## htsjdk.samtools.metrics.StringHeader # MarkDuplicates INPUT=[/project/berglandlab/DEST/dest_mapped/DESTv1/AT_Kar_See_1_2016-08-01/AT_Kar_See_1_2016-08-01.sorted_merged.bam] OUTPUT=/project/berglandlab/DEST/dest_mapped/DESTv1/AT_Kar_See_1_2016-08-01/AT_Kar_See_1_2016-08-01.dedup.bam METRICS_FILE=/project/berglandlab/DEST/dest_mapped/DESTv1/AT_Kar_See_1_2016-08-01/AT_Kar_See_1_2016-08-01.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 09:09:42 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 35301497 12438060 0 0 8907835 1063968 0 0.183387 68494072 ## HISTOGRAM java.lang.Double BIN VALUE all_sets non_optical_sets 1.0 1 10302625 10302625 2.0 1.83394 687006 687006 3.0 2.529397 53459 53459 4.0 3.109367 6460 6460 5.0 3.593027 2101 2101 6.0 3.996371 1277 1277 7.0 4.332735 863 863 8.0 4.613243 588 588 9.0 4.84717 394 394 10.0 5.042252 358 358 11.0 5.204938 272 272 12.0 5.340608 220 220 13.0 5.45375 163 163 14.0 5.548103 215 215 15.0 5.626787 174 174 16.0 5.692406 123 123 17.0 5.747128 134 134 18.0 5.792763 110 110 19.0 5.830819 116 116 20.0 5.862556 104 104 21.0 5.889023 101 101 22.0 5.911095 89 89 23.0 5.929501 93 93 24.0 5.944851 74 74 25.0 5.957652 84 84 26.0 5.968327 71 71 27.0 5.97723 77 77 28.0 5.984654 70 70 29.0 5.990845 79 79 30.0 5.996008 74 74 31.0 6.000314 79 79 32.0 6.003905 60 60 33.0 6.006899 61 61 34.0 6.009397 57 57 35.0 6.011479 35 35 36.0 6.013216 59 59 37.0 6.014664 46 46 38.0 6.015872 39 39 39.0 6.016879 33 33 40.0 6.017719 32 32 41.0 6.01842 49 49 42.0 6.019004 36 36 43.0 6.019491 37 37 44.0 6.019897 30 30 45.0 6.020236 40 40 46.0 6.020519 26 26 47.0 6.020754 29 29 48.0 6.020951 23 23 49.0 6.021115 23 23 50.0 6.021251 22 22 51.0 6.021365 27 27 52.0 6.02146 24 24 53.0 6.02154 22 22 54.0 6.021606 17 17 55.0 6.021661 19 19 56.0 6.021707 24 24 57.0 6.021745 14 14 58.0 6.021777 12 12 59.0 6.021804 21 21 60.0 6.021826 15 15 61.0 6.021844 13 13 62.0 6.02186 14 14 63.0 6.021873 13 13 64.0 6.021884 15 15 65.0 6.021893 11 11 66.0 6.0219 17 17 67.0 6.021906 11 11 68.0 6.021911 11 11 69.0 6.021916 16 16 70.0 6.021919 12 12 71.0 6.021922 8 8 72.0 6.021925 13 13 73.0 6.021927 8 8 74.0 6.021929 9 9 75.0 6.02193 15 15 76.0 6.021931 7 7 77.0 6.021932 5 5 78.0 6.021933 11 11 79.0 6.021934 10 10 80.0 6.021935 11 11 81.0 6.021935 8 8 82.0 6.021936 13 13 83.0 6.021936 8 8 84.0 6.021936 8 8 85.0 6.021936 8 8 86.0 6.021937 6 6 87.0 6.021937 8 8 88.0 6.021937 9 9 89.0 6.021937 13 13 90.0 6.021937 7 7 91.0 6.021937 10 10 92.0 6.021937 12 12 93.0 6.021937 7 7 94.0 6.021937 5 5 95.0 6.021937 12 12 96.0 6.021937 10 10 97.0 6.021937 10 10 98.0 6.021937 8 8 99.0 6.021937 8 8 100.0 6.021937 5 5 101.0 0 7 7 102.0 0 7 7 103.0 0 8 8 104.0 0 4 4 105.0 0 9 9 106.0 0 9 9 107.0 0 6 6 108.0 0 10 10 109.0 0 6 6 110.0 0 6 6 111.0 0 5 5 112.0 0 6 6 113.0 0 7 7 114.0 0 8 8 115.0 0 6 6 116.0 0 8 8 117.0 0 12 12 118.0 0 6 6 119.0 0 7 7 120.0 0 7 7 121.0 0 7 7 122.0 0 6 6 123.0 0 9 9 124.0 0 4 4 125.0 0 3 3 126.0 0 11 11 127.0 0 7 7 128.0 0 6 6 129.0 0 2 2 130.0 0 7 7 131.0 0 3 3 132.0 0 9 9 133.0 0 4 4 134.0 0 6 6 135.0 0 2 2 136.0 0 2 2 137.0 0 9 9 138.0 0 4 4 139.0 0 2 2 140.0 0 1 1 141.0 0 2 2 142.0 0 3 3 143.0 0 5 5 144.0 0 4 4 145.0 0 2 2 146.0 0 2 2 147.0 0 4 4 148.0 0 6 6 149.0 0 2 2 150.0 0 2 2 151.0 0 1 1 152.0 0 5 5 153.0 0 4 4 155.0 0 1 1 156.0 0 4 4 157.0 0 4 4 158.0 0 3 3 159.0 0 2 2 160.0 0 7 7 161.0 0 2 2 162.0 0 2 2 164.0 0 2 2 165.0 0 4 4 166.0 0 3 3 167.0 0 2 2 168.0 0 4 4 169.0 0 1 1 171.0 0 3 3 173.0 0 6 6 174.0 0 2 2 175.0 0 1 1 176.0 0 3 3 177.0 0 2 2 178.0 0 2 2 180.0 0 3 3 182.0 0 2 2 183.0 0 1 1 184.0 0 4 4 185.0 0 2 2 186.0 0 1 1 188.0 0 3 3 189.0 0 2 2 190.0 0 1 1 191.0 0 2 2 192.0 0 2 2 193.0 0 2 2 194.0 0 2 2 195.0 0 2 2 196.0 0 1 1 197.0 0 2 2 198.0 0 3 3 202.0 0 2 2 203.0 0 4 4 204.0 0 2 2 205.0 0 1 1 206.0 0 2 2 207.0 0 1 1 210.0 0 2 2 212.0 0 1 1 213.0 0 1 1 214.0 0 1 1 215.0 0 1 1 216.0 0 1 1 217.0 0 1 1 224.0 0 3 3 225.0 0 1 1 226.0 0 2 2 227.0 0 2 2 229.0 0 1 1 233.0 0 2 2 234.0 0 2 2 235.0 0 1 1 238.0 0 1 1 239.0 0 1 1 240.0 0 2 2 241.0 0 1 1 242.0 0 1 1 243.0 0 4 4 244.0 0 1 1 247.0 0 1 1 254.0 0 3 3 260.0 0 1 1 266.0 0 1 1 268.0 0 1 1 269.0 0 1 1 270.0 0 1 1 271.0 0 2 2 272.0 0 1 1 277.0 0 2 2 278.0 0 1 1 280.0 0 1 1 282.0 0 3 3 285.0 0 1 1 296.0 0 2 2 299.0 0 1 1 300.0 0 1 1 304.0 0 2 2 307.0 0 1 1 308.0 0 1 1 309.0 0 1 1 315.0 0 1 1 320.0 0 1 1 323.0 0 1 1 331.0 0 1 1 336.0 0 1 1 337.0 0 1 1 344.0 0 1 1 349.0 0 1 1 351.0 0 1 1 355.0 0 1 1 369.0 0 1 1 370.0 0 1 1 371.0 0 1 1 372.0 0 1 1 375.0 0 1 1 376.0 0 1 1 379.0 0 1 1 380.0 0 1 1 381.0 0 1 1 389.0 0 1 1 392.0 0 1 1 393.0 0 1 1 397.0 0 1 1 400.0 0 1 1 401.0 0 1 1 402.0 0 1 1 416.0 0 1 1 418.0 0 1 1 420.0 0 1 1 426.0 0 1 1 437.0 0 1 1 438.0 0 1 1 440.0 0 1 1 445.0 0 1 1 454.0 0 1 1 459.0 0 1 1 463.0 0 1 1 471.0 0 1 1 474.0 0 1 1 477.0 0 1 1 481.0 0 1 1 510.0 0 1 1 517.0 0 2 2 520.0 0 1 1 522.0 0 1 1 526.0 0 1 1 529.0 0 1 1 539.0 0 1 1 551.0 0 1 1 553.0 0 1 1 560.0 0 1 1 562.0 0 1 1 577.0 0 1 1 620.0 0 1 1 653.0 0 1 1 739.0 0 1 1 782.0 0 1 1 788.0 0 1 1 968.0 0 1 1 1022.0 0 1 1 1058.0 0 1 1 1107.0 0 1 1 1841.0 0 1 1 3092.0 0 1 1