## htsjdk.samtools.metrics.StringHeader # MarkDuplicates INPUT=[/project/berglandlab/DEST/dest_mapped/DESTv1/RU_Nov_Val_1_2016-09-29/RU_Nov_Val_1_2016-09-29.sorted_merged.bam] OUTPUT=/project/berglandlab/DEST/dest_mapped/DESTv1/RU_Nov_Val_1_2016-09-29/RU_Nov_Val_1_2016-09-29.dedup.bam METRICS_FILE=/project/berglandlab/DEST/dest_mapped/DESTv1/RU_Nov_Val_1_2016-09-29/RU_Nov_Val_1_2016-09-29.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 09:17:06 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 33191784 14397453 0 0 9074418 1235851 0 0.186268 78992789 ## HISTOGRAM java.lang.Double BIN VALUE all_sets non_optical_sets 1.0 1 11846689 11846689 2.0 1.833382 818201 818201 3.0 2.527908 65140 65140 4.0 3.106714 8279 8279 5.0 3.58908 2860 2860 6.0 3.991076 1661 1661 7.0 4.326091 1190 1190 8.0 4.605288 828 828 9.0 4.837965 618 618 10.0 5.031874 513 513 11.0 5.193474 381 381 12.0 5.328149 308 308 13.0 5.440385 282 282 14.0 5.53392 257 257 15.0 5.611871 225 225 16.0 5.676833 181 181 17.0 5.730972 162 162 18.0 5.77609 152 152 19.0 5.813691 145 145 20.0 5.845027 132 132 21.0 5.871142 127 127 22.0 5.892905 115 115 23.0 5.911042 108 108 24.0 5.926158 102 102 25.0 5.938755 91 91 26.0 5.949253 104 104 27.0 5.958001 84 84 28.0 5.965293 81 81 29.0 5.971369 77 77 30.0 5.976433 80 80 31.0 5.980653 62 62 32.0 5.98417 59 59 33.0 5.987101 63 63 34.0 5.989543 49 49 35.0 5.991579 48 48 36.0 5.993276 61 61 37.0 5.994689 45 45 38.0 5.995868 49 49 39.0 5.99685 40 40 40.0 5.997668 43 43 41.0 5.99835 52 52 42.0 5.998918 44 44 43.0 5.999392 36 36 44.0 5.999787 39 39 45.0 6.000116 31 31 46.0 6.00039 39 39 47.0 6.000618 17 17 48.0 6.000809 33 33 49.0 6.000967 20 20 50.0 6.0011 28 28 51.0 6.00121 21 21 52.0 6.001302 26 26 53.0 6.001378 26 26 54.0 6.001442 23 23 55.0 6.001495 14 14 56.0 6.001539 24 24 57.0 6.001576 20 20 58.0 6.001607 17 17 59.0 6.001633 16 16 60.0 6.001654 10 10 61.0 6.001672 19 19 62.0 6.001687 15 15 63.0 6.001699 19 19 64.0 6.001709 15 15 65.0 6.001718 17 17 66.0 6.001725 12 12 67.0 6.001731 14 14 68.0 6.001736 13 13 69.0 6.00174 9 9 70.0 6.001744 9 9 71.0 6.001747 16 16 72.0 6.001749 14 14 73.0 6.001751 15 15 74.0 6.001753 9 9 75.0 6.001754 13 13 76.0 6.001755 15 15 77.0 6.001756 7 7 78.0 6.001757 12 12 79.0 6.001758 10 10 80.0 6.001758 11 11 81.0 6.001759 9 9 82.0 6.001759 18 18 83.0 6.001759 9 9 84.0 6.00176 13 13 85.0 6.00176 10 10 86.0 6.00176 8 8 87.0 6.00176 7 7 88.0 6.00176 12 12 89.0 6.00176 7 7 90.0 6.001761 10 10 91.0 6.001761 8 8 92.0 6.001761 4 4 93.0 6.001761 7 7 94.0 6.001761 11 11 95.0 6.001761 10 10 96.0 6.001761 7 7 97.0 6.001761 6 6 98.0 6.001761 6 6 99.0 6.001761 10 10 100.0 6.001761 7 7 101.0 0 7 7 102.0 0 14 14 103.0 0 2 2 104.0 0 7 7 105.0 0 14 14 106.0 0 4 4 107.0 0 13 13 108.0 0 6 6 109.0 0 11 11 110.0 0 6 6 111.0 0 11 11 112.0 0 13 13 113.0 0 7 7 114.0 0 8 8 115.0 0 8 8 116.0 0 4 4 117.0 0 4 4 118.0 0 5 5 119.0 0 9 9 120.0 0 8 8 121.0 0 8 8 122.0 0 4 4 124.0 0 3 3 125.0 0 3 3 126.0 0 7 7 127.0 0 3 3 128.0 0 6 6 129.0 0 9 9 130.0 0 5 5 131.0 0 3 3 132.0 0 1 1 133.0 0 2 2 134.0 0 3 3 135.0 0 2 2 136.0 0 3 3 137.0 0 4 4 138.0 0 3 3 139.0 0 1 1 140.0 0 2 2 141.0 0 5 5 142.0 0 2 2 143.0 0 4 4 144.0 0 4 4 145.0 0 3 3 146.0 0 4 4 147.0 0 3 3 148.0 0 4 4 149.0 0 3 3 150.0 0 3 3 151.0 0 3 3 152.0 0 5 5 153.0 0 4 4 154.0 0 2 2 155.0 0 1 1 156.0 0 4 4 157.0 0 3 3 158.0 0 3 3 159.0 0 2 2 160.0 0 2 2 161.0 0 2 2 165.0 0 3 3 166.0 0 1 1 167.0 0 6 6 169.0 0 3 3 170.0 0 2 2 171.0 0 2 2 172.0 0 4 4 173.0 0 3 3 174.0 0 3 3 175.0 0 1 1 176.0 0 3 3 177.0 0 2 2 178.0 0 1 1 179.0 0 4 4 180.0 0 2 2 181.0 0 4 4 182.0 0 1 1 184.0 0 1 1 185.0 0 2 2 186.0 0 3 3 187.0 0 4 4 189.0 0 3 3 191.0 0 2 2 192.0 0 3 3 194.0 0 4 4 195.0 0 1 1 196.0 0 4 4 197.0 0 1 1 198.0 0 1 1 199.0 0 1 1 200.0 0 1 1 202.0 0 2 2 203.0 0 1 1 204.0 0 2 2 206.0 0 1 1 207.0 0 1 1 211.0 0 5 5 214.0 0 2 2 215.0 0 2 2 220.0 0 1 1 221.0 0 1 1 227.0 0 2 2 228.0 0 1 1 229.0 0 1 1 230.0 0 1 1 232.0 0 1 1 233.0 0 1 1 235.0 0 1 1 238.0 0 1 1 240.0 0 1 1 242.0 0 3 3 243.0 0 1 1 246.0 0 1 1 247.0 0 1 1 253.0 0 1 1 254.0 0 2 2 255.0 0 2 2 256.0 0 1 1 263.0 0 1 1 265.0 0 1 1 266.0 0 1 1 270.0 0 1 1 271.0 0 2 2 272.0 0 1 1 276.0 0 1 1 278.0 0 1 1 280.0 0 1 1 281.0 0 1 1 282.0 0 1 1 283.0 0 1 1 284.0 0 1 1 285.0 0 1 1 287.0 0 1 1 292.0 0 2 2 294.0 0 1 1 296.0 0 1 1 298.0 0 1 1 305.0 0 1 1 307.0 0 1 1 312.0 0 1 1 316.0 0 1 1 318.0 0 1 1 319.0 0 1 1 324.0 0 1 1 336.0 0 1 1 337.0 0 1 1 346.0 0 1 1 348.0 0 1 1 356.0 0 1 1 364.0 0 1 1 370.0 0 1 1 373.0 0 1 1 374.0 0 1 1 375.0 0 1 1 376.0 0 1 1 380.0 0 1 1 384.0 0 1 1 386.0 0 1 1 387.0 0 1 1 389.0 0 1 1 414.0 0 1 1 420.0 0 1 1 423.0 0 1 1 426.0 0 1 1 428.0 0 1 1 447.0 0 1 1 449.0 0 1 1 457.0 0 2 2 466.0 0 1 1 471.0 0 1 1 472.0 0 1 1 475.0 0 1 1 478.0 0 1 1 492.0 0 2 2 495.0 0 1 1 501.0 0 1 1 505.0 0 1 1 509.0 0 2 2 512.0 0 1 1 527.0 0 1 1 569.0 0 1 1 578.0 0 1 1 603.0 0 1 1 622.0 0 1 1 635.0 0 1 1 1202.0 0 1 1 1475.0 0 1 1