## htsjdk.samtools.metrics.StringHeader # MarkDuplicates INPUT=[/project/berglandlab/DEST/dest_mapped/DESTv1/UA_Ode_Ode_1_2013-10-15/UA_Ode_Ode_1_2013-10-15.sorted_merged.bam] OUTPUT=/project/berglandlab/DEST/dest_mapped/DESTv1/UA_Ode_Ode_1_2013-10-15/UA_Ode_Ode_1_2013-10-15.dedup.bam METRICS_FILE=/project/berglandlab/DEST/dest_mapped/DESTv1/UA_Ode_Ode_1_2013-10-15/UA_Ode_Ode_1_2013-10-15.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 18:56:03 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 2037634 44053018 0 0 918893 12209931 0 0.281093 63984583 ## HISTOGRAM java.lang.Double BIN VALUE all_sets non_optical_sets 1.0 1 21876273 21876273 2.0 1.502332 6680908 6680908 3.0 1.754669 1764447 1764447 4.0 1.881426 416411 416411 5.0 1.9451 94156 94156 6.0 1.977086 22033 22033 7.0 1.993153 6295 6295 8.0 2.001224 2488 2488 9.0 2.005279 1314 1314 10.0 2.007315 909 909 11.0 2.008339 625 625 12.0 2.008852 453 453 13.0 2.009111 378 378 14.0 2.00924 323 323 15.0 2.009305 234 234 16.0 2.009338 192 192 17.0 2.009355 170 170 18.0 2.009363 146 146 19.0 2.009367 133 133 20.0 2.009369 124 124 21.0 2.00937 106 106 22.0 2.009371 93 93 23.0 2.009371 94 94 24.0 2.009371 71 71 25.0 2.009371 58 58 26.0 2.009371 65 65 27.0 2.009371 51 51 28.0 2.009371 72 72 29.0 2.009371 56 56 30.0 2.009371 66 66 31.0 2.009371 57 57 32.0 2.009371 30 30 33.0 2.009371 32 32 34.0 2.009371 32 32 35.0 2.009371 34 34 36.0 2.009371 46 46 37.0 2.009371 32 32 38.0 2.009371 24 24 39.0 2.009371 25 25 40.0 2.009371 21 21 41.0 2.009371 28 28 42.0 2.009371 18 18 43.0 2.009371 31 31 44.0 2.009371 22 22 45.0 2.009371 18 18 46.0 2.009371 20 20 47.0 2.009371 20 20 48.0 2.009371 16 16 49.0 2.009371 9 9 50.0 2.009371 19 19 51.0 2.009371 23 23 52.0 2.009371 10 10 53.0 2.009371 15 15 54.0 2.009371 7 7 55.0 2.009371 14 14 56.0 2.009371 12 12 57.0 2.009371 9 9 58.0 2.009371 12 12 59.0 2.009371 7 7 60.0 2.009371 12 12 61.0 2.009371 14 14 62.0 2.009371 12 12 63.0 2.009371 16 16 64.0 2.009371 16 16 65.0 2.009371 10 10 66.0 2.009371 10 10 67.0 2.009371 8 8 68.0 2.009371 10 10 69.0 2.009371 10 10 70.0 2.009371 6 6 71.0 2.009371 4 4 72.0 2.009371 9 9 73.0 2.009371 12 12 74.0 2.009371 4 4 75.0 2.009371 12 12 76.0 2.009371 11 11 77.0 2.009371 8 8 78.0 2.009371 5 5 79.0 2.009371 6 6 80.0 2.009371 9 9 81.0 2.009371 4 4 82.0 2.009371 2 2 83.0 2.009371 6 6 84.0 2.009371 3 3 85.0 2.009371 6 6 86.0 2.009371 5 5 87.0 2.009371 7 7 88.0 2.009371 6 6 89.0 2.009371 2 2 90.0 2.009371 7 7 91.0 2.009371 6 6 92.0 2.009371 4 4 93.0 2.009371 1 1 94.0 2.009371 5 5 95.0 2.009371 4 4 96.0 2.009371 3 3 97.0 2.009371 4 4 98.0 2.009371 5 5 99.0 2.009371 10 10 100.0 2.009371 4 4 101.0 0 3 3 102.0 0 6 6 103.0 0 5 5 104.0 0 4 4 105.0 0 7 7 106.0 0 5 5 107.0 0 1 1 108.0 0 6 6 109.0 0 2 2 110.0 0 1 1 111.0 0 2 2 112.0 0 5 5 113.0 0 5 5 114.0 0 5 5 115.0 0 3 3 116.0 0 3 3 117.0 0 4 4 118.0 0 6 6 119.0 0 2 2 120.0 0 1 1 121.0 0 2 2 123.0 0 2 2 124.0 0 3 3 125.0 0 2 2 126.0 0 3 3 127.0 0 2 2 128.0 0 4 4 129.0 0 3 3 130.0 0 1 1 131.0 0 4 4 132.0 0 1 1 133.0 0 4 4 134.0 0 3 3 136.0 0 4 4 137.0 0 2 2 138.0 0 1 1 139.0 0 3 3 140.0 0 1 1 141.0 0 1 1 142.0 0 2 2 143.0 0 3 3 146.0 0 2 2 147.0 0 2 2 148.0 0 2 2 149.0 0 3 3 150.0 0 1 1 151.0 0 2 2 153.0 0 1 1 154.0 0 1 1 155.0 0 2 2 156.0 0 2 2 157.0 0 1 1 158.0 0 1 1 159.0 0 2 2 160.0 0 1 1 162.0 0 1 1 163.0 0 1 1 165.0 0 1 1 166.0 0 1 1 167.0 0 3 3 168.0 0 2 2 169.0 0 1 1 171.0 0 2 2 172.0 0 2 2 174.0 0 1 1 175.0 0 2 2 176.0 0 1 1 177.0 0 2 2 178.0 0 3 3 179.0 0 2 2 180.0 0 2 2 183.0 0 2 2 185.0 0 1 1 186.0 0 1 1 187.0 0 1 1 188.0 0 1 1 189.0 0 6 6 190.0 0 1 1 192.0 0 1 1 193.0 0 1 1 194.0 0 1 1 195.0 0 3 3 197.0 0 1 1 203.0 0 4 4 204.0 0 3 3 205.0 0 1 1 206.0 0 1 1 207.0 0 1 1 209.0 0 1 1 211.0 0 1 1 212.0 0 2 2 213.0 0 1 1 214.0 0 2 2 215.0 0 2 2 220.0 0 1 1 221.0 0 1 1 222.0 0 2 2 223.0 0 2 2 226.0 0 3 3 229.0 0 1 1 230.0 0 2 2 231.0 0 1 1 232.0 0 1 1 234.0 0 1 1 236.0 0 1 1 237.0 0 1 1 239.0 0 1 1 240.0 0 1 1 242.0 0 1 1 245.0 0 2 2 247.0 0 1 1 253.0 0 2 2 256.0 0 1 1 258.0 0 1 1 260.0 0 2 2 262.0 0 1 1 263.0 0 1 1 264.0 0 1 1 266.0 0 3 3 268.0 0 1 1 270.0 0 2 2 271.0 0 1 1 272.0 0 1 1 276.0 0 1 1 280.0 0 1 1 283.0 0 2 2 285.0 0 1 1 288.0 0 1 1 290.0 0 1 1 294.0 0 2 2 295.0 0 1 1 307.0 0 1 1 313.0 0 1 1 315.0 0 2 2 320.0 0 1 1 322.0 0 1 1 323.0 0 4 4 334.0 0 1 1 342.0 0 1 1 346.0 0 1 1 348.0 0 1 1 350.0 0 1 1 354.0 0 1 1 359.0 0 1 1 367.0 0 1 1 368.0 0 1 1 370.0 0 1 1 374.0 0 1 1 379.0 0 1 1 381.0 0 2 2 382.0 0 1 1 388.0 0 1 1 391.0 0 1 1 392.0 0 1 1 394.0 0 1 1 396.0 0 1 1 398.0 0 3 3 404.0 0 1 1 406.0 0 1 1 407.0 0 1 1 410.0 0 1 1 420.0 0 1 1 422.0 0 1 1 438.0 0 1 1 457.0 0 1 1 459.0 0 1 1 470.0 0 1 1 474.0 0 1 1 477.0 0 1 1 483.0 0 1 1 499.0 0 1 1 505.0 0 1 1 507.0 0 1 1 532.0 0 1 1 535.0 0 1 1 587.0 0 1 1 601.0 0 1 1 606.0 0 1 1 608.0 0 1 1 624.0 0 1 1 649.0 0 2 2 661.0 0 1 1 670.0 0 1 1 671.0 0 1 1 690.0 0 1 1 700.0 0 1 1 720.0 0 1 1 740.0 0 1 1 774.0 0 1 1 775.0 0 1 1 784.0 0 1 1 788.0 0 1 1 829.0 0 1 1 836.0 0 1 1 1162.0 0 1 1 1428.0 0 1 1 1809.0 0 1 1 2048.0 0 1 1 2216.0 0 1 1 2386.0 0 1 1