## htsjdk.samtools.metrics.StringHeader # MarkDuplicates INPUT=[/project/berglandlab/DEST/dest_mapped/DESTv1/FI_Pir_Aka_1_2015-10-01/FI_Pir_Aka_1_2015-10-01.sorted_merged.bam] OUTPUT=/project/berglandlab/DEST/dest_mapped/DESTv1/FI_Pir_Aka_1_2015-10-01/FI_Pir_Aka_1_2015-10-01.dedup.bam METRICS_FILE=/project/berglandlab/DEST/dest_mapped/DESTv1/FI_Pir_Aka_1_2015-10-01/FI_Pir_Aka_1_2015-10-01.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 09:25:04 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 8498688 34629488 0 0 3549229 3126819 0 0.126069 180034830 ## HISTOGRAM java.lang.Double BIN VALUE all_sets non_optical_sets 1.0 1 28212326 28212326 2.0 1.825019 2468355 2468355 3.0 2.505675 186358 186358 4.0 3.06723 15645 15645 5.0 3.530523 2679 2679 6.0 3.912749 1231 1231 7.0 4.228092 824 824 8.0 4.488256 609 609 9.0 4.702897 474 474 10.0 4.87998 396 396 11.0 5.026076 321 321 12.0 5.146608 253 253 13.0 5.24605 177 177 14.0 5.328091 182 182 15.0 5.395776 140 140 16.0 5.451618 169 169 17.0 5.497689 165 165 18.0 5.535698 125 125 19.0 5.567056 123 123 20.0 5.592927 104 104 21.0 5.614271 105 105 22.0 5.631881 132 132 23.0 5.646409 90 90 24.0 5.658395 82 82 25.0 5.668283 73 73 26.0 5.676442 92 92 27.0 5.683172 67 67 28.0 5.688725 74 74 29.0 5.693307 49 49 30.0 5.697086 68 68 31.0 5.700205 51 51 32.0 5.702777 67 67 33.0 5.7049 60 60 34.0 5.706651 50 50 35.0 5.708096 49 49 36.0 5.709288 42 42 37.0 5.710271 39 39 38.0 5.711082 43 43 39.0 5.711751 42 42 40.0 5.712304 48 48 41.0 5.712759 38 38 42.0 5.713135 49 49 43.0 5.713445 35 35 44.0 5.713701 39 39 45.0 5.713912 27 27 46.0 5.714086 28 28 47.0 5.71423 30 30 48.0 5.714348 34 34 49.0 5.714446 28 28 50.0 5.714527 30 30 51.0 5.714593 25 25 52.0 5.714648 28 28 53.0 5.714694 27 27 54.0 5.714731 19 19 55.0 5.714762 14 14 56.0 5.714787 18 18 57.0 5.714808 25 25 58.0 5.714826 24 24 59.0 5.71484 21 21 60.0 5.714852 19 19 61.0 5.714861 22 22 62.0 5.714869 24 24 63.0 5.714876 12 12 64.0 5.714881 19 19 65.0 5.714886 14 14 66.0 5.71489 20 20 67.0 5.714893 9 9 68.0 5.714895 21 21 69.0 5.714897 14 14 70.0 5.714899 13 13 71.0 5.714901 22 22 72.0 5.714902 12 12 73.0 5.714903 24 24 74.0 5.714903 9 9 75.0 5.714904 13 13 76.0 5.714905 22 22 77.0 5.714905 7 7 78.0 5.714905 11 11 79.0 5.714906 14 14 80.0 5.714906 8 8 81.0 5.714906 19 19 82.0 5.714906 7 7 83.0 5.714907 11 11 84.0 5.714907 14 14 85.0 5.714907 7 7 86.0 5.714907 12 12 87.0 5.714907 10 10 88.0 5.714907 10 10 89.0 5.714907 10 10 90.0 5.714907 8 8 91.0 5.714907 9 9 92.0 5.714907 7 7 93.0 5.714907 14 14 94.0 5.714907 6 6 95.0 5.714907 5 5 96.0 5.714907 5 5 97.0 5.714907 8 8 98.0 5.714907 7 7 99.0 5.714907 4 4 100.0 5.714907 10 10 101.0 0 4 4 102.0 0 8 8 103.0 0 11 11 104.0 0 10 10 105.0 0 7 7 106.0 0 3 3 107.0 0 6 6 108.0 0 6 6 109.0 0 13 13 110.0 0 4 4 111.0 0 5 5 112.0 0 5 5 113.0 0 6 6 114.0 0 7 7 115.0 0 1 1 116.0 0 6 6 117.0 0 3 3 118.0 0 3 3 119.0 0 6 6 120.0 0 4 4 121.0 0 3 3 122.0 0 6 6 123.0 0 7 7 124.0 0 3 3 125.0 0 2 2 126.0 0 3 3 127.0 0 3 3 128.0 0 3 3 129.0 0 7 7 130.0 0 3 3 131.0 0 2 2 132.0 0 5 5 133.0 0 2 2 134.0 0 10 10 135.0 0 6 6 136.0 0 4 4 137.0 0 8 8 138.0 0 1 1 139.0 0 3 3 140.0 0 2 2 141.0 0 5 5 142.0 0 2 2 143.0 0 5 5 144.0 0 3 3 145.0 0 4 4 146.0 0 2 2 147.0 0 3 3 148.0 0 2 2 150.0 0 1 1 151.0 0 2 2 152.0 0 1 1 153.0 0 3 3 154.0 0 1 1 155.0 0 3 3 156.0 0 3 3 157.0 0 3 3 158.0 0 4 4 159.0 0 2 2 160.0 0 1 1 161.0 0 4 4 162.0 0 2 2 163.0 0 2 2 164.0 0 3 3 165.0 0 6 6 166.0 0 4 4 167.0 0 2 2 168.0 0 4 4 169.0 0 4 4 170.0 0 1 1 172.0 0 4 4 173.0 0 1 1 174.0 0 1 1 177.0 0 4 4 179.0 0 5 5 182.0 0 2 2 184.0 0 2 2 185.0 0 3 3 187.0 0 2 2 188.0 0 3 3 189.0 0 1 1 191.0 0 2 2 193.0 0 1 1 194.0 0 4 4 195.0 0 1 1 196.0 0 1 1 197.0 0 2 2 198.0 0 3 3 200.0 0 1 1 201.0 0 4 4 202.0 0 2 2 203.0 0 1 1 205.0 0 1 1 206.0 0 1 1 208.0 0 1 1 209.0 0 1 1 211.0 0 3 3 213.0 0 1 1 214.0 0 1 1 215.0 0 4 4 216.0 0 1 1 217.0 0 1 1 218.0 0 2 2 219.0 0 1 1 220.0 0 1 1 224.0 0 2 2 225.0 0 1 1 226.0 0 2 2 228.0 0 1 1 229.0 0 2 2 230.0 0 2 2 231.0 0 3 3 234.0 0 3 3 236.0 0 2 2 237.0 0 1 1 238.0 0 1 1 239.0 0 1 1 240.0 0 1 1 241.0 0 4 4 242.0 0 2 2 245.0 0 1 1 246.0 0 1 1 249.0 0 1 1 250.0 0 1 1 251.0 0 1 1 258.0 0 1 1 259.0 0 1 1 261.0 0 1 1 264.0 0 3 3 269.0 0 1 1 271.0 0 1 1 273.0 0 1 1 281.0 0 1 1 283.0 0 2 2 287.0 0 1 1 290.0 0 1 1 291.0 0 2 2 293.0 0 1 1 295.0 0 1 1 297.0 0 1 1 298.0 0 1 1 301.0 0 1 1 307.0 0 1 1 311.0 0 1 1 313.0 0 1 1 314.0 0 2 2 315.0 0 2 2 317.0 0 1 1 319.0 0 1 1 321.0 0 1 1 331.0 0 1 1 334.0 0 1 1 335.0 0 1 1 338.0 0 1 1 344.0 0 2 2 345.0 0 1 1 348.0 0 1 1 355.0 0 1 1 364.0 0 1 1 371.0 0 1 1 387.0 0 2 2 394.0 0 1 1 395.0 0 1 1 396.0 0 1 1 399.0 0 1 1 405.0 0 1 1 411.0 0 1 1 414.0 0 1 1 416.0 0 1 1 426.0 0 1 1 427.0 0 1 1 437.0 0 1 1 441.0 0 1 1 479.0 0 1 1 480.0 0 1 1 533.0 0 1 1 584.0 0 1 1 615.0 0 1 1 618.0 0 1 1 638.0 0 1 1 747.0 0 1 1