## htsjdk.samtools.metrics.StringHeader # MarkDuplicates INPUT=[/project/berglandlab/DEST/dest_mapped/DESTv1/CH_Vau_Cha_1_2016-08-15/CH_Vau_Cha_1_2016-08-15.sorted_merged.bam] OUTPUT=/project/berglandlab/DEST/dest_mapped/DESTv1/CH_Vau_Cha_1_2016-08-15/CH_Vau_Cha_1_2016-08-15.dedup.bam METRICS_FILE=/project/berglandlab/DEST/dest_mapped/DESTv1/CH_Vau_Cha_1_2016-08-15/CH_Vau_Cha_1_2016-08-15.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 08:43:43 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 28947355 8327288 0 0 7272593 721994 0 0.191145 45204526 ## HISTOGRAM java.lang.Double BIN VALUE all_sets non_optical_sets 1.0 1 6884194 6884194 2.0 1.831758 410648 410648 3.0 2.52358 30494 30494 4.0 3.099008 4217 4217 5.0 3.577625 1558 1558 6.0 3.975719 1042 1042 7.0 4.306836 679 679 8.0 4.582246 597 597 9.0 4.81132 399 399 10.0 5.001855 309 309 11.0 5.160334 259 259 12.0 5.292149 219 219 13.0 5.401788 184 184 14.0 5.492981 170 170 15.0 5.568832 144 144 16.0 5.631921 137 137 17.0 5.684396 133 133 18.0 5.728043 123 123 19.0 5.764346 123 123 20.0 5.794542 94 94 21.0 5.819657 103 103 22.0 5.840547 84 84 23.0 5.857923 93 93 24.0 5.872375 107 107 25.0 5.884395 82 82 26.0 5.894394 86 86 27.0 5.90271 70 70 28.0 5.909627 72 72 29.0 5.91538 56 56 30.0 5.920166 63 63 31.0 5.924146 55 55 32.0 5.927457 56 56 33.0 5.93021 55 55 34.0 5.9325 47 47 35.0 5.934406 50 50 36.0 5.93599 43 43 37.0 5.937308 33 33 38.0 5.938404 36 36 39.0 5.939316 43 43 40.0 5.940074 26 26 41.0 5.940705 28 28 42.0 5.94123 37 37 43.0 5.941666 31 31 44.0 5.942029 18 18 45.0 5.942331 31 31 46.0 5.942582 27 27 47.0 5.942791 24 24 48.0 5.942965 19 19 49.0 5.943109 19 19 50.0 5.943229 16 16 51.0 5.943329 25 25 52.0 5.943413 22 22 53.0 5.943482 19 19 54.0 5.943539 24 24 55.0 5.943587 15 15 56.0 5.943627 16 16 57.0 5.94366 16 16 58.0 5.943687 16 16 59.0 5.94371 19 19 60.0 5.943729 29 29 61.0 5.943745 12 12 62.0 5.943758 18 18 63.0 5.943769 20 20 64.0 5.943779 13 13 65.0 5.943786 18 18 66.0 5.943792 12 12 67.0 5.943798 10 10 68.0 5.943802 15 15 69.0 5.943806 9 9 70.0 5.943809 16 16 71.0 5.943811 7 7 72.0 5.943813 10 10 73.0 5.943815 15 15 74.0 5.943816 16 16 75.0 5.943818 13 13 76.0 5.943819 6 6 77.0 5.943819 9 9 78.0 5.94382 13 13 79.0 5.943821 10 10 80.0 5.943821 7 7 81.0 5.943822 8 8 82.0 5.943822 12 12 83.0 5.943822 3 3 84.0 5.943822 5 5 85.0 5.943823 7 7 86.0 5.943823 14 14 87.0 5.943823 10 10 88.0 5.943823 6 6 89.0 5.943823 8 8 90.0 5.943823 9 9 91.0 5.943823 12 12 92.0 5.943823 8 8 93.0 5.943823 10 10 94.0 5.943823 6 6 95.0 5.943823 9 9 96.0 5.943823 13 13 97.0 5.943824 15 15 98.0 5.943824 6 6 99.0 5.943824 4 4 100.0 5.943824 4 4 101.0 0 5 5 102.0 0 5 5 103.0 0 7 7 104.0 0 6 6 105.0 0 9 9 106.0 0 8 8 107.0 0 8 8 108.0 0 7 7 109.0 0 9 9 110.0 0 6 6 111.0 0 4 4 112.0 0 6 6 113.0 0 5 5 114.0 0 3 3 115.0 0 5 5 116.0 0 4 4 117.0 0 7 7 118.0 0 1 1 119.0 0 3 3 120.0 0 3 3 121.0 0 6 6 123.0 0 3 3 124.0 0 3 3 125.0 0 2 2 127.0 0 5 5 128.0 0 6 6 129.0 0 4 4 130.0 0 5 5 131.0 0 8 8 132.0 0 4 4 133.0 0 1 1 134.0 0 4 4 135.0 0 5 5 136.0 0 3 3 137.0 0 2 2 138.0 0 2 2 139.0 0 2 2 140.0 0 2 2 141.0 0 3 3 142.0 0 3 3 143.0 0 2 2 144.0 0 2 2 145.0 0 4 4 146.0 0 3 3 147.0 0 3 3 148.0 0 2 2 149.0 0 4 4 150.0 0 1 1 151.0 0 6 6 152.0 0 1 1 153.0 0 4 4 154.0 0 1 1 155.0 0 3 3 156.0 0 1 1 157.0 0 3 3 158.0 0 3 3 159.0 0 4 4 160.0 0 2 2 162.0 0 2 2 163.0 0 5 5 165.0 0 3 3 166.0 0 3 3 170.0 0 5 5 172.0 0 3 3 174.0 0 4 4 176.0 0 3 3 177.0 0 1 1 179.0 0 2 2 180.0 0 2 2 181.0 0 2 2 182.0 0 1 1 183.0 0 1 1 185.0 0 4 4 187.0 0 2 2 188.0 0 2 2 191.0 0 3 3 192.0 0 2 2 193.0 0 1 1 194.0 0 2 2 195.0 0 1 1 196.0 0 3 3 197.0 0 1 1 198.0 0 1 1 200.0 0 1 1 202.0 0 2 2 204.0 0 2 2 205.0 0 1 1 208.0 0 1 1 210.0 0 1 1 213.0 0 2 2 214.0 0 1 1 215.0 0 1 1 219.0 0 1 1 220.0 0 1 1 221.0 0 1 1 223.0 0 3 3 224.0 0 2 2 225.0 0 1 1 226.0 0 1 1 229.0 0 2 2 230.0 0 1 1 231.0 0 1 1 232.0 0 1 1 234.0 0 2 2 237.0 0 1 1 240.0 0 1 1 241.0 0 1 1 243.0 0 1 1 245.0 0 2 2 247.0 0 1 1 249.0 0 1 1 250.0 0 1 1 253.0 0 2 2 254.0 0 1 1 256.0 0 1 1 258.0 0 2 2 259.0 0 1 1 260.0 0 1 1 261.0 0 3 3 262.0 0 2 2 263.0 0 2 2 264.0 0 1 1 272.0 0 1 1 274.0 0 2 2 279.0 0 1 1 281.0 0 1 1 282.0 0 1 1 283.0 0 2 2 286.0 0 1 1 287.0 0 2 2 289.0 0 2 2 294.0 0 3 3 296.0 0 1 1 297.0 0 1 1 300.0 0 1 1 306.0 0 1 1 310.0 0 1 1 312.0 0 1 1 313.0 0 1 1 316.0 0 1 1 319.0 0 1 1 320.0 0 1 1 322.0 0 1 1 325.0 0 1 1 326.0 0 3 3 333.0 0 2 2 338.0 0 1 1 341.0 0 1 1 344.0 0 1 1 350.0 0 2 2 352.0 0 1 1 359.0 0 1 1 364.0 0 1 1 368.0 0 1 1 369.0 0 1 1 383.0 0 1 1 384.0 0 1 1 385.0 0 2 2 386.0 0 1 1 388.0 0 1 1 395.0 0 1 1 407.0 0 1 1 419.0 0 1 1 420.0 0 1 1 424.0 0 1 1 426.0 0 1 1 430.0 0 2 2 431.0 0 1 1 436.0 0 1 1 454.0 0 1 1 489.0 0 1 1 492.0 0 1 1 504.0 0 1 1 511.0 0 1 1 522.0 0 1 1 531.0 0 1 1 539.0 0 1 1 540.0 0 2 2 557.0 0 1 1 559.0 0 1 1 562.0 0 1 1 580.0 0 1 1 618.0 0 1 1 648.0 0 1 1 695.0 0 1 1 766.0 0 1 1 791.0 0 1 1 802.0 0 1 1 841.0 0 1 1 862.0 0 1 1 874.0 0 1 1 877.0 0 1 1 887.0 0 1 1 1011.0 0 1 1 1016.0 0 1 1 1102.0 0 1 1 1283.0 0 1 1 1322.0 0 1 1 2609.0 0 1 1 5258.0 0 1 1