## htsjdk.samtools.metrics.StringHeader # MarkDuplicates TAG_DUPLICATE_SET_MEMBERS=true TAGGING_POLICY=All INPUT=[one.sorted.bam] OUTPUT=one.markdup.bam METRICS_FILE=one.markdup_metrics.txt REMOVE_DUPLICATES=false OPTICAL_DUPLICATE_PIXEL_DISTANCE=2500 TMP_DIR=[/tmp/nxf.bfq8ROwoxh] VALIDATION_STRINGENCY=SILENT MAX_RECORDS_IN_RAM=250000 CREATE_INDEX=true MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false 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 ASSUME_SORTED=false DUPLICATE_SCORING_STRATEGY=SUM_OF_BASE_QUALITIES PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false COMPRESSION_LEVEL=5 CREATE_MD5_FILE=false USE_JDK_DEFLATER=false USE_JDK_INFLATER=false ## htsjdk.samtools.metrics.StringHeader # Started on: Mon Jun 08 19:30:54 UTC 2026 ## METRICS CLASS picard.sam.DuplicationMetrics LIBRARY UNPAIRED_READS_EXAMINED READ_PAIRS_EXAMINED SECONDARY_OR_SUPPLEMENTARY_RDS UNMAPPED_READS UNPAIRED_READ_DUPLICATES READ_PAIR_DUPLICATES READ_PAIR_OPTICAL_DUPLICATES PERCENT_DUPLICATION ESTIMATED_LIBRARY_SIZE one 5 875093 3 1675 4 696570 4600 0.795995 179949 ## HISTOGRAM java.lang.Double BIN CoverageMult all_sets optical_sets non_optical_sets 1.0 1.000199 48274 0 48511 2.0 1.007928 45768 4129 46000 3.0 1.007987 23129 203 22994 4.0 1.007988 14312 19 14246 5.0 1.007988 9564 2 9540 6.0 1.007988 6676 0 6626 7.0 1.007988 5071 0 5054 8.0 1.007988 3747 0 3730 9.0 1.007988 2810 0 2792 10.0 1.007988 2284 0 2283 11.0 1.007988 1876 0 1834 12.0 1.007988 1663 0 1659 13.0 1.007988 1387 0 1372 14.0 1.007988 1051 0 1051 15.0 1.007988 973 0 974 16.0 1.007988 872 0 880 17.0 1.007988 736 0 711 18.0 1.007988 655 0 649 19.0 1.007988 514 0 495 20.0 1.007988 485 0 495 21.0 1.007988 440 0 438 22.0 1.007988 419 0 424 23.0 1.007988 380 0 379 24.0 1.007988 331 0 319 25.0 1.007988 268 0 267 26.0 1.007988 282 0 282 27.0 1.007988 226 0 225 28.0 1.007988 274 0 283 29.0 1.007988 239 0 226 30.0 1.007988 183 0 179 31.0 1.007988 189 0 194 32.0 1.007988 173 0 163 33.0 1.007988 168 0 169 34.0 1.007988 135 0 143 35.0 1.007988 123 0 110 36.0 1.007988 126 0 137 37.0 1.007988 132 0 123 38.0 1.007988 149 0 151 39.0 1.007988 89 0 86 40.0 1.007988 110 0 118 41.0 1.007988 94 0 86 42.0 1.007988 73 0 78 43.0 1.007988 75 0 65 44.0 1.007988 59 0 62 45.0 1.007988 70 0 68 46.0 1.007988 76 0 82 47.0 1.007988 94 0 89 48.0 1.007988 88 0 94 49.0 1.007988 70 0 72 50.0 1.007988 54 0 43 51.0 1.007988 54 0 58 52.0 1.007988 48 0 48 53.0 1.007988 60 0 60 54.0 1.007988 53 0 56 55.0 1.007988 53 0 45 56.0 1.007988 62 0 64 57.0 1.007988 50 0 58 58.0 1.007988 62 0 45 59.0 1.007988 42 0 45 60.0 1.007988 39 0 49 61.0 1.007988 39 0 34 62.0 1.007988 25 0 26 63.0 1.007988 42 0 36 64.0 1.007988 34 0 33 65.0 1.007988 34 0 37 66.0 1.007988 28 0 30 67.0 1.007988 39 0 38 68.0 1.007988 35 0 43 69.0 1.007988 40 0 33 70.0 1.007988 35 0 41 71.0 1.007988 32 0 24 72.0 1.007988 25 0 26 73.0 1.007988 29 0 30 74.0 1.007988 21 0 25 75.0 1.007988 36 0 38 76.0 1.007988 35 0 30 77.0 1.007988 28 0 28 78.0 1.007988 27 0 24 79.0 1.007988 32 0 29 80.0 1.007988 22 0 20 81.0 1.007988 15 0 14 82.0 1.007988 13 0 11 83.0 1.007988 10 0 14 84.0 1.007988 17 0 22 85.0 1.007988 28 0 27 86.0 1.007988 13 0 14 87.0 1.007988 31 0 28 88.0 1.007988 11 0 11 89.0 1.007988 17 0 18 90.0 1.007988 19 0 15 91.0 1.007988 16 0 13 92.0 1.007988 7 0 7 93.0 1.007988 10 0 11 94.0 1.007988 16 0 28 95.0 1.007988 28 0 23 96.0 1.007988 16 0 10 97.0 1.007988 9 0 5 98.0 1.007988 7 0 11 99.0 1.007988 12 0 10 100.0 1.007988 12 0 16 101.0 0 7 0 1 102.0 0 1 0 3 103.0 0 3 0 1 104.0 0 2 0 1 105.0 0 1 0 0 107.0 0 1 0 2 108.0 0 1 0 0 110.0 0 1 0 1 115.0 0 0 0 1 116.0 0 1 0 0 120.0 0 1 0 1