## htsjdk.samtools.metrics.StringHeader # MarkDuplicates INPUT=[/project/berglandlab/DEST/dest_mapped/DESTv1/FR_Gua_Des_1_2015-12-16/FR_Gua_Des_1_2015-12-16.sorted_merged.bam] OUTPUT=/project/berglandlab/DEST/dest_mapped/DESTv1/FR_Gua_Des_1_2015-12-16/FR_Gua_Des_1_2015-12-16.dedup.bam METRICS_FILE=/project/berglandlab/DEST/dest_mapped/DESTv1/FR_Gua_Des_1_2015-12-16/FR_Gua_Des_1_2015-12-16.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 09:08:40 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 8109209 30415680 0 0 2959726 2722997 0 0.121927 159572952 ## HISTOGRAM java.lang.Double BIN VALUE all_sets non_optical_sets 1.0 1 24795417 24795417 2.0 1.826458 2135093 2135093 3.0 2.50949 162653 162653 4.0 3.073987 14357 14357 5.0 3.540519 2718 2718 6.0 3.926089 1363 1363 7.0 4.244746 915 915 8.0 4.508102 598 598 9.0 4.725755 489 489 10.0 4.905636 371 371 11.0 5.0543 312 312 12.0 5.177164 252 252 13.0 5.278706 233 233 14.0 5.362627 175 175 15.0 5.431983 174 174 16.0 5.489303 145 145 17.0 5.536676 130 130 18.0 5.575828 125 125 19.0 5.608185 138 138 20.0 5.634927 118 118 21.0 5.657028 98 98 22.0 5.675293 91 91 23.0 5.690389 98 98 24.0 5.702865 91 91 25.0 5.713176 96 96 26.0 5.721697 106 106 27.0 5.72874 91 91 28.0 5.73456 68 68 29.0 5.73937 79 79 30.0 5.743346 75 75 31.0 5.746632 83 83 32.0 5.749347 56 56 33.0 5.751591 56 56 34.0 5.753446 60 60 35.0 5.754979 47 47 36.0 5.756245 55 55 37.0 5.757292 46 46 38.0 5.758158 43 43 39.0 5.758873 46 46 40.0 5.759464 45 45 41.0 5.759952 36 36 42.0 5.760356 41 41 43.0 5.76069 46 46 44.0 5.760965 34 34 45.0 5.761193 25 25 46.0 5.761382 36 36 47.0 5.761537 24 24 48.0 5.761666 27 27 49.0 5.761772 21 21 50.0 5.76186 31 31 51.0 5.761933 26 26 52.0 5.761993 29 29 53.0 5.762042 19 19 54.0 5.762083 29 29 55.0 5.762117 17 17 56.0 5.762145 23 23 57.0 5.762168 24 24 58.0 5.762187 18 18 59.0 5.762203 21 21 60.0 5.762216 18 18 61.0 5.762227 17 17 62.0 5.762236 22 22 63.0 5.762243 15 15 64.0 5.762249 14 14 65.0 5.762255 16 16 66.0 5.762259 14 14 67.0 5.762262 13 13 68.0 5.762265 18 18 69.0 5.762267 8 8 70.0 5.762269 12 12 71.0 5.762271 16 16 72.0 5.762272 11 11 73.0 5.762273 11 11 74.0 5.762274 15 15 75.0 5.762275 14 14 76.0 5.762276 10 10 77.0 5.762276 8 8 78.0 5.762276 7 7 79.0 5.762277 7 7 80.0 5.762277 14 14 81.0 5.762277 16 16 82.0 5.762278 9 9 83.0 5.762278 9 9 84.0 5.762278 10 10 85.0 5.762278 13 13 86.0 5.762278 11 11 87.0 5.762278 7 7 88.0 5.762278 9 9 89.0 5.762278 11 11 90.0 5.762278 5 5 91.0 5.762278 11 11 92.0 5.762278 8 8 93.0 5.762278 7 7 94.0 5.762278 10 10 95.0 5.762278 8 8 96.0 5.762278 5 5 97.0 5.762278 8 8 98.0 5.762278 9 9 99.0 5.762278 4 4 100.0 5.762278 9 9 101.0 0 6 6 102.0 0 11 11 103.0 0 9 9 104.0 0 4 4 105.0 0 5 5 106.0 0 7 7 107.0 0 7 7 108.0 0 6 6 109.0 0 11 11 110.0 0 5 5 111.0 0 2 2 112.0 0 7 7 113.0 0 9 9 114.0 0 7 7 115.0 0 9 9 116.0 0 4 4 117.0 0 4 4 118.0 0 2 2 119.0 0 5 5 120.0 0 4 4 121.0 0 2 2 122.0 0 7 7 123.0 0 3 3 124.0 0 7 7 125.0 0 3 3 126.0 0 5 5 127.0 0 6 6 128.0 0 4 4 129.0 0 2 2 130.0 0 8 8 131.0 0 5 5 132.0 0 4 4 133.0 0 3 3 134.0 0 3 3 136.0 0 3 3 137.0 0 2 2 138.0 0 1 1 139.0 0 4 4 140.0 0 5 5 141.0 0 3 3 142.0 0 2 2 143.0 0 5 5 144.0 0 4 4 145.0 0 2 2 146.0 0 2 2 147.0 0 1 1 148.0 0 2 2 149.0 0 2 2 150.0 0 5 5 151.0 0 5 5 152.0 0 2 2 154.0 0 1 1 155.0 0 3 3 156.0 0 4 4 157.0 0 1 1 160.0 0 3 3 161.0 0 1 1 162.0 0 1 1 164.0 0 1 1 165.0 0 1 1 166.0 0 1 1 167.0 0 2 2 168.0 0 2 2 170.0 0 1 1 171.0 0 6 6 174.0 0 2 2 176.0 0 2 2 177.0 0 1 1 178.0 0 1 1 179.0 0 2 2 180.0 0 3 3 181.0 0 1 1 182.0 0 1 1 183.0 0 3 3 184.0 0 2 2 185.0 0 3 3 186.0 0 1 1 187.0 0 1 1 188.0 0 2 2 189.0 0 1 1 192.0 0 2 2 194.0 0 1 1 196.0 0 1 1 197.0 0 1 1 199.0 0 3 3 200.0 0 1 1 201.0 0 1 1 202.0 0 1 1 203.0 0 3 3 204.0 0 1 1 205.0 0 1 1 206.0 0 4 4 207.0 0 2 2 208.0 0 3 3 209.0 0 3 3 210.0 0 2 2 211.0 0 1 1 214.0 0 1 1 217.0 0 1 1 218.0 0 1 1 219.0 0 1 1 220.0 0 1 1 221.0 0 1 1 224.0 0 3 3 225.0 0 1 1 226.0 0 1 1 228.0 0 1 1 229.0 0 1 1 231.0 0 1 1 232.0 0 1 1 234.0 0 1 1 241.0 0 1 1 242.0 0 1 1 244.0 0 1 1 245.0 0 1 1 248.0 0 1 1 251.0 0 1 1 252.0 0 2 2 259.0 0 1 1 265.0 0 1 1 276.0 0 1 1 281.0 0 1 1 282.0 0 1 1 287.0 0 1 1 291.0 0 1 1 293.0 0 1 1 296.0 0 1 1 299.0 0 1 1 301.0 0 2 2 303.0 0 1 1 310.0 0 1 1 314.0 0 2 2 318.0 0 1 1 324.0 0 1 1 326.0 0 1 1 332.0 0 1 1 346.0 0 2 2 353.0 0 1 1 360.0 0 1 1 365.0 0 1 1 375.0 0 1 1 386.0 0 1 1 392.0 0 1 1 395.0 0 1 1 397.0 0 1 1 408.0 0 1 1 424.0 0 1 1 456.0 0 1 1