## htsjdk.samtools.metrics.StringHeader # MarkDuplicates MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=999 INPUT=[/ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/ghe/2023_s2s_run/results_no_replicates/star/GRCh38.p13-D19_adherent_DMSO_1.samtools-coordinate-unsieved.bam] OUTPUT=/ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/ghe/2023_s2s_run/results_no_replicates/star/GRCh38.p13-D19_adherent_DMSO_1.samtools-coordinate-dupmarked.bam METRICS_FILE=/ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/ghe/2023_s2s_run/results_no_replicates/qc/markdup/GRCh38.p13-D19_adherent_DMSO_1.samtools-coordinate.metrics.txt TMP_DIR=[/scratch/slrinzema/tmp] MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 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_QUALITY_SUM_STRATEGY=false USE_END_IN_UNPAIRED_READS=false USE_UNPAIRED_CLIPPED_END=false UNPAIRED_END_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 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 VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false USE_JDK_DEFLATER=false USE_JDK_INFLATER=false ## htsjdk.samtools.metrics.StringHeader # Started on: Fri Oct 06 02:55:38 CEST 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 Unknown Library 638 21398983 58350996 0 546 9526391 0 0.445186 16189974 ## HISTOGRAM java.lang.Double BIN CoverageMult all_sets non_optical_sets 1.0 1 7752201 7752201 2.0 1.26667 2709841 2709841 3.0 1.337783 850849 850849 4.0 1.356747 258098 258098 5.0 1.361804 90278 90278 6.0 1.363152 42885 42885 7.0 1.363512 26314 26314 8.0 1.363608 19107 19107 9.0 1.363633 14556 14556 10.0 1.36364 11771 11771 11.0 1.363642 9331 9331 12.0 1.363643 7891 7891 13.0 1.363643 6669 6669 14.0 1.363643 5734 5734 15.0 1.363643 5051 5051 16.0 1.363643 4395 4395 17.0 1.363643 3893 3893 18.0 1.363643 3561 3561 19.0 1.363643 3089 3089 20.0 1.363643 2775 2775 21.0 1.363643 2450 2450 22.0 1.363643 2356 2356 23.0 1.363643 2078 2078 24.0 1.363643 1785 1785 25.0 1.363643 1725 1725 26.0 1.363643 1531 1531 27.0 1.363643 1464 1464 28.0 1.363643 1423 1423 29.0 1.363643 1263 1263 30.0 1.363643 1175 1175 31.0 1.363643 1072 1072 32.0 1.363643 1055 1055 33.0 1.363643 1024 1024 34.0 1.363643 901 901 35.0 1.363643 819 819 36.0 1.363643 778 778 37.0 1.363643 763 763 38.0 1.363643 719 719 39.0 1.363643 650 650 40.0 1.363643 689 689 41.0 1.363643 611 611 42.0 1.363643 590 590 43.0 1.363643 605 605 44.0 1.363643 568 568 45.0 1.363643 490 490 46.0 1.363643 456 456 47.0 1.363643 431 431 48.0 1.363643 455 455 49.0 1.363643 394 394 50.0 1.363643 347 347 51.0 1.363643 372 372 52.0 1.363643 352 352 53.0 1.363643 361 361 54.0 1.363643 292 292 55.0 1.363643 340 340 56.0 1.363643 273 273 57.0 1.363643 273 273 58.0 1.363643 300 300 59.0 1.363643 275 275 60.0 1.363643 222 222 61.0 1.363643 283 283 62.0 1.363643 241 241 63.0 1.363643 233 233 64.0 1.363643 242 242 65.0 1.363643 190 190 66.0 1.363643 215 215 67.0 1.363643 201 201 68.0 1.363643 187 187 69.0 1.363643 168 168 70.0 1.363643 188 188 71.0 1.363643 158 158 72.0 1.363643 163 163 73.0 1.363643 203 203 74.0 1.363643 154 154 75.0 1.363643 153 153 76.0 1.363643 139 139 77.0 1.363643 161 161 78.0 1.363643 131 131 79.0 1.363643 137 137 80.0 1.363643 145 145 81.0 1.363643 140 140 82.0 1.363643 118 118 83.0 1.363643 110 110 84.0 1.363643 132 132 85.0 1.363643 127 127 86.0 1.363643 107 107 87.0 1.363643 118 118 88.0 1.363643 99 99 89.0 1.363643 97 97 90.0 1.363643 114 114 91.0 1.363643 100 100 92.0 1.363643 87 87 93.0 1.363643 97 97 94.0 1.363643 88 88 95.0 1.363643 88 88 96.0 1.363643 78 78 97.0 1.363643 87 87 98.0 1.363643 85 85 99.0 1.363643 81 81 100.0 1.363643 77 77 101.0 0 76 76 102.0 0 56 56 103.0 0 78 78 104.0 0 80 80 105.0 0 65 65 106.0 0 71 71 107.0 0 61 61 108.0 0 50 50 109.0 0 62 62 110.0 0 56 56 111.0 0 80 80 112.0 0 56 56 113.0 0 54 54 114.0 0 54 54 115.0 0 59 59 116.0 0 50 50 117.0 0 55 55 118.0 0 62 62 119.0 0 53 53 120.0 0 39 39 121.0 0 45 45 122.0 0 43 43 123.0 0 38 38 124.0 0 35 35 125.0 0 44 44 126.0 0 61 61 127.0 0 40 40 128.0 0 46 46 129.0 0 48 48 130.0 0 42 42 131.0 0 34 34 132.0 0 41 41 133.0 0 41 41 134.0 0 28 28 135.0 0 33 33 136.0 0 51 51 137.0 0 33 33 138.0 0 43 43 139.0 0 31 31 140.0 0 28 28 141.0 0 36 36 142.0 0 27 27 143.0 0 30 30 144.0 0 34 34 145.0 0 23 23 146.0 0 32 32 147.0 0 29 29 148.0 0 27 27 149.0 0 28 28 150.0 0 25 25 151.0 0 36 36 152.0 0 28 28 153.0 0 20 20 154.0 0 25 25 155.0 0 24 24 156.0 0 18 18 157.0 0 25 25 158.0 0 25 25 159.0 0 27 27 160.0 0 16 16 161.0 0 22 22 162.0 0 30 30 163.0 0 23 23 164.0 0 21 21 165.0 0 14 14 166.0 0 26 26 167.0 0 16 16 168.0 0 22 22 169.0 0 24 24 170.0 0 30 30 171.0 0 21 21 172.0 0 19 19 173.0 0 20 20 174.0 0 23 23 175.0 0 23 23 176.0 0 23 23 177.0 0 19 19 178.0 0 22 22 179.0 0 15 15 180.0 0 16 16 181.0 0 19 19 182.0 0 22 22 183.0 0 19 19 184.0 0 10 10 185.0 0 11 11 186.0 0 19 19 187.0 0 15 15 188.0 0 22 22 189.0 0 15 15 190.0 0 16 16 191.0 0 12 12 192.0 0 17 17 193.0 0 22 22 194.0 0 21 21 195.0 0 19 19 196.0 0 24 24 197.0 0 5 5 198.0 0 23 23 199.0 0 12 12 200.0 0 13 13 201.0 0 8 8 202.0 0 12 12 203.0 0 16 16 204.0 0 14 14 205.0 0 15 15 206.0 0 15 15 207.0 0 10 10 208.0 0 15 15 209.0 0 15 15 210.0 0 5 5 211.0 0 13 13 212.0 0 9 9 213.0 0 11 11 214.0 0 7 7 215.0 0 12 12 216.0 0 12 12 217.0 0 13 13 218.0 0 5 5 219.0 0 11 11 220.0 0 6 6 221.0 0 8 8 222.0 0 8 8 223.0 0 6 6 224.0 0 9 9 225.0 0 10 10 226.0 0 10 10 227.0 0 11 11 228.0 0 15 15 229.0 0 10 10 230.0 0 13 13 231.0 0 11 11 232.0 0 6 6 233.0 0 10 10 234.0 0 10 10 235.0 0 11 11 236.0 0 5 5 237.0 0 3 3 238.0 0 11 11 239.0 0 11 11 240.0 0 3 3 241.0 0 8 8 242.0 0 15 15 243.0 0 9 9 244.0 0 11 11 245.0 0 5 5 246.0 0 8 8 247.0 0 7 7 248.0 0 10 10 249.0 0 7 7 250.0 0 10 10 251.0 0 9 9 252.0 0 6 6 253.0 0 8 8 254.0 0 8 8 255.0 0 6 6 256.0 0 6 6 257.0 0 6 6 258.0 0 6 6 259.0 0 5 5 260.0 0 6 6 261.0 0 9 9 262.0 0 7 7 263.0 0 8 8 264.0 0 5 5 265.0 0 6 6 266.0 0 6 6 267.0 0 10 10 268.0 0 8 8 269.0 0 12 12 270.0 0 6 6 271.0 0 11 11 272.0 0 12 12 273.0 0 9 9 274.0 0 7 7 275.0 0 12 12 276.0 0 4 4 277.0 0 3 3 278.0 0 1 1 279.0 0 11 11 280.0 0 7 7 281.0 0 5 5 282.0 0 3 3 283.0 0 3 3 284.0 0 12 12 285.0 0 6 6 286.0 0 4 4 287.0 0 7 7 288.0 0 2 2 289.0 0 4 4 290.0 0 9 9 291.0 0 4 4 292.0 0 4 4 293.0 0 3 3 294.0 0 5 5 295.0 0 6 6 296.0 0 5 5 297.0 0 4 4 298.0 0 3 3 299.0 0 7 7 300.0 0 5 5 301.0 0 4 4 302.0 0 6 6 303.0 0 4 4 304.0 0 9 9 305.0 0 4 4 306.0 0 6 6 307.0 0 4 4 308.0 0 3 3 309.0 0 5 5 310.0 0 8 8 311.0 0 3 3 312.0 0 6 6 313.0 0 4 4 314.0 0 8 8 315.0 0 5 5 316.0 0 1 1 317.0 0 2 2 318.0 0 2 2 319.0 0 7 7 320.0 0 2 2 321.0 0 5 5 322.0 0 4 4 323.0 0 2 2 324.0 0 8 8 325.0 0 1 1 326.0 0 4 4 327.0 0 6 6 328.0 0 1 1 329.0 0 4 4 330.0 0 3 3 331.0 0 4 4 332.0 0 3 3 333.0 0 6 6 334.0 0 6 6 335.0 0 4 4 336.0 0 6 6 337.0 0 4 4 338.0 0 3 3 339.0 0 2 2 340.0 0 2 2 341.0 0 4 4 342.0 0 2 2 343.0 0 4 4 344.0 0 3 3 345.0 0 3 3 346.0 0 5 5 347.0 0 3 3 348.0 0 2 2 349.0 0 1 1 350.0 0 3 3 351.0 0 4 4 352.0 0 1 1 353.0 0 2 2 354.0 0 3 3 355.0 0 7 7 357.0 0 1 1 358.0 0 6 6 359.0 0 3 3 360.0 0 3 3 361.0 0 2 2 362.0 0 4 4 363.0 0 4 4 364.0 0 4 4 366.0 0 1 1 367.0 0 2 2 369.0 0 3 3 370.0 0 6 6 372.0 0 4 4 373.0 0 4 4 374.0 0 1 1 375.0 0 4 4 376.0 0 1 1 377.0 0 3 3 378.0 0 1 1 379.0 0 2 2 380.0 0 2 2 381.0 0 2 2 382.0 0 2 2 383.0 0 1 1 384.0 0 5 5 385.0 0 2 2 386.0 0 2 2 387.0 0 1 1 388.0 0 5 5 389.0 0 2 2 390.0 0 3 3 391.0 0 1 1 392.0 0 2 2 393.0 0 2 2 394.0 0 3 3 395.0 0 3 3 396.0 0 5 5 397.0 0 1 1 398.0 0 2 2 399.0 0 2 2 400.0 0 1 1 401.0 0 1 1 404.0 0 2 2 405.0 0 4 4 406.0 0 2 2 407.0 0 2 2 408.0 0 6 6 410.0 0 3 3 411.0 0 1 1 412.0 0 3 3 414.0 0 2 2 415.0 0 4 4 416.0 0 5 5 417.0 0 2 2 418.0 0 1 1 419.0 0 6 6 420.0 0 4 4 421.0 0 2 2 422.0 0 2 2 423.0 0 2 2 424.0 0 3 3 426.0 0 2 2 427.0 0 2 2 428.0 0 1 1 429.0 0 5 5 430.0 0 4 4 432.0 0 2 2 435.0 0 1 1 437.0 0 1 1 438.0 0 1 1 439.0 0 2 2 440.0 0 2 2 441.0 0 3 3 443.0 0 3 3 445.0 0 4 4 446.0 0 2 2 447.0 0 1 1 448.0 0 1 1 449.0 0 3 3 450.0 0 2 2 451.0 0 1 1 452.0 0 1 1 453.0 0 1 1 454.0 0 2 2 455.0 0 1 1 456.0 0 1 1 457.0 0 1 1 459.0 0 2 2 460.0 0 1 1 461.0 0 1 1 462.0 0 1 1 463.0 0 4 4 464.0 0 1 1 466.0 0 1 1 469.0 0 1 1 470.0 0 2 2 471.0 0 1 1 472.0 0 1 1 473.0 0 2 2 475.0 0 3 3 477.0 0 1 1 478.0 0 1 1 480.0 0 2 2 481.0 0 1 1 482.0 0 3 3 483.0 0 2 2 484.0 0 1 1 487.0 0 1 1 490.0 0 1 1 491.0 0 1 1 494.0 0 1 1 495.0 0 1 1 496.0 0 2 2 497.0 0 1 1 499.0 0 2 2 500.0 0 2 2 501.0 0 1 1 502.0 0 1 1 504.0 0 1 1 505.0 0 1 1 506.0 0 3 3 509.0 0 2 2 513.0 0 1 1 514.0 0 4 4 515.0 0 1 1 516.0 0 1 1 518.0 0 2 2 520.0 0 1 1 521.0 0 1 1 524.0 0 1 1 525.0 0 1 1 526.0 0 1 1 535.0 0 1 1 536.0 0 2 2 537.0 0 1 1 540.0 0 2 2 541.0 0 3 3 542.0 0 1 1 543.0 0 1 1 544.0 0 1 1 545.0 0 2 2 546.0 0 3 3 547.0 0 1 1 549.0 0 1 1 550.0 0 2 2 552.0 0 1 1 556.0 0 1 1 557.0 0 1 1 558.0 0 1 1 561.0 0 1 1 563.0 0 1 1 566.0 0 1 1 569.0 0 2 2 571.0 0 1 1 573.0 0 3 3 576.0 0 4 4 579.0 0 2 2 580.0 0 1 1 585.0 0 1 1 586.0 0 1 1 593.0 0 2 2 594.0 0 3 3 596.0 0 2 2 597.0 0 2 2 600.0 0 1 1 602.0 0 2 2 603.0 0 2 2 604.0 0 1 1 611.0 0 1 1 612.0 0 1 1 618.0 0 1 1 620.0 0 2 2 621.0 0 1 1 624.0 0 2 2 626.0 0 1 1 628.0 0 1 1 629.0 0 1 1 630.0 0 1 1 631.0 0 2 2 635.0 0 1 1 636.0 0 1 1 638.0 0 2 2 639.0 0 2 2 640.0 0 1 1 643.0 0 2 2 646.0 0 1 1 648.0 0 1 1 654.0 0 1 1 659.0 0 1 1 661.0 0 2 2 662.0 0 1 1 663.0 0 2 2 665.0 0 1 1 666.0 0 1 1 669.0 0 1 1 676.0 0 1 1 678.0 0 1 1 680.0 0 1 1 681.0 0 1 1 686.0 0 1 1 688.0 0 1 1 694.0 0 1 1 697.0 0 1 1 698.0 0 3 3 699.0 0 1 1 700.0 0 1 1 701.0 0 1 1 705.0 0 1 1 707.0 0 1 1 709.0 0 1 1 710.0 0 1 1 711.0 0 2 2 713.0 0 1 1 715.0 0 1 1 729.0 0 1 1 730.0 0 1 1 739.0 0 1 1 750.0 0 1 1 752.0 0 1 1 755.0 0 1 1 760.0 0 1 1 765.0 0 1 1 767.0 0 1 1 770.0 0 1 1 772.0 0 1 1 773.0 0 1 1 775.0 0 2 2 776.0 0 1 1 777.0 0 1 1 779.0 0 1 1 782.0 0 1 1 786.0 0 1 1 796.0 0 1 1 799.0 0 2 2 805.0 0 1 1 821.0 0 1 1 827.0 0 1 1 833.0 0 1 1 839.0 0 1 1 847.0 0 1 1 859.0 0 1 1 860.0 0 1 1 872.0 0 1 1 878.0 0 1 1 886.0 0 1 1 898.0 0 1 1 902.0 0 1 1 916.0 0 1 1 923.0 0 1 1 946.0 0 1 1 951.0 0 1 1 967.0 0 1 1 977.0 0 1 1 978.0 0 1 1 999.0 0 1 1 1018.0 0 1 1 1024.0 0 1 1 1026.0 0 1 1 1052.0 0 1 1 1053.0 0 1 1 1054.0 0 1 1 1080.0 0 1 1 1098.0 0 1 1 1106.0 0 1 1 1112.0 0 1 1 1115.0 0 1 1 1128.0 0 1 1 1132.0 0 1 1 1145.0 0 1 1 1151.0 0 1 1 1164.0 0 1 1 1174.0 0 1 1 1206.0 0 1 1 1212.0 0 1 1 1234.0 0 1 1 1236.0 0 1 1 1240.0 0 1 1 1270.0 0 1 1 1284.0 0 1 1 1300.0 0 1 1 1305.0 0 1 1 1306.0 0 1 1 1312.0 0 1 1 1320.0 0 1 1 1349.0 0 1 1 1393.0 0 1 1 1400.0 0 1 1 1429.0 0 1 1 1435.0 0 1 1 1438.0 0 1 1 1451.0 0 1 1 1481.0 0 1 1 1509.0 0 1 1 1523.0 0 1 1 1524.0 0 1 1 1571.0 0 2 2 1619.0 0 1 1 1714.0 0 1 1 1762.0 0 1 1 1885.0 0 1 1 1901.0 0 1 1 1958.0 0 1 1 1961.0 0 1 1 2048.0 0 1 1 2082.0 0 1 1 2167.0 0 1 1 2169.0 0 1 1 2472.0 0 1 1 2492.0 0 1 1 2552.0 0 1 1 2646.0 0 1 1 4204.0 0 1 1