## htsjdk.samtools.metrics.StringHeader # MarkDuplicates INPUT=[/project/berglandlab/DEST/dest_mapped/DESTv1/UA_Kie_Cho_1_2014-09-13/UA_Kie_Cho_1_2014-09-13.sorted_merged.bam] OUTPUT=/project/berglandlab/DEST/dest_mapped/DESTv1/UA_Kie_Cho_1_2014-09-13/UA_Kie_Cho_1_2014-09-13.dedup.bam METRICS_FILE=/project/berglandlab/DEST/dest_mapped/DESTv1/UA_Kie_Cho_1_2014-09-13/UA_Kie_Cho_1_2014-09-13.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 08:53:29 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 4210099 24176702 0 0 1011417 698988 0 0.045838 410015357 ## HISTOGRAM java.lang.Double BIN VALUE all_sets non_optical_sets 1.0 1 22513492 22513492 2.0 1.942739 528609 528609 3.0 2.831497 11051 11051 4.0 3.669364 846 846 5.0 4.459254 430 430 6.0 5.203915 287 287 7.0 5.905935 223 223 8.0 6.567758 182 182 9.0 7.191685 139 139 10.0 7.779885 122 122 11.0 8.334404 116 116 12.0 8.857171 119 119 13.0 9.350005 82 82 14.0 9.814618 66 66 15.0 10.252627 91 91 16.0 10.665556 83 83 17.0 11.05484 53 53 18.0 11.421834 69 69 19.0 11.767813 46 46 20.0 12.093981 49 49 21.0 12.401473 53 53 22.0 12.691358 34 34 23.0 12.964643 44 44 24.0 13.22228 31 31 25.0 13.465165 33 33 26.0 13.694142 32 32 27.0 13.910007 43 43 28.0 14.113512 29 29 29.0 14.305365 43 43 30.0 14.486231 34 34 31.0 14.656741 29 29 32.0 14.817488 21 21 33.0 14.96903 14 14 34.0 15.111895 28 28 35.0 15.246579 17 17 36.0 15.373551 15 15 37.0 15.493253 27 27 38.0 15.6061 19 19 39.0 15.712486 17 17 40.0 15.81278 14 14 41.0 15.907331 20 20 42.0 15.996469 16 16 43.0 16.080502 17 17 44.0 16.159723 14 14 45.0 16.234408 19 19 46.0 16.304816 19 19 47.0 16.371193 13 13 48.0 16.433769 8 8 49.0 16.492762 17 17 50.0 16.548377 10 10 51.0 16.600808 16 16 52.0 16.650236 13 13 53.0 16.696834 14 14 54.0 16.740764 9 9 55.0 16.782178 13 13 56.0 16.821221 9 9 57.0 16.858028 7 7 58.0 16.892728 10 10 59.0 16.925441 12 12 60.0 16.95628 13 13 61.0 16.985354 6 6 62.0 17.012763 7 7 63.0 17.038602 9 9 64.0 17.062962 5 5 65.0 17.085927 9 9 66.0 17.107577 7 7 67.0 17.127987 9 9 68.0 17.147229 7 7 69.0 17.165369 3 3 70.0 17.18247 9 9 71.0 17.198592 6 6 72.0 17.213791 8 8 73.0 17.228119 6 6 74.0 17.241627 8 8 75.0 17.254362 9 9 76.0 17.266367 3 3 77.0 17.277685 2 2 78.0 17.288355 3 3 79.0 17.298414 3 3 80.0 17.307897 8 8 81.0 17.316837 5 5 82.0 17.325265 8 8 83.0 17.33321 9 9 84.0 17.340701 8 8 85.0 17.347762 6 6 86.0 17.354419 5 5 87.0 17.360695 9 9 88.0 17.366612 7 7 89.0 17.37219 6 6 90.0 17.377448 5 5 91.0 17.382406 6 6 92.0 17.387079 5 5 93.0 17.391485 7 7 94.0 17.395639 4 4 95.0 17.399555 5 5 96.0 17.403246 2 2 97.0 17.406726 1 1 98.0 17.410007 6 6 99.0 17.4131 4 4 100.0 17.416016 9 9 101.0 0 5 5 102.0 0 8 8 103.0 0 4 4 104.0 0 4 4 105.0 0 3 3 106.0 0 2 2 107.0 0 5 5 108.0 0 6 6 109.0 0 6 6 110.0 0 2 2 111.0 0 3 3 112.0 0 3 3 113.0 0 6 6 114.0 0 1 1 115.0 0 5 5 116.0 0 3 3 117.0 0 2 2 118.0 0 3 3 119.0 0 4 4 120.0 0 3 3 121.0 0 3 3 122.0 0 3 3 123.0 0 3 3 125.0 0 2 2 126.0 0 3 3 127.0 0 3 3 128.0 0 2 2 129.0 0 2 2 130.0 0 2 2 131.0 0 1 1 132.0 0 2 2 133.0 0 1 1 134.0 0 4 4 135.0 0 3 3 136.0 0 3 3 137.0 0 4 4 138.0 0 3 3 139.0 0 1 1 140.0 0 4 4 142.0 0 3 3 143.0 0 3 3 144.0 0 3 3 145.0 0 3 3 147.0 0 1 1 148.0 0 1 1 149.0 0 1 1 150.0 0 3 3 151.0 0 3 3 152.0 0 2 2 154.0 0 2 2 155.0 0 6 6 156.0 0 2 2 157.0 0 1 1 159.0 0 2 2 161.0 0 4 4 162.0 0 4 4 163.0 0 1 1 165.0 0 4 4 166.0 0 1 1 168.0 0 1 1 169.0 0 4 4 171.0 0 2 2 172.0 0 1 1 173.0 0 1 1 175.0 0 1 1 176.0 0 1 1 177.0 0 2 2 178.0 0 4 4 179.0 0 3 3 180.0 0 2 2 181.0 0 2 2 183.0 0 2 2 184.0 0 2 2 185.0 0 1 1 186.0 0 2 2 187.0 0 1 1 189.0 0 1 1 191.0 0 1 1 192.0 0 2 2 193.0 0 2 2 194.0 0 1 1 195.0 0 4 4 197.0 0 1 1 198.0 0 1 1 199.0 0 3 3 200.0 0 1 1 201.0 0 3 3 202.0 0 1 1 203.0 0 1 1 204.0 0 1 1 205.0 0 3 3 206.0 0 1 1 208.0 0 3 3 209.0 0 2 2 210.0 0 1 1 213.0 0 2 2 214.0 0 1 1 215.0 0 1 1 217.0 0 1 1 218.0 0 4 4 219.0 0 2 2 220.0 0 1 1 224.0 0 2 2 225.0 0 1 1 228.0 0 1 1 229.0 0 1 1 230.0 0 2 2 231.0 0 2 2 232.0 0 1 1 234.0 0 3 3 236.0 0 1 1 237.0 0 1 1 243.0 0 1 1 244.0 0 2 2 246.0 0 1 1 248.0 0 1 1 249.0 0 3 3 250.0 0 1 1 251.0 0 2 2 252.0 0 1 1 257.0 0 1 1 258.0 0 1 1 260.0 0 1 1 262.0 0 3 3 265.0 0 1 1 266.0 0 1 1 267.0 0 1 1 268.0 0 1 1 269.0 0 1 1 272.0 0 2 2 273.0 0 2 2 277.0 0 1 1 278.0 0 2 2 279.0 0 1 1 280.0 0 2 2 281.0 0 2 2 282.0 0 1 1 285.0 0 1 1 287.0 0 1 1 289.0 0 1 1 291.0 0 2 2 293.0 0 1 1 294.0 0 1 1 297.0 0 1 1 299.0 0 1 1 301.0 0 1 1 304.0 0 1 1 314.0 0 1 1 316.0 0 1 1 319.0 0 1 1 320.0 0 1 1 322.0 0 1 1 323.0 0 2 2 327.0 0 1 1 329.0 0 1 1 333.0 0 1 1 334.0 0 1 1 337.0 0 1 1 339.0 0 1 1 345.0 0 2 2 346.0 0 1 1 349.0 0 1 1 354.0 0 1 1 356.0 0 1 1 360.0 0 1 1 372.0 0 2 2 374.0 0 1 1 375.0 0 1 1 378.0 0 2 2 379.0 0 2 2 381.0 0 1 1 390.0 0 1 1 396.0 0 1 1 398.0 0 1 1 403.0 0 1 1 406.0 0 1 1 407.0 0 1 1 409.0 0 1 1 425.0 0 1 1 436.0 0 1 1 445.0 0 1 1 453.0 0 1 1 460.0 0 1 1 465.0 0 1 1 470.0 0 1 1 477.0 0 1 1 483.0 0 1 1 488.0 0 1 1 496.0 0 1 1 500.0 0 1 1 501.0 0 1 1 505.0 0 1 1 524.0 0 1 1 525.0 0 1 1 538.0 0 1 1 542.0 0 1 1 580.0 0 1 1 588.0 0 1 1 634.0 0 1 1 681.0 0 1 1 787.0 0 1 1 818.0 0 1 1