:35 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 13:17:35 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 13:17:35 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. INFO 2025-04-24 13:17:35 MarkDuplicatesWithMateCigar Processed 2 records INFO 2025-04-24 13:17:35 MarkDuplicatesWithMateCigar Marking 0 records as duplicates. [Thu Apr 24 13:17:35 EDT 2025] picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 [Thu Apr 24 13:17:35 EDT 2025] UmiAwareMarkDuplicatesWithMateCigar --MAX_EDIT_DISTANCE_TO_JOIN 1 --UMI_METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.tmp14783636515035411898/umi_metrics.txt --MOLECULAR_IDENTIFIER_TAG MI --INPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.tmp14783636515035411898/input.sam --OUTPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.tmp14783636515035411898/output.sam --METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.tmp14783636515035411898/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --UMI_TAG_NAME RX --ALLOW_MISSING_UMIS false --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 UmiAwareMarkDuplicatesWithMateCigar --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 --MAX_RECORDS_IN_RAM 1000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:17:35 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 13:17:35 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 13:17:35 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. INFO 2025-04-24 13:17:35 MarkDuplicatesWithMateCigar Processed 6 records INFO 2025-04-24 13:17:35 MarkDuplicatesWithMateCigar Marking 2 records as duplicates. [Thu Apr 24 13:17:35 EDT 2025] picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 [Thu Apr 24 13:17:35 EDT 2025] UmiAwareMarkDuplicatesWithMateCigar --MAX_EDIT_DISTANCE_TO_JOIN 1 --UMI_METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.tmp5394905399942912617/umi_metrics.txt --MOLECULAR_IDENTIFIER_TAG MI --INPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.tmp5394905399942912617/input.sam --OUTPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.tmp5394905399942912617/output.sam --METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.tmp5394905399942912617/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --UMI_TAG_NAME RX --ALLOW_MISSING_UMIS false --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 UmiAwareMarkDuplicatesWithMateCigar --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 --MAX_RECORDS_IN_RAM 1000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:17:35 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 13:17:35 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 13:17:35 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. INFO 2025-04-24 13:17:35 MarkDuplicatesWithMateCigar Processed 10 records INFO 2025-04-24 13:17:35 MarkDuplicatesWithMateCigar Marking 6 records as duplicates. [Thu Apr 24 13:17:35 EDT 2025] picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 [Thu Apr 24 13:17:35 EDT 2025] UmiAwareMarkDuplicatesWithMateCigar --MAX_EDIT_DISTANCE_TO_JOIN 2 --UMI_METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.tmp16835122127437048699/umi_metrics.txt --MOLECULAR_IDENTIFIER_TAG MI --INPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.tmp16835122127437048699/input.sam --OUTPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.tmp16835122127437048699/output.sam --METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.tmp16835122127437048699/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --UMI_TAG_NAME RX --ALLOW_MISSING_UMIS false --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 UmiAwareMarkDuplicatesWithMateCigar --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 --MAX_RECORDS_IN_RAM 1000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:17:35 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 13:17:35 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 13:17:35 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. INFO 2025-04-24 13:17:35 MarkDuplicatesWithMateCigar Processed 10 records INFO 2025-04-24 13:17:35 MarkDuplicatesWithMateCigar Marking 8 records as duplicates. [Thu Apr 24 13:17:35 EDT 2025] picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 [Thu Apr 24 13:17:35 EDT 2025] UmiAwareMarkDuplicatesWithMateCigar --MAX_EDIT_DISTANCE_TO_JOIN 1 --UMI_METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.tmp12648903802869634850/umi_metrics.txt --MOLECULAR_IDENTIFIER_TAG MI --INPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.tmp12648903802869634850/input.sam --OUTPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.tmp12648903802869634850/output.sam --METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.tmp12648903802869634850/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --UMI_TAG_NAME RX --ALLOW_MISSING_UMIS false --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 UmiAwareMarkDuplicatesWithMateCigar --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 --MAX_RECORDS_IN_RAM 1000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:17:35 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 13:17:35 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 13:17:35 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. INFO 2025-04-24 13:17:35 MarkDuplicatesWithMateCigar Processed 14 records INFO 2025-04-24 13:17:35 MarkDuplicatesWithMateCigar Marking 10 records as duplicates. [Thu Apr 24 13:17:35 EDT 2025] picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 [Thu Apr 24 13:17:35 EDT 2025] UmiAwareMarkDuplicatesWithMateCigar --MAX_EDIT_DISTANCE_TO_JOIN 1 --UMI_METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.tmp3346340852434478392/umi_metrics.txt --MOLECULAR_IDENTIFIER_TAG MI --INPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.tmp3346340852434478392/input.sam --OUTPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.tmp3346340852434478392/output.sam --METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.tmp3346340852434478392/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --UMI_TAG_NAME RX --ALLOW_MISSING_UMIS false --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 UmiAwareMarkDuplicatesWithMateCigar --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 --MAX_RECORDS_IN_RAM 1000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:17:35 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 13:17:35 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 13:17:35 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. INFO 2025-04-24 13:17:35 MarkDuplicatesWithMateCigar Processed 16 records INFO 2025-04-24 13:17:35 MarkDuplicatesWithMateCigar Marking 14 records as duplicates. [Thu Apr 24 13:17:35 EDT 2025] picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 [Thu Apr 24 13:17:35 EDT 2025] UmiAwareMarkDuplicatesWithMateCigar --MAX_EDIT_DISTANCE_TO_JOIN 0 --UMI_METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.tmp12353829725340593187/umi_metrics.txt --MOLECULAR_IDENTIFIER_TAG MI --INPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.tmp12353829725340593187/input.sam --OUTPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.tmp12353829725340593187/output.sam --METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.tmp12353829725340593187/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --UMI_TAG_NAME RX --ALLOW_MISSING_UMIS false --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 UmiAwareMarkDuplicatesWithMateCigar --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 --MAX_RECORDS_IN_RAM 1000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:17:35 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 13:17:35 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 13:17:35 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. INFO 2025-04-24 13:17:35 MarkDuplicatesWithMateCigar Processed 16 records INFO 2025-04-24 13:17:35 MarkDuplicatesWithMateCigar Marking 8 records as duplicates. [Thu Apr 24 13:17:35 EDT 2025] picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 [Thu Apr 24 13:17:35 EDT 2025] UmiAwareMarkDuplicatesWithMateCigar --MAX_EDIT_DISTANCE_TO_JOIN 4 --UMI_METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.tmp11751164414127296516/umi_metrics.txt --MOLECULAR_IDENTIFIER_TAG MI --INPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.tmp11751164414127296516/input.sam --OUTPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.tmp11751164414127296516/output.sam --METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.tmp11751164414127296516/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --UMI_TAG_NAME RX --ALLOW_MISSING_UMIS false --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 UmiAwareMarkDuplicatesWithMateCigar --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 --MAX_RECORDS_IN_RAM 1000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:17:35 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 13:17:35 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 13:17:35 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. INFO 2025-04-24 13:17:35 MarkDuplicatesWithMateCigar Processed 6 records INFO 2025-04-24 13:17:35 MarkDuplicatesWithMateCigar Marking 4 records as duplicates. [Thu Apr 24 13:17:35 EDT 2025] picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 [Thu Apr 24 13:17:35 EDT 2025] UmiAwareMarkDuplicatesWithMateCigar --MAX_EDIT_DISTANCE_TO_JOIN 1 --UMI_METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.tmp11684330514586116686/umi_metrics.txt --MOLECULAR_IDENTIFIER_TAG MI --INPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.tmp11684330514586116686/input.sam --OUTPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.tmp11684330514586116686/output.sam --METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.tmp11684330514586116686/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --UMI_TAG_NAME RX --ALLOW_MISSING_UMIS false --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 UmiAwareMarkDuplicatesWithMateCigar --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 --MAX_RECORDS_IN_RAM 1000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:17:35 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 13:17:35 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 13:17:35 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. INFO 2025-04-24 13:17:35 MarkDuplicatesWithMateCigar Processed 4 records INFO 2025-04-24 13:17:35 MarkDuplicatesWithMateCigar Marking 2 records as duplicates. [Thu Apr 24 13:17:35 EDT 2025] picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 [Thu Apr 24 13:17:35 EDT 2025] UmiAwareMarkDuplicatesWithMateCigar --MAX_EDIT_DISTANCE_TO_JOIN 1 --UMI_METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.tmp8210558227314162228/umi_metrics.txt --MOLECULAR_IDENTIFIER_TAG MI --INPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.tmp8210558227314162228/input.sam --OUTPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.tmp8210558227314162228/output.sam --METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.tmp8210558227314162228/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --UMI_TAG_NAME RX --ALLOW_MISSING_UMIS false --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 UmiAwareMarkDuplicatesWithMateCigar --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 --MAX_RECORDS_IN_RAM 1000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:17:35 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 13:17:35 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 13:17:35 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. INFO 2025-04-24 13:17:35 MarkDuplicatesWithMateCigar Processed 10 records INFO 2025-04-24 13:17:35 MarkDuplicatesWithMateCigar Marking 8 records as duplicates. [Thu Apr 24 13:17:35 EDT 2025] picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 [Thu Apr 24 13:17:35 EDT 2025] UmiAwareMarkDuplicatesWithMateCigar --MAX_EDIT_DISTANCE_TO_JOIN 1 --UMI_METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.tmp5836127896429129736/umi_metrics.txt --MOLECULAR_IDENTIFIER_TAG MI --INPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.tmp5836127896429129736/input.sam --OUTPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.tmp5836127896429129736/output.sam --METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.tmp5836127896429129736/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --UMI_TAG_NAME RX --ALLOW_MISSING_UMIS false --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 UmiAwareMarkDuplicatesWithMateCigar --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 --MAX_RECORDS_IN_RAM 1000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:17:35 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 13:17:35 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 13:17:35 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. INFO 2025-04-24 13:17:35 MarkDuplicatesWithMateCigar Processed 10 records INFO 2025-04-24 13:17:35 MarkDuplicatesWithMateCigar Marking 8 records as duplicates. [Thu Apr 24 13:17:35 EDT 2025] picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 [Thu Apr 24 13:17:35 EDT 2025] UmiAwareMarkDuplicatesWithMateCigar --MAX_EDIT_DISTANCE_TO_JOIN 1 --UMI_METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.tmp2671293341374397807/umi_metrics.txt --MOLECULAR_IDENTIFIER_TAG MI --INPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.tmp2671293341374397807/input.sam --OUTPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.tmp2671293341374397807/output.sam --METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.tmp2671293341374397807/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --UMI_TAG_NAME RX --ALLOW_MISSING_UMIS false --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 UmiAwareMarkDuplicatesWithMateCigar --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 --MAX_RECORDS_IN_RAM 1000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:17:35 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 13:17:35 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 13:17:35 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. INFO 2025-04-24 13:17:35 MarkDuplicatesWithMateCigar Processed 10 records INFO 2025-04-24 13:17:35 MarkDuplicatesWithMateCigar Marking 6 records as duplicates. [Thu Apr 24 13:17:35 EDT 2025] picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 [Thu Apr 24 13:17:35 EDT 2025] UmiAwareMarkDuplicatesWithMateCigar --MAX_EDIT_DISTANCE_TO_JOIN 2 --UMI_METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.tmp4918192721702259268/umi_metrics.txt --MOLECULAR_IDENTIFIER_TAG MI --INPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.tmp4918192721702259268/input.sam --OUTPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.tmp4918192721702259268/output.sam --METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.tmp4918192721702259268/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --UMI_TAG_NAME RX --ALLOW_MISSING_UMIS false --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 UmiAwareMarkDuplicatesWithMateCigar --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 --MAX_RECORDS_IN_RAM 1000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:17:35 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 13:17:35 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 13:17:35 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. INFO 2025-04-24 13:17:35 MarkDuplicatesWithMateCigar Processed 10 records INFO 2025-04-24 13:17:35 MarkDuplicatesWithMateCigar Marking 8 records as duplicates. [Thu Apr 24 13:17:35 EDT 2025] picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 [Thu Apr 24 13:17:35 EDT 2025] UmiAwareMarkDuplicatesWithMateCigar --MAX_EDIT_DISTANCE_TO_JOIN 2 --UMI_METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.tmp9877920107455082112/umi_metrics.txt --MOLECULAR_IDENTIFIER_TAG MI --INPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.tmp9877920107455082112/input.sam --OUTPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.tmp9877920107455082112/output.sam --METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.tmp9877920107455082112/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --UMI_TAG_NAME RX --ALLOW_MISSING_UMIS false --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 UmiAwareMarkDuplicatesWithMateCigar --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 --MAX_RECORDS_IN_RAM 1000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:17:35 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 13:17:35 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 13:17:35 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. INFO 2025-04-24 13:17:35 MarkDuplicatesWithMateCigar Processed 14 records INFO 2025-04-24 13:17:35 MarkDuplicatesWithMateCigar Marking 12 records as duplicates. [Thu Apr 24 13:17:35 EDT 2025] picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 [Thu Apr 24 13:17:35 EDT 2025] UmiAwareMarkDuplicatesWithMateCigar --MAX_EDIT_DISTANCE_TO_JOIN 0 --UMI_METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.tmp11979080754348577906/umi_metrics.txt --MOLECULAR_IDENTIFIER_TAG MI --INPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.tmp11979080754348577906/input.sam --OUTPUT /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.tmp11979080754348577906/output.sam --METRICS_FILE /tmp/UmiAwareMarkDuplicatesWithMateCigarTester.tmp11979080754348577906/metrics.txt --DUPLICATE_SCORING_STRATEGY TOTAL_MAPPED_REFERENCE_LENGTH --UMI_TAG_NAME RX --ALLOW_MISSING_UMIS false --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 UmiAwareMarkDuplicatesWithMateCigar --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 --MAX_RECORDS_IN_RAM 1000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:17:35 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 13:17:35 AbstractOpticalDuplicateFinderCommandLineProgram A field field parsed out of a read name was expected to contain an integer and did not. Read name: READ5. Cause: String 'READ5' did not start with a parsable number. INFO 2025-04-24 13:17:35 MarkDuplicatesWithMateCigar Found 0 optical duplicate clusters. INFO 2025-04-24 13:17:35 MarkDuplicatesWithMateCigar Processed 32 records INFO 2025-04-24 13:17:35 MarkDuplicatesWithMateCigar Marking 0 records as duplicates. [Thu Apr 24 13:17:35 EDT 2025] picard.sam.markduplicates.UmiAwareMarkDuplicatesWithMateCigar done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824