## htsjdk.samtools.metrics.StringHeader # MarkDuplicates INPUT=[/project/berglandlab/DEST/dest_mapped/pipeline_output//WI_cp_13_spring/WI_cp_13_spring.sorted_merged.bam] OUTPUT=/project/berglandlab/DEST/dest_mapped/pipeline_output/WI_cp_13_spring/WI_cp_13_spring.dedup.bam METRICS_FILE=/project/berglandlab/DEST/dest_mapped/pipeline_output/WI_cp_13_spring/WI_cp_13_spring.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: Thu Jun 11 07:11:31 UTC 2020 ## 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 2142457 96310466 0 0 1262881 14622078 0 0.156636 284192413 ## HISTOGRAM java.lang.Double BIN VALUE all_sets non_optical_sets 1.0 1 67357441 67357441 2.0 1.71256 10346864 10346864 3.0 2.220301 1493440 1493440 4.0 2.582097 221280 221280 5.0 2.839898 38490 38490 6.0 3.023596 9873 9873 7.0 3.154492 3857 3857 8.0 3.247764 2252 2252 9.0 3.314225 1456 1456 10.0 3.361583 1049 1049 11.0 3.395328 825 825 12.0 3.419374 674 674 13.0 3.436507 536 536 14.0 3.448716 496 496 15.0 3.457416 391 391 16.0 3.463615 341 341 17.0 3.468032 303 303 18.0 3.471179 255 255 19.0 3.473422 228 228 20.0 3.47502 233 233 21.0 3.476159 203 203 22.0 3.47697 174 174 23.0 3.477548 129 129 24.0 3.47796 136 136 25.0 3.478254 124 124 26.0 3.478463 110 110 27.0 3.478612 110 110 28.0 3.478718 102 102 29.0 3.478794 75 75 30.0 3.478848 98 98 31.0 3.478887 71 71 32.0 3.478914 81 81 33.0 3.478933 80 80 34.0 3.478947 66 66 35.0 3.478957 70 70 36.0 3.478964 67 67 37.0 3.478969 58 58 38.0 3.478973 52 52 39.0 3.478975 56 56 40.0 3.478977 51 51 41.0 3.478979 44 44 42.0 3.478979 45 45 43.0 3.47898 42 42 44.0 3.478981 37 37 45.0 3.478981 38 38 46.0 3.478981 38 38 47.0 3.478981 30 30 48.0 3.478981 40 40 49.0 3.478982 32 32 50.0 3.478982 41 41 51.0 3.478982 27 27 52.0 3.478982 31 31 53.0 3.478982 26 26 54.0 3.478982 30 30 55.0 3.478982 23 23 56.0 3.478982 21 21 57.0 3.478982 31 31 58.0 3.478982 24 24 59.0 3.478982 14 14 60.0 3.478982 20 20 61.0 3.478982 23 23 62.0 3.478982 22 22 63.0 3.478982 25 25 64.0 3.478982 27 27 65.0 3.478982 25 25 66.0 3.478982 20 20 67.0 3.478982 22 22 68.0 3.478982 15 15 69.0 3.478982 29 29 70.0 3.478982 15 15 71.0 3.478982 19 19 72.0 3.478982 24 24 73.0 3.478982 20 20 74.0 3.478982 22 22 75.0 3.478982 20 20 76.0 3.478982 16 16 77.0 3.478982 18 18 78.0 3.478982 10 10 79.0 3.478982 12 12 80.0 3.478982 13 13 81.0 3.478982 18 18 82.0 3.478982 15 15 83.0 3.478982 11 11 84.0 3.478982 12 12 85.0 3.478982 17 17 86.0 3.478982 10 10 87.0 3.478982 13 13 88.0 3.478982 8 8 89.0 3.478982 11 11 90.0 3.478982 4 4 91.0 3.478982 8 8 92.0 3.478982 4 4 93.0 3.478982 11 11 94.0 3.478982 8 8 95.0 3.478982 9 9 96.0 3.478982 12 12 97.0 3.478982 10 10 98.0 3.478982 9 9 99.0 3.478982 12 12 100.0 3.478982 5 5 101.0 0 11 11 102.0 0 10 10 103.0 0 9 9 104.0 0 11 11 105.0 0 5 5 106.0 0 12 12 107.0 0 3 3 108.0 0 5 5 109.0 0 6 6 110.0 0 2 2 111.0 0 6 6 112.0 0 7 7 113.0 0 5 5 114.0 0 8 8 115.0 0 7 7 116.0 0 6 6 117.0 0 4 4 118.0 0 9 9 119.0 0 7 7 120.0 0 8 8 121.0 0 5 5 122.0 0 6 6 123.0 0 6 6 124.0 0 3 3 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221.0 0 1 1 222.0 0 1 1 223.0 0 1 1 224.0 0 1 1 226.0 0 4 4 229.0 0 5 5 230.0 0 4 4 231.0 0 1 1 232.0 0 4 4 233.0 0 2 2 235.0 0 4 4 236.0 0 4 4 238.0 0 1 1 240.0 0 2 2 242.0 0 1 1 243.0 0 1 1 244.0 0 1 1 246.0 0 1 1 248.0 0 2 2 251.0 0 4 4 252.0 0 1 1 253.0 0 2 2 254.0 0 3 3 256.0 0 2 2 257.0 0 1 1 261.0 0 1 1 263.0 0 1 1 264.0 0 2 2 265.0 0 2 2 266.0 0 2 2 268.0 0 2 2 270.0 0 2 2 272.0 0 1 1 273.0 0 1 1 274.0 0 3 3 275.0 0 1 1 277.0 0 1 1 278.0 0 1 1 279.0 0 2 2 280.0 0 1 1 282.0 0 1 1 283.0 0 2 2 284.0 0 1 1 285.0 0 1 1 286.0 0 2 2 288.0 0 1 1 290.0 0 1 1 291.0 0 1 1 293.0 0 1 1 295.0 0 1 1 299.0 0 1 1 300.0 0 1 1 301.0 0 2 2 304.0 0 1 1 305.0 0 1 1 309.0 0 1 1 310.0 0 1 1 311.0 0 1 1 313.0 0 1 1 318.0 0 3 3 319.0 0 2 2 324.0 0 1 1 325.0 0 1 1 326.0 0 1 1 328.0 0 1 1 333.0 0 1 1 339.0 0 1 1 340.0 0 1 1 341.0 0 1 1 343.0 0 1 1 344.0 0 1 1 345.0 0 1 1 348.0 0 1 1 350.0 0 1 1 356.0 0 1 1 357.0 0 1 1 361.0 0 1 1 369.0 0 1 1 375.0 0 1 1 377.0 0 2 2 378.0 0 1 1 379.0 0 1 1 385.0 0 1 1 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1708.0 0 1 1 1715.0 0 1 1 1786.0 0 1 1 1927.0 0 1 1 1968.0 0 1 1 2496.0 0 1 1 2508.0 0 1 1 2559.0 0 1 1 3422.0 0 1 1