## htsjdk.samtools.metrics.StringHeader # MarkDuplicates INPUT=[/project/berglandlab/DEST/dest_mapped/DESTv1/UA_Ode_Ode_1_2016-09-15/UA_Ode_Ode_1_2016-09-15.sorted_merged.bam] OUTPUT=/project/berglandlab/DEST/dest_mapped/DESTv1/UA_Ode_Ode_1_2016-09-15/UA_Ode_Ode_1_2016-09-15.dedup.bam METRICS_FILE=/project/berglandlab/DEST/dest_mapped/DESTv1/UA_Ode_Ode_1_2016-09-15/UA_Ode_Ode_1_2016-09-15.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 17:31:44 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 27542373 8163095 0 0 6516025 702377 0 0.180557 44674195 ## HISTOGRAM java.lang.Double BIN VALUE all_sets non_optical_sets 1.0 1 6745813 6745813 2.0 1.832997 419786 419786 3.0 2.526881 32377 32377 4.0 3.104885 4434 4434 5.0 3.58636 1681 1681 6.0 3.987428 1036 1036 7.0 4.321516 762 762 8.0 4.599811 524 524 9.0 4.831629 376 376 10.0 5.024733 333 333 11.0 5.185588 292 292 12.0 5.31958 214 214 13.0 5.431195 207 207 14.0 5.52417 201 201 15.0 5.601618 163 163 16.0 5.666132 151 151 17.0 5.719872 128 128 18.0 5.764637 101 101 19.0 5.801926 132 132 20.0 5.832988 117 117 21.0 5.858862 109 109 22.0 5.880415 109 109 23.0 5.898369 93 93 24.0 5.913325 98 98 25.0 5.925783 89 89 26.0 5.93616 72 72 27.0 5.944804 63 63 28.0 5.952005 76 76 29.0 5.958003 67 67 30.0 5.963 60 60 31.0 5.967162 41 41 32.0 5.970629 48 48 33.0 5.973517 50 50 34.0 5.975922 44 44 35.0 5.977926 44 44 36.0 5.979596 39 39 37.0 5.980986 34 34 38.0 5.982144 19 19 39.0 5.983109 27 27 40.0 5.983913 37 37 41.0 5.984582 30 30 42.0 5.98514 22 22 43.0 5.985605 23 23 44.0 5.985992 20 20 45.0 5.986314 24 24 46.0 5.986582 28 28 47.0 5.986806 14 14 48.0 5.986992 27 27 49.0 5.987148 20 20 50.0 5.987277 15 15 51.0 5.987385 10 10 52.0 5.987474 26 26 53.0 5.987549 16 16 54.0 5.987611 11 11 55.0 5.987663 15 15 56.0 5.987706 18 18 57.0 5.987742 19 19 58.0 5.987772 12 12 59.0 5.987797 20 20 60.0 5.987818 10 10 61.0 5.987835 14 14 62.0 5.98785 17 17 63.0 5.987862 15 15 64.0 5.987872 16 16 65.0 5.98788 10 10 66.0 5.987887 12 12 67.0 5.987893 12 12 68.0 5.987898 13 13 69.0 5.987902 13 13 70.0 5.987905 11 11 71.0 5.987908 13 13 72.0 5.98791 16 16 73.0 5.987912 13 13 74.0 5.987914 11 11 75.0 5.987915 11 11 76.0 5.987916 8 8 77.0 5.987917 8 8 78.0 5.987918 4 4 79.0 5.987918 12 12 80.0 5.987919 11 11 81.0 5.987919 5 5 82.0 5.98792 6 6 83.0 5.98792 10 10 84.0 5.98792 5 5 85.0 5.987921 6 6 86.0 5.987921 13 13 87.0 5.987921 5 5 88.0 5.987921 8 8 89.0 5.987921 8 8 90.0 5.987921 10 10 91.0 5.987921 9 9 92.0 5.987921 2 2 93.0 5.987921 8 8 94.0 5.987921 8 8 95.0 5.987921 7 7 96.0 5.987922 9 9 97.0 5.987922 4 4 98.0 5.987922 8 8 99.0 5.987922 3 3 100.0 5.987922 6 6 101.0 0 5 5 102.0 0 2 2 103.0 0 4 4 104.0 0 7 7 105.0 0 9 9 106.0 0 3 3 107.0 0 6 6 108.0 0 8 8 109.0 0 3 3 110.0 0 1 1 111.0 0 2 2 112.0 0 5 5 113.0 0 4 4 114.0 0 3 3 115.0 0 3 3 116.0 0 2 2 117.0 0 4 4 118.0 0 2 2 119.0 0 2 2 120.0 0 4 4 121.0 0 6 6 122.0 0 4 4 123.0 0 2 2 124.0 0 2 2 125.0 0 3 3 126.0 0 2 2 127.0 0 4 4 128.0 0 4 4 129.0 0 3 3 130.0 0 3 3 131.0 0 4 4 132.0 0 4 4 133.0 0 6 6 134.0 0 4 4 135.0 0 2 2 136.0 0 4 4 137.0 0 3 3 139.0 0 1 1 140.0 0 2 2 141.0 0 2 2 142.0 0 2 2 143.0 0 1 1 144.0 0 3 3 145.0 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 3 3 151.0 0 1 1 152.0 0 1 1 154.0 0 1 1 155.0 0 3 3 156.0 0 2 2 157.0 0 1 1 159.0 0 1 1 160.0 0 3 3 161.0 0 1 1 163.0 0 3 3 164.0 0 1 1 165.0 0 2 2 166.0 0 1 1 168.0 0 1 1 171.0 0 1 1 172.0 0 2 2 173.0 0 1 1 177.0 0 4 4 178.0 0 1 1 179.0 0 1 1 181.0 0 2 2 182.0 0 1 1 184.0 0 1 1 185.0 0 2 2 186.0 0 2 2 187.0 0 1 1 188.0 0 1 1 189.0 0 3 3 190.0 0 1 1 191.0 0 1 1 192.0 0 1 1 193.0 0 4 4 194.0 0 1 1 195.0 0 2 2 196.0 0 1 1 199.0 0 1 1 201.0 0 1 1 203.0 0 1 1 204.0 0 1 1 205.0 0 1 1 207.0 0 1 1 209.0 0 2 2 211.0 0 1 1 212.0 0 1 1 213.0 0 1 1 215.0 0 1 1 216.0 0 1 1 217.0 0 2 2 219.0 0 2 2 220.0 0 1 1 222.0 0 1 1 223.0 0 1 1 225.0 0 2 2 228.0 0 1 1 231.0 0 1 1 232.0 0 1 1 233.0 0 1 1 234.0 0 2 2 237.0 0 2 2 245.0 0 1 1 247.0 0 1 1 250.0 0 2 2 252.0 0 1 1 255.0 0 1 1 258.0 0 1 1 259.0 0 1 1 260.0 0 1 1 262.0 0 1 1 265.0 0 1 1 270.0 0 2 2 271.0 0 1 1 274.0 0 1 1 275.0 0 2 2 277.0 0 1 1 279.0 0 1 1 280.0 0 1 1 282.0 0 1 1 284.0 0 2 2 286.0 0 1 1 287.0 0 1 1 289.0 0 1 1 292.0 0 1 1 293.0 0 1 1 294.0 0 1 1 298.0 0 1 1 303.0 0 1 1 307.0 0 1 1 309.0 0 1 1 310.0 0 1 1 313.0 0 1 1 314.0 0 1 1 318.0 0 1 1 320.0 0 1 1 326.0 0 1 1 333.0 0 1 1 335.0 0 1 1 338.0 0 1 1 343.0 0 1 1 344.0 0 1 1 345.0 0 1 1 348.0 0 1 1 351.0 0 1 1 358.0 0 1 1 360.0 0 1 1 363.0 0 1 1 366.0 0 1 1 374.0 0 1 1 386.0 0 1 1 402.0 0 1 1 403.0 0 1 1 416.0 0 1 1 427.0 0 1 1 434.0 0 1 1 443.0 0 1 1 448.0 0 1 1 456.0 0 1 1 474.0 0 1 1 491.0 0 1 1 503.0 0 1 1 518.0 0 1 1 528.0 0 1 1 535.0 0 1 1 540.0 0 1 1 624.0 0 1 1 657.0 0 1 1 659.0 0 1 1 673.0 0 1 1 725.0 0 1 1 729.0 0 1 1 816.0 0 1 1 842.0 0 1 1 913.0 0 1 1 924.0 0 1 1 993.0 0 1 1 1094.0 0 1 1 1961.0 0 1 1 4445.0 0 1 1