## htsjdk.samtools.metrics.StringHeader # MarkDuplicates INPUT=[/project/berglandlab/DEST/dest_mapped/DESTv1/RU_Cri_Yal_1_2015-08-24/RU_Cri_Yal_1_2015-08-24.sorted_merged.bam] OUTPUT=/project/berglandlab/DEST/dest_mapped/DESTv1/RU_Cri_Yal_1_2015-08-24/RU_Cri_Yal_1_2015-08-24.dedup.bam METRICS_FILE=/project/berglandlab/DEST/dest_mapped/DESTv1/RU_Cri_Yal_1_2015-08-24/RU_Cri_Yal_1_2015-08-24.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 08:57:37 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 33622334 9108931 0 0 8468464 782110 0 0.193531 49962216 ## HISTOGRAM java.lang.Double BIN VALUE all_sets non_optical_sets 1.0 1 7545755 7545755 2.0 1.833338 465348 465348 3.0 2.527789 36637 36637 4.0 3.106502 5008 5008 5.0 3.588765 1931 1931 6.0 3.990653 1169 1169 7.0 4.325561 845 845 8.0 4.604653 571 571 9.0 4.837231 454 454 10.0 5.031046 354 354 11.0 5.19256 289 289 12.0 5.327156 255 255 13.0 5.43932 217 217 14.0 5.53279 188 188 15.0 5.610682 179 179 16.0 5.675592 173 173 17.0 5.729685 154 154 18.0 5.774762 141 141 19.0 5.812326 115 115 20.0 5.84363 121 121 21.0 5.869717 96 96 22.0 5.891456 95 95 23.0 5.909572 108 108 24.0 5.924669 101 101 25.0 5.93725 77 77 26.0 5.947734 95 95 27.0 5.95647 77 77 28.0 5.963751 68 68 29.0 5.969818 64 64 30.0 5.974874 52 52 31.0 5.979087 56 56 32.0 5.982599 48 48 33.0 5.985525 54 54 34.0 5.987963 43 43 35.0 5.989995 36 36 36.0 5.991688 40 40 37.0 5.993099 33 33 38.0 5.994275 48 48 39.0 5.995255 43 43 40.0 5.996072 28 28 41.0 5.996752 29 29 42.0 5.997319 31 31 43.0 5.997792 25 25 44.0 5.998186 27 27 45.0 5.998514 23 23 46.0 5.998787 23 23 47.0 5.999015 22 22 48.0 5.999205 18 18 49.0 5.999364 19 19 50.0 5.999495 35 35 51.0 5.999605 12 12 52.0 5.999697 23 23 53.0 5.999773 13 13 54.0 5.999837 19 19 55.0 5.99989 15 15 56.0 5.999934 16 16 57.0 5.999971 19 19 58.0 6.000002 17 17 59.0 6.000027 14 14 60.0 6.000048 14 14 61.0 6.000066 20 20 62.0 6.000081 7 7 63.0 6.000093 25 25 64.0 6.000104 14 14 65.0 6.000112 10 10 66.0 6.000119 13 13 67.0 6.000125 14 14 68.0 6.00013 11 11 69.0 6.000134 7 7 70.0 6.000138 10 10 71.0 6.000141 16 16 72.0 6.000143 6 6 73.0 6.000145 16 16 74.0 6.000147 9 9 75.0 6.000148 13 13 76.0 6.000149 12 12 77.0 6.00015 16 16 78.0 6.000151 14 14 79.0 6.000152 7 7 80.0 6.000152 10 10 81.0 6.000153 12 12 82.0 6.000153 12 12 83.0 6.000153 14 14 84.0 6.000154 10 10 85.0 6.000154 11 11 86.0 6.000154 4 4 87.0 6.000154 8 8 88.0 6.000154 6 6 89.0 6.000154 6 6 90.0 6.000154 7 7 91.0 6.000155 9 9 92.0 6.000155 10 10 93.0 6.000155 10 10 94.0 6.000155 6 6 95.0 6.000155 10 10 96.0 6.000155 7 7 97.0 6.000155 2 2 98.0 6.000155 12 12 99.0 6.000155 4 4 100.0 6.000155 7 7 101.0 0 3 3 102.0 0 3 3 103.0 0 6 6 104.0 0 7 7 105.0 0 5 5 106.0 0 7 7 107.0 0 4 4 108.0 0 5 5 109.0 0 7 7 110.0 0 7 7 111.0 0 5 5 112.0 0 9 9 113.0 0 5 5 114.0 0 1 1 115.0 0 3 3 116.0 0 3 3 117.0 0 1 1 118.0 0 4 4 119.0 0 1 1 120.0 0 3 3 121.0 0 3 3 122.0 0 4 4 123.0 0 7 7 124.0 0 3 3 125.0 0 4 4 126.0 0 3 3 127.0 0 4 4 128.0 0 3 3 130.0 0 4 4 131.0 0 2 2 132.0 0 1 1 133.0 0 2 2 134.0 0 1 1 135.0 0 3 3 136.0 0 4 4 137.0 0 5 5 138.0 0 3 3 139.0 0 7 7 140.0 0 1 1 141.0 0 1 1 142.0 0 4 4 143.0 0 6 6 144.0 0 2 2 145.0 0 5 5 146.0 0 2 2 147.0 0 3 3 148.0 0 2 2 149.0 0 2 2 150.0 0 3 3 151.0 0 3 3 152.0 0 4 4 153.0 0 2 2 154.0 0 5 5 155.0 0 4 4 156.0 0 1 1 159.0 0 1 1 160.0 0 4 4 161.0 0 2 2 163.0 0 1 1 164.0 0 2 2 166.0 0 4 4 167.0 0 3 3 168.0 0 1 1 169.0 0 2 2 171.0 0 2 2 172.0 0 4 4 174.0 0 2 2 176.0 0 1 1 178.0 0 2 2 181.0 0 1 1 183.0 0 3 3 184.0 0 2 2 185.0 0 1 1 186.0 0 2 2 188.0 0 1 1 189.0 0 1 1 190.0 0 2 2 193.0 0 1 1 194.0 0 1 1 197.0 0 1 1 198.0 0 1 1 199.0 0 1 1 201.0 0 1 1 202.0 0 1 1 205.0 0 2 2 206.0 0 2 2 207.0 0 4 4 210.0 0 2 2 211.0 0 3 3 212.0 0 1 1 215.0 0 1 1 216.0 0 1 1 217.0 0 1 1 219.0 0 3 3 220.0 0 1 1 221.0 0 2 2 225.0 0 1 1 227.0 0 1 1 234.0 0 1 1 236.0 0 2 2 239.0 0 2 2 241.0 0 1 1 243.0 0 1 1 244.0 0 4 4 247.0 0 1 1 248.0 0 1 1 249.0 0 1 1 251.0 0 1 1 252.0 0 1 1 254.0 0 1 1 255.0 0 1 1 257.0 0 1 1 258.0 0 1 1 261.0 0 1 1 263.0 0 1 1 264.0 0 1 1 266.0 0 1 1 267.0 0 1 1 268.0 0 1 1 269.0 0 1 1 270.0 0 1 1 274.0 0 1 1 276.0 0 1 1 277.0 0 2 2 280.0 0 1 1 282.0 0 1 1 285.0 0 2 2 288.0 0 1 1 289.0 0 1 1 290.0 0 1 1 293.0 0 1 1 299.0 0 1 1 303.0 0 1 1 305.0 0 1 1 307.0 0 1 1 309.0 0 1 1 310.0 0 1 1 314.0 0 1 1 315.0 0 1 1 316.0 0 2 2 318.0 0 1 1 325.0 0 1 1 330.0 0 1 1 331.0 0 1 1 335.0 0 1 1 340.0 0 1 1 342.0 0 1 1 343.0 0 1 1 344.0 0 1 1 346.0 0 2 2 353.0 0 1 1 357.0 0 1 1 359.0 0 1 1 360.0 0 1 1 362.0 0 1 1 364.0 0 1 1 365.0 0 1 1 376.0 0 1 1 380.0 0 1 1 382.0 0 1 1 383.0 0 1 1 385.0 0 2 2 387.0 0 1 1 393.0 0 1 1 431.0 0 1 1 432.0 0 1 1 435.0 0 2 2 437.0 0 1 1 447.0 0 1 1 453.0 0 1 1 459.0 0 1 1 498.0 0 1 1 538.0 0 1 1 553.0 0 1 1 559.0 0 1 1 568.0 0 1 1 637.0 0 2 2 679.0 0 2 2 700.0 0 1 1 762.0 0 1 1 769.0 0 1 1 799.0 0 1 1 815.0 0 1 1 834.0 0 1 1 842.0 0 1 1 1037.0 0 1 1 1041.0 0 1 1 1125.0 0 1 1 1254.0 0 1 1 2079.0 0 1 1 4322.0 0 1 1