## htsjdk.samtools.metrics.StringHeader # MarkDuplicates INPUT=[/project/berglandlab/DEST/dest_mapped/DESTv1/RU_Cri_Yal_1_2016-08-20/RU_Cri_Yal_1_2016-08-20.sorted_merged.bam] OUTPUT=/project/berglandlab/DEST/dest_mapped/DESTv1/RU_Cri_Yal_1_2016-08-20/RU_Cri_Yal_1_2016-08-20.dedup.bam METRICS_FILE=/project/berglandlab/DEST/dest_mapped/DESTv1/RU_Cri_Yal_1_2016-08-20/RU_Cri_Yal_1_2016-08-20.mark_duplicates_report.txt REMOVE_DUPLICATES=true VALIDATION_STRINGENCY=SILENT 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 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= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false ## htsjdk.samtools.metrics.StringHeader # Started on: Fri Jan 20 08:48:39 UTC 2023 ## 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 lib1 32043477 8445710 0 0 7981800 744626 0 0.193544 45037867 ## HISTOGRAM java.lang.Double BIN VALUE all_sets non_optical_sets 1.0 1 6959933 6959933 2.0 1.829009 442271 442271 3.0 2.516264 35541 35541 4.0 3.086005 4861 4861 5.0 3.558325 1789 1789 6.0 3.949882 1047 1047 7.0 4.274487 756 756 8.0 4.543587 547 547 9.0 4.766673 385 385 10.0 4.951613 343 343 11.0 5.10493 248 248 12.0 5.232032 214 214 13.0 5.3374 190 190 14.0 5.424751 173 173 15.0 5.497165 154 154 16.0 5.557198 145 145 17.0 5.606965 155 155 18.0 5.648223 119 119 19.0 5.682426 118 118 20.0 5.71078 118 118 21.0 5.734287 106 106 22.0 5.753773 94 94 23.0 5.769928 93 93 24.0 5.783321 83 83 25.0 5.794423 79 79 26.0 5.803627 64 64 27.0 5.811257 96 96 28.0 5.817583 65 65 29.0 5.822827 67 67 30.0 5.827174 52 52 31.0 5.830778 53 53 32.0 5.833765 44 44 33.0 5.836242 50 50 34.0 5.838295 46 46 35.0 5.839998 46 46 36.0 5.841409 53 53 37.0 5.842579 38 38 38.0 5.843548 36 36 39.0 5.844352 31 31 40.0 5.845019 35 35 41.0 5.845571 23 23 42.0 5.84603 25 25 43.0 5.846409 25 25 44.0 5.846724 25 25 45.0 5.846985 23 23 46.0 5.847201 15 15 47.0 5.847381 28 28 48.0 5.847529 23 23 49.0 5.847653 23 23 50.0 5.847755 23 23 51.0 5.84784 12 12 52.0 5.84791 13 13 53.0 5.847968 13 13 54.0 5.848016 22 22 55.0 5.848056 14 14 56.0 5.84809 16 16 57.0 5.848117 11 11 58.0 5.84814 8 8 59.0 5.848159 16 16 60.0 5.848174 20 20 61.0 5.848187 10 10 62.0 5.848198 15 15 63.0 5.848207 13 13 64.0 5.848214 23 23 65.0 5.848221 9 9 66.0 5.848226 8 8 67.0 5.84823 10 10 68.0 5.848233 8 8 69.0 5.848236 14 14 70.0 5.848239 14 14 71.0 5.848241 12 12 72.0 5.848242 14 14 73.0 5.848244 13 13 74.0 5.848245 11 11 75.0 5.848246 16 16 76.0 5.848247 8 8 77.0 5.848247 10 10 78.0 5.848248 21 21 79.0 5.848248 15 15 80.0 5.848249 13 13 81.0 5.848249 14 14 82.0 5.848249 13 13 83.0 5.848249 9 9 84.0 5.848249 12 12 85.0 5.84825 6 6 86.0 5.84825 9 9 87.0 5.84825 5 5 88.0 5.84825 6 6 89.0 5.84825 7 7 90.0 5.84825 10 10 91.0 5.84825 8 8 92.0 5.84825 8 8 93.0 5.84825 9 9 94.0 5.84825 3 3 95.0 5.84825 6 6 96.0 5.84825 3 3 97.0 5.84825 8 8 98.0 5.84825 1 1 99.0 5.84825 8 8 100.0 5.84825 5 5 101.0 0 6 6 102.0 0 5 5 103.0 0 6 6 104.0 0 4 4 105.0 0 5 5 106.0 0 3 3 107.0 0 6 6 108.0 0 3 3 109.0 0 6 6 110.0 0 3 3 111.0 0 6 6 112.0 0 4 4 113.0 0 6 6 114.0 0 6 6 115.0 0 3 3 116.0 0 12 12 117.0 0 2 2 118.0 0 4 4 119.0 0 5 5 120.0 0 3 3 121.0 0 4 4 122.0 0 3 3 123.0 0 3 3 124.0 0 2 2 125.0 0 2 2 126.0 0 5 5 127.0 0 3 3 128.0 0 2 2 129.0 0 5 5 130.0 0 2 2 131.0 0 2 2 132.0 0 4 4 133.0 0 2 2 134.0 0 1 1 135.0 0 5 5 136.0 0 8 8 137.0 0 3 3 138.0 0 3 3 139.0 0 2 2 140.0 0 4 4 141.0 0 1 1 142.0 0 7 7 143.0 0 5 5 144.0 0 3 3 145.0 0 2 2 147.0 0 3 3 148.0 0 7 7 149.0 0 1 1 150.0 0 3 3 152.0 0 1 1 153.0 0 1 1 154.0 0 2 2 155.0 0 3 3 156.0 0 1 1 158.0 0 3 3 159.0 0 1 1 160.0 0 1 1 161.0 0 1 1 163.0 0 3 3 164.0 0 4 4 165.0 0 1 1 166.0 0 3 3 167.0 0 1 1 168.0 0 2 2 172.0 0 2 2 173.0 0 2 2 176.0 0 1 1 177.0 0 1 1 178.0 0 2 2 179.0 0 2 2 181.0 0 3 3 183.0 0 2 2 184.0 0 3 3 185.0 0 3 3 186.0 0 1 1 188.0 0 1 1 189.0 0 1 1 190.0 0 1 1 191.0 0 2 2 192.0 0 3 3 195.0 0 1 1 197.0 0 1 1 198.0 0 1 1 199.0 0 1 1 200.0 0 1 1 204.0 0 1 1 208.0 0 2 2 210.0 0 3 3 211.0 0 2 2 212.0 0 1 1 215.0 0 1 1 217.0 0 1 1 220.0 0 1 1 221.0 0 1 1 222.0 0 1 1 224.0 0 1 1 225.0 0 1 1 226.0 0 1 1 227.0 0 2 2 231.0 0 1 1 232.0 0 1 1 234.0 0 2 2 235.0 0 3 3 236.0 0 3 3 238.0 0 3 3 239.0 0 1 1 243.0 0 1 1 249.0 0 3 3 250.0 0 4 4 251.0 0 1 1 255.0 0 1 1 256.0 0 1 1 260.0 0 1 1 261.0 0 2 2 270.0 0 2 2 273.0 0 2 2 277.0 0 1 1 278.0 0 1 1 282.0 0 1 1 285.0 0 1 1 286.0 0 2 2 289.0 0 1 1 294.0 0 1 1 297.0 0 3 3 301.0 0 1 1 302.0 0 1 1 307.0 0 1 1 309.0 0 1 1 310.0 0 1 1 311.0 0 2 2 312.0 0 1 1 313.0 0 1 1 314.0 0 1 1 317.0 0 1 1 323.0 0 1 1 328.0 0 1 1 332.0 0 1 1 336.0 0 1 1 338.0 0 1 1 343.0 0 1 1 344.0 0 1 1 345.0 0 1 1 346.0 0 1 1 354.0 0 1 1 361.0 0 2 2 366.0 0 1 1 369.0 0 1 1 374.0 0 1 1 376.0 0 1 1 377.0 0 1 1 378.0 0 1 1 380.0 0 1 1 395.0 0 1 1 415.0 0 1 1 417.0 0 1 1 425.0 0 1 1 437.0 0 1 1 448.0 0 1 1 454.0 0 1 1 464.0 0 1 1 470.0 0 1 1 472.0 0 1 1 479.0 0 1 1 514.0 0 1 1 520.0 0 2 2 533.0 0 1 1 559.0 0 1 1 581.0 0 1 1 587.0 0 1 1 623.0 0 1 1 625.0 0 1 1 652.0 0 1 1 724.0 0 1 1 736.0 0 1 1 762.0 0 1 1 766.0 0 1 1 769.0 0 1 1 909.0 0 1 1 952.0 0 1 1 1009.0 0 1 1 1138.0 0 1 1 1864.0 0 1 1 3809.0 0 1 1