## htsjdk.samtools.metrics.StringHeader # MarkDuplicates INPUT=[/project/berglandlab/DEST/dest_mapped/DESTv1/DE_Bad_Bro_1_2014-06-26/DE_Bad_Bro_1_2014-06-26.sorted_merged.bam] OUTPUT=/project/berglandlab/DEST/dest_mapped/DESTv1/DE_Bad_Bro_1_2014-06-26/DE_Bad_Bro_1_2014-06-26.dedup.bam METRICS_FILE=/project/berglandlab/DEST/dest_mapped/DESTv1/DE_Bad_Bro_1_2014-06-26/DE_Bad_Bro_1_2014-06-26.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 08:53:35 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 4787460 32226982 0 0 1423789 871972 0 0.045749 584742760 ## HISTOGRAM java.lang.Double BIN VALUE all_sets non_optical_sets 1.0 1 30135773 30135773 2.0 1.946378 729778 729778 3.0 2.84201 13624 13624 4.0 3.689616 790 790 5.0 4.491772 369 369 6.0 5.250914 293 293 7.0 5.96935 275 275 8.0 6.649263 194 194 9.0 7.292717 183 183 10.0 7.901667 143 143 11.0 8.477965 129 129 12.0 9.023361 116 116 13.0 9.539511 104 104 14.0 10.027984 114 114 15.0 10.490265 94 94 16.0 10.927757 92 92 17.0 11.34179 74 74 18.0 11.733622 61 61 19.0 12.104443 51 51 20.0 12.45538 63 63 21.0 12.787499 52 52 22.0 13.101809 43 43 23.0 13.399265 40 40 24.0 13.680772 39 39 25.0 13.947183 42 42 26.0 14.199309 33 33 27.0 14.437915 41 41 28.0 14.663727 39 39 29.0 14.87743 37 37 30.0 15.079674 18 18 31.0 15.271073 26 26 32.0 15.45221 28 28 33.0 15.623633 25 25 34.0 15.785864 36 36 35.0 15.939397 21 21 36.0 16.084696 22 22 37.0 16.222204 29 29 38.0 16.352339 15 15 39.0 16.475496 17 17 40.0 16.592049 21 21 41.0 16.702352 17 17 42.0 16.80674 13 13 43.0 16.905531 19 19 44.0 16.999024 9 9 45.0 17.087505 16 16 46.0 17.17124 16 16 47.0 17.250486 19 19 48.0 17.325483 12 12 49.0 17.396458 7 7 50.0 17.463627 11 11 51.0 17.527194 13 13 52.0 17.587353 7 7 53.0 17.644286 12 12 54.0 17.698166 11 11 55.0 17.749157 10 10 56.0 17.797414 6 6 57.0 17.843083 14 14 58.0 17.886303 12 12 59.0 17.927206 14 14 60.0 17.965915 7 7 61.0 18.002549 5 5 62.0 18.037218 12 12 63.0 18.070028 6 6 64.0 18.101079 8 8 65.0 18.130465 3 3 66.0 18.158276 5 5 67.0 18.184595 5 5 68.0 18.209502 3 3 69.0 18.233075 7 7 70.0 18.255383 7 7 71.0 18.276495 6 6 72.0 18.296474 11 11 73.0 18.315383 7 7 74.0 18.333278 7 7 75.0 18.350213 8 8 76.0 18.36624 6 6 77.0 18.381407 9 9 78.0 18.395761 9 9 79.0 18.409346 6 6 80.0 18.422202 1 1 81.0 18.434369 8 8 82.0 18.445883 3 3 83.0 18.45678 6 6 84.0 18.467093 5 5 85.0 18.476853 5 5 86.0 18.486089 3 3 87.0 18.49483 3 3 88.0 18.503102 3 3 89.0 18.510931 1 1 90.0 18.51834 5 5 91.0 18.525352 4 4 92.0 18.531987 5 5 93.0 18.538267 4 4 94.0 18.54421 1 1 95.0 18.549835 2 2 96.0 18.555158 3 3 97.0 18.560195 0 0 98.0 18.564962 4 4 99.0 18.569474 3 3 100.0 18.573744 2 2 101.0 0 3 3 102.0 0 1 1 103.0 0 1 1 104.0 0 1 1 105.0 0 2 2 107.0 0 3 3 108.0 0 4 4 109.0 0 4 4 110.0 0 2 2 111.0 0 5 5 112.0 0 2 2 113.0 0 4 4 114.0 0 2 2 115.0 0 1 1 116.0 0 2 2 117.0 0 2 2 118.0 0 2 2 119.0 0 1 1 120.0 0 2 2 121.0 0 3 3 122.0 0 2 2 123.0 0 3 3 125.0 0 1 1 127.0 0 1 1 128.0 0 1 1 129.0 0 1 1 131.0 0 1 1 133.0 0 5 5 134.0 0 3 3 135.0 0 1 1 136.0 0 3 3 137.0 0 2 2 138.0 0 1 1 142.0 0 4 4 143.0 0 5 5 144.0 0 2 2 145.0 0 2 2 147.0 0 2 2 148.0 0 1 1 149.0 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 3 3 156.0 0 1 1 157.0 0 2 2 158.0 0 2 2 159.0 0 3 3 160.0 0 1 1 161.0 0 4 4 162.0 0 2 2 163.0 0 1 1 164.0 0 2 2 165.0 0 1 1 166.0 0 1 1 167.0 0 3 3 168.0 0 2 2 169.0 0 2 2 170.0 0 1 1 171.0 0 1 1 172.0 0 1 1 173.0 0 1 1 174.0 0 1 1 175.0 0 1 1 176.0 0 1 1 177.0 0 1 1 179.0 0 1 1 182.0 0 3 3 183.0 0 1 1 184.0 0 2 2 185.0 0 1 1 187.0 0 1 1 188.0 0 4 4 189.0 0 2 2 193.0 0 3 3 194.0 0 1 1 195.0 0 1 1 196.0 0 1 1 197.0 0 1 1 198.0 0 2 2 200.0 0 2 2 201.0 0 1 1 204.0 0 1 1 205.0 0 1 1 206.0 0 1 1 207.0 0 2 2 209.0 0 1 1 210.0 0 2 2 212.0 0 1 1 214.0 0 1 1 216.0 0 1 1 217.0 0 2 2 219.0 0 2 2 221.0 0 1 1 223.0 0 1 1 224.0 0 1 1 226.0 0 1 1 230.0 0 1 1 231.0 0 1 1 232.0 0 1 1 233.0 0 2 2 235.0 0 1 1 239.0 0 2 2 243.0 0 1 1 247.0 0 1 1 248.0 0 1 1 249.0 0 1 1 251.0 0 1 1 254.0 0 1 1 257.0 0 1 1 260.0 0 1 1 264.0 0 1 1 266.0 0 1 1 267.0 0 1 1 269.0 0 2 2 271.0 0 3 3 272.0 0 1 1 274.0 0 1 1 279.0 0 1 1 286.0 0 1 1 292.0 0 1 1 293.0 0 1 1 302.0 0 1 1 305.0 0 1 1 306.0 0 1 1 324.0 0 1 1 325.0 0 1 1 327.0 0 2 2 331.0 0 1 1 332.0 0 1 1 344.0 0 1 1 345.0 0 1 1 347.0 0 1 1 348.0 0 1 1 349.0 0 1 1 356.0 0 1 1 371.0 0 1 1 373.0 0 1 1 382.0 0 1 1 388.0 0 1 1 389.0 0 1 1 393.0 0 1 1 405.0 0 1 1 419.0 0 1 1 421.0 0 1 1 425.0 0 1 1 428.0 0 1 1 439.0 0 1 1 480.0 0 1 1 486.0 0 1 1 559.0 0 1 1 562.0 0 1 1