## htsjdk.samtools.metrics.StringHeader # MarkDuplicates INPUT=[/project/berglandlab/DEST/dest_mapped/DESTv1/RU_Nov_Val_1_2016-10-24/RU_Nov_Val_1_2016-10-24.sorted_merged.bam] OUTPUT=/project/berglandlab/DEST/dest_mapped/DESTv1/RU_Nov_Val_1_2016-10-24/RU_Nov_Val_1_2016-10-24.dedup.bam METRICS_FILE=/project/berglandlab/DEST/dest_mapped/DESTv1/RU_Nov_Val_1_2016-10-24/RU_Nov_Val_1_2016-10-24.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 09:27:02 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 41795066 13269919 0 0 11212117 1125285 0 0.19701 73753914 ## HISTOGRAM java.lang.Double BIN VALUE all_sets non_optical_sets 1.0 1 11017799 11017799 2.0 1.835336 747554 747554 3.0 2.533122 61226 61226 4.0 3.116007 7419 7419 5.0 3.602912 2215 2215 6.0 4.009641 1237 1237 7.0 4.349396 822 822 8.0 4.633206 666 666 9.0 4.870283 473 473 10.0 5.068321 370 370 11.0 5.23375 310 310 12.0 5.371938 279 279 13.0 5.487372 214 214 14.0 5.583798 204 204 15.0 5.664346 155 155 16.0 5.731631 168 168 17.0 5.787836 148 148 18.0 5.834786 124 124 19.0 5.874005 122 122 20.0 5.906767 99 99 21.0 5.934133 126 126 22.0 5.956994 124 124 23.0 5.97609 110 110 24.0 5.992041 85 85 25.0 6.005366 83 83 26.0 6.016497 99 99 27.0 6.025795 76 76 28.0 6.033562 81 81 29.0 6.04005 61 61 30.0 6.045469 79 79 31.0 6.049997 58 58 32.0 6.053778 58 58 33.0 6.056937 58 58 34.0 6.059576 54 54 35.0 6.061781 49 49 36.0 6.063622 44 44 37.0 6.06516 40 40 38.0 6.066445 47 47 39.0 6.067518 28 28 40.0 6.068415 21 21 41.0 6.069164 35 35 42.0 6.069789 26 26 43.0 6.070312 32 32 44.0 6.070749 20 20 45.0 6.071113 26 26 46.0 6.071418 28 28 47.0 6.071672 27 27 48.0 6.071885 17 17 49.0 6.072062 26 26 50.0 6.072211 24 24 51.0 6.072335 14 14 52.0 6.072438 13 13 53.0 6.072525 19 19 54.0 6.072597 11 11 55.0 6.072657 22 22 56.0 6.072707 14 14 57.0 6.07275 14 14 58.0 6.072785 14 14 59.0 6.072814 8 8 60.0 6.072839 16 16 61.0 6.072859 19 19 62.0 6.072876 14 14 63.0 6.072891 8 8 64.0 6.072902 12 12 65.0 6.072912 19 19 66.0 6.072921 13 13 67.0 6.072928 14 14 68.0 6.072934 14 14 69.0 6.072938 17 17 70.0 6.072942 11 11 71.0 6.072946 18 18 72.0 6.072949 15 15 73.0 6.072951 9 9 74.0 6.072953 8 8 75.0 6.072955 8 8 76.0 6.072956 6 6 77.0 6.072957 11 11 78.0 6.072958 7 7 79.0 6.072959 6 6 80.0 6.07296 9 9 81.0 6.07296 8 8 82.0 6.072961 8 8 83.0 6.072961 3 3 84.0 6.072961 11 11 85.0 6.072962 9 9 86.0 6.072962 8 8 87.0 6.072962 8 8 88.0 6.072962 17 17 89.0 6.072962 13 13 90.0 6.072963 9 9 91.0 6.072963 5 5 92.0 6.072963 9 9 93.0 6.072963 11 11 94.0 6.072963 12 12 95.0 6.072963 11 11 96.0 6.072963 4 4 97.0 6.072963 5 5 98.0 6.072963 12 12 99.0 6.072963 5 5 100.0 6.072963 7 7 101.0 0 6 6 102.0 0 9 9 103.0 0 6 6 104.0 0 6 6 105.0 0 6 6 106.0 0 3 3 107.0 0 5 5 108.0 0 4 4 109.0 0 8 8 110.0 0 8 8 111.0 0 7 7 112.0 0 7 7 114.0 0 4 4 115.0 0 4 4 116.0 0 8 8 117.0 0 10 10 118.0 0 3 3 119.0 0 7 7 120.0 0 5 5 121.0 0 3 3 123.0 0 4 4 124.0 0 5 5 125.0 0 2 2 126.0 0 6 6 127.0 0 5 5 128.0 0 3 3 129.0 0 1 1 130.0 0 3 3 131.0 0 5 5 132.0 0 5 5 133.0 0 6 6 134.0 0 1 1 135.0 0 5 5 136.0 0 5 5 137.0 0 1 1 138.0 0 3 3 139.0 0 2 2 140.0 0 3 3 141.0 0 2 2 142.0 0 3 3 144.0 0 2 2 145.0 0 2 2 146.0 0 2 2 147.0 0 2 2 148.0 0 2 2 149.0 0 1 1 150.0 0 3 3 151.0 0 4 4 152.0 0 3 3 153.0 0 4 4 154.0 0 1 1 155.0 0 2 2 156.0 0 3 3 157.0 0 3 3 158.0 0 1 1 159.0 0 1 1 160.0 0 1 1 161.0 0 1 1 162.0 0 2 2 163.0 0 5 5 164.0 0 1 1 165.0 0 1 1 166.0 0 1 1 167.0 0 1 1 168.0 0 1 1 169.0 0 1 1 170.0 0 1 1 171.0 0 2 2 172.0 0 1 1 173.0 0 1 1 174.0 0 2 2 175.0 0 1 1 177.0 0 1 1 178.0 0 2 2 179.0 0 1 1 180.0 0 2 2 181.0 0 3 3 182.0 0 1 1 183.0 0 2 2 184.0 0 1 1 186.0 0 1 1 187.0 0 1 1 188.0 0 2 2 189.0 0 2 2 191.0 0 1 1 193.0 0 3 3 194.0 0 1 1 195.0 0 3 3 196.0 0 4 4 197.0 0 2 2 198.0 0 1 1 199.0 0 1 1 201.0 0 1 1 202.0 0 2 2 203.0 0 1 1 204.0 0 1 1 206.0 0 1 1 207.0 0 1 1 209.0 0 1 1 210.0 0 3 3 211.0 0 1 1 212.0 0 1 1 217.0 0 1 1 219.0 0 1 1 220.0 0 2 2 221.0 0 1 1 222.0 0 3 3 224.0 0 3 3 225.0 0 1 1 228.0 0 1 1 229.0 0 1 1 230.0 0 1 1 232.0 0 2 2 233.0 0 1 1 234.0 0 1 1 235.0 0 1 1 236.0 0 1 1 241.0 0 1 1 243.0 0 1 1 246.0 0 1 1 248.0 0 1 1 254.0 0 1 1 257.0 0 1 1 258.0 0 1 1 262.0 0 1 1 265.0 0 1 1 267.0 0 1 1 268.0 0 1 1 269.0 0 1 1 270.0 0 1 1 279.0 0 1 1 283.0 0 1 1 285.0 0 1 1 286.0 0 1 1 287.0 0 1 1 289.0 0 1 1 291.0 0 1 1 292.0 0 1 1 295.0 0 2 2 296.0 0 1 1 297.0 0 1 1 300.0 0 1 1 301.0 0 2 2 302.0 0 3 3 303.0 0 1 1 305.0 0 1 1 307.0 0 1 1 308.0 0 1 1 313.0 0 1 1 315.0 0 1 1 319.0 0 1 1 320.0 0 2 2 322.0 0 1 1 324.0 0 1 1 328.0 0 1 1 331.0 0 2 2 345.0 0 1 1 346.0 0 1 1 348.0 0 1 1 351.0 0 1 1 357.0 0 1 1 362.0 0 1 1 373.0 0 1 1 377.0 0 1 1 378.0 0 1 1 391.0 0 1 1 393.0 0 1 1 407.0 0 1 1 413.0 0 1 1 424.0 0 1 1 430.0 0 1 1 434.0 0 1 1 438.0 0 1 1 441.0 0 1 1 442.0 0 1 1 453.0 0 1 1 454.0 0 3 3 467.0 0 1 1 493.0 0 1 1 496.0 0 1 1 500.0 0 1 1 585.0 0 1 1 611.0 0 1 1 710.0 0 1 1 783.0 0 1 1 853.0 0 1 1 879.0 0 1 1 987.0 0 1 1 1100.0 0 1 1 1214.0 0 1 1 1257.0 0 1 1 1414.0 0 1 1 1450.0 0 1 1 1548.0 0 1 1 1751.0 0 1 1 3041.0 0 1 1