## htsjdk.samtools.metrics.StringHeader # MarkDuplicates INPUT=[/project/berglandlab/DEST/dest_mapped/DESTv1/UA_Kie_Kyi_1_2015-08-10/UA_Kie_Kyi_1_2015-08-10.sorted_merged.bam] OUTPUT=/project/berglandlab/DEST/dest_mapped/DESTv1/UA_Kie_Kyi_1_2015-08-10/UA_Kie_Kyi_1_2015-08-10.dedup.bam METRICS_FILE=/project/berglandlab/DEST/dest_mapped/DESTv1/UA_Kie_Kyi_1_2015-08-10/UA_Kie_Kyi_1_2015-08-10.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 17:37:37 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 40916292 9863059 0 0 11325090 797856 0 0.213065 57629306 ## HISTOGRAM java.lang.Double BIN VALUE all_sets non_optical_sets 1.0 1 8264065 8264065 2.0 1.842698 474297 474297 3.0 2.552838 35707 35707 4.0 3.151272 5027 5027 5.0 3.65557 1882 1882 6.0 4.080542 1179 1179 7.0 4.438665 874 874 8.0 4.740454 594 594 9.0 4.994771 446 446 10.0 5.209084 372 372 11.0 5.389685 288 288 12.0 5.541877 220 220 13.0 5.670129 214 214 14.0 5.778206 176 176 15.0 5.869283 155 155 16.0 5.946033 167 167 17.0 6.010711 155 155 18.0 6.065214 127 127 19.0 6.111144 118 118 20.0 6.149849 117 117 21.0 6.182466 114 114 22.0 6.209952 107 107 23.0 6.233114 92 92 24.0 6.252633 84 84 25.0 6.269082 94 94 26.0 6.282943 88 88 27.0 6.294623 80 80 28.0 6.304467 71 71 29.0 6.312762 66 66 30.0 6.319752 67 67 31.0 6.325643 62 62 32.0 6.330607 57 57 33.0 6.33479 61 61 34.0 6.338315 46 46 35.0 6.341286 48 48 36.0 6.343789 48 48 37.0 6.345898 38 38 38.0 6.347676 45 45 39.0 6.349174 38 38 40.0 6.350437 35 35 41.0 6.3515 35 35 42.0 6.352397 37 37 43.0 6.353152 24 24 44.0 6.353789 25 25 45.0 6.354326 32 32 46.0 6.354778 20 20 47.0 6.355159 29 29 48.0 6.35548 16 16 49.0 6.35575 14 14 50.0 6.355978 21 21 51.0 6.35617 14 14 52.0 6.356332 29 29 53.0 6.356469 21 21 54.0 6.356584 13 13 55.0 6.356681 15 15 56.0 6.356762 20 20 57.0 6.356831 14 14 58.0 6.356889 14 14 59.0 6.356938 15 15 60.0 6.356979 15 15 61.0 6.357014 14 14 62.0 6.357043 15 15 63.0 6.357068 14 14 64.0 6.357088 11 11 65.0 6.357106 10 10 66.0 6.357121 11 11 67.0 6.357133 7 7 68.0 6.357144 18 18 69.0 6.357152 17 17 70.0 6.35716 14 14 71.0 6.357166 10 10 72.0 6.357171 17 17 73.0 6.357176 12 12 74.0 6.35718 14 14 75.0 6.357183 13 13 76.0 6.357185 16 16 77.0 6.357188 9 9 78.0 6.35719 12 12 79.0 6.357191 8 8 80.0 6.357193 7 7 81.0 6.357194 7 7 82.0 6.357195 19 19 83.0 6.357195 10 10 84.0 6.357196 11 11 85.0 6.357197 9 9 86.0 6.357197 13 13 87.0 6.357198 9 9 88.0 6.357198 11 11 89.0 6.357198 12 12 90.0 6.357198 10 10 91.0 6.357199 5 5 92.0 6.357199 3 3 93.0 6.357199 9 9 94.0 6.357199 10 10 95.0 6.357199 2 2 96.0 6.357199 8 8 97.0 6.357199 10 10 98.0 6.357199 5 5 99.0 6.357199 4 4 100.0 6.357199 8 8 101.0 0 12 12 102.0 0 10 10 103.0 0 9 9 104.0 0 6 6 105.0 0 4 4 106.0 0 8 8 107.0 0 7 7 108.0 0 4 4 109.0 0 5 5 110.0 0 5 5 111.0 0 2 2 112.0 0 6 6 113.0 0 6 6 114.0 0 5 5 115.0 0 3 3 116.0 0 3 3 117.0 0 1 1 119.0 0 5 5 120.0 0 4 4 121.0 0 4 4 122.0 0 4 4 123.0 0 3 3 124.0 0 6 6 125.0 0 6 6 126.0 0 2 2 127.0 0 5 5 128.0 0 2 2 129.0 0 4 4 130.0 0 3 3 131.0 0 5 5 132.0 0 6 6 133.0 0 3 3 134.0 0 1 1 135.0 0 3 3 136.0 0 5 5 137.0 0 1 1 138.0 0 2 2 139.0 0 1 1 140.0 0 2 2 142.0 0 1 1 143.0 0 6 6 144.0 0 4 4 145.0 0 2 2 146.0 0 2 2 147.0 0 3 3 148.0 0 1 1 149.0 0 4 4 150.0 0 6 6 151.0 0 2 2 152.0 0 1 1 153.0 0 2 2 154.0 0 3 3 155.0 0 3 3 156.0 0 1 1 157.0 0 3 3 158.0 0 1 1 159.0 0 1 1 160.0 0 2 2 161.0 0 1 1 162.0 0 4 4 163.0 0 2 2 164.0 0 2 2 165.0 0 5 5 166.0 0 4 4 167.0 0 2 2 168.0 0 2 2 169.0 0 3 3 170.0 0 1 1 172.0 0 2 2 174.0 0 1 1 175.0 0 3 3 176.0 0 1 1 178.0 0 5 5 181.0 0 2 2 182.0 0 1 1 183.0 0 2 2 184.0 0 2 2 186.0 0 1 1 188.0 0 4 4 191.0 0 2 2 192.0 0 1 1 193.0 0 1 1 195.0 0 2 2 196.0 0 2 2 197.0 0 1 1 198.0 0 3 3 199.0 0 1 1 200.0 0 1 1 201.0 0 2 2 202.0 0 1 1 204.0 0 1 1 207.0 0 1 1 213.0 0 1 1 214.0 0 1 1 215.0 0 1 1 217.0 0 1 1 221.0 0 1 1 222.0 0 1 1 225.0 0 2 2 226.0 0 2 2 227.0 0 1 1 228.0 0 1 1 229.0 0 2 2 230.0 0 1 1 239.0 0 3 3 241.0 0 1 1 242.0 0 1 1 243.0 0 1 1 244.0 0 2 2 245.0 0 3 3 247.0 0 2 2 249.0 0 2 2 254.0 0 1 1 256.0 0 1 1 257.0 0 1 1 259.0 0 1 1 261.0 0 1 1 266.0 0 1 1 267.0 0 2 2 270.0 0 1 1 273.0 0 1 1 275.0 0 1 1 277.0 0 1 1 282.0 0 2 2 284.0 0 1 1 285.0 0 1 1 286.0 0 1 1 289.0 0 1 1 290.0 0 1 1 291.0 0 1 1 293.0 0 2 2 294.0 0 1 1 296.0 0 1 1 298.0 0 1 1 300.0 0 1 1 303.0 0 1 1 304.0 0 1 1 305.0 0 1 1 307.0 0 1 1 310.0 0 1 1 315.0 0 2 2 316.0 0 1 1 319.0 0 1 1 326.0 0 1 1 329.0 0 1 1 332.0 0 1 1 334.0 0 1 1 336.0 0 1 1 343.0 0 2 2 350.0 0 1 1 353.0 0 1 1 356.0 0 1 1 357.0 0 1 1 358.0 0 1 1 362.0 0 1 1 364.0 0 1 1 367.0 0 1 1 373.0 0 1 1 374.0 0 1 1 378.0 0 2 2 382.0 0 1 1 383.0 0 1 1 384.0 0 1 1 388.0 0 1 1 389.0 0 1 1 390.0 0 1 1 394.0 0 1 1 400.0 0 1 1 407.0 0 1 1 411.0 0 1 1 422.0 0 1 1 426.0 0 1 1 428.0 0 1 1 457.0 0 1 1 470.0 0 1 1 483.0 0 1 1 499.0 0 1 1 505.0 0 1 1 507.0 0 1 1 517.0 0 1 1 526.0 0 1 1 558.0 0 2 2 565.0 0 1 1 575.0 0 1 1 581.0 0 1 1 675.0 0 1 1 691.0 0 1 1 734.0 0 1 1 743.0 0 1 1 744.0 0 1 1 800.0 0 1 1 833.0 0 1 1 842.0 0 1 1 850.0 0 1 1 918.0 0 1 1 1062.0 0 1 1 1085.0 0 1 1 1162.0 0 1 1 1209.0 0 1 1 1894.0 0 1 1 4302.0 0 1 1