## htsjdk.samtools.metrics.StringHeader # MarkDuplicates INPUT=[/project/berglandlab/DEST/dest_mapped/DESTv1/UA_Ode_Ode_1_2015-07-26/UA_Ode_Ode_1_2015-07-26.sorted_merged.bam] OUTPUT=/project/berglandlab/DEST/dest_mapped/DESTv1/UA_Ode_Ode_1_2015-07-26/UA_Ode_Ode_1_2015-07-26.dedup.bam METRICS_FILE=/project/berglandlab/DEST/dest_mapped/DESTv1/UA_Ode_Ode_1_2015-07-26/UA_Ode_Ode_1_2015-07-26.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 17:25:55 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 28691798 11001151 0 0 7391103 947747 0 0.183189 60126690 ## HISTOGRAM java.lang.Double BIN VALUE all_sets non_optical_sets 1.0 1 9091904 9091904 2.0 1.832796 613703 613703 3.0 2.526346 48242 48242 4.0 3.103932 5884 5884 5.0 3.584943 1931 1931 6.0 3.985527 1184 1184 7.0 4.319132 829 829 8.0 4.596958 638 638 9.0 4.828329 449 449 10.0 5.021015 367 367 11.0 5.181483 315 315 12.0 5.31512 259 259 13.0 5.426412 218 218 14.0 5.519096 203 203 15.0 5.596283 181 181 16.0 5.660564 167 167 17.0 5.714097 124 124 18.0 5.758679 140 140 19.0 5.795806 130 130 20.0 5.826726 110 110 21.0 5.852476 118 118 22.0 5.873921 91 91 23.0 5.891779 97 97 24.0 5.906652 87 87 25.0 5.919038 83 83 26.0 5.929353 84 84 27.0 5.937944 69 69 28.0 5.945097 64 64 29.0 5.951055 70 70 30.0 5.956017 55 55 31.0 5.960149 66 66 32.0 5.96359 66 66 33.0 5.966456 51 51 34.0 5.968842 34 34 35.0 5.97083 44 44 36.0 5.972485 50 50 37.0 5.973864 43 43 38.0 5.975012 48 48 39.0 5.975968 42 42 40.0 5.976764 38 38 41.0 5.977427 33 33 42.0 5.977979 22 22 43.0 5.978439 27 27 44.0 5.978822 22 22 45.0 5.979141 23 23 46.0 5.979407 28 28 47.0 5.979628 23 23 48.0 5.979812 24 24 49.0 5.979965 27 27 50.0 5.980093 16 16 51.0 5.9802 15 15 52.0 5.980288 17 17 53.0 5.980362 19 19 54.0 5.980423 26 26 55.0 5.980475 19 19 56.0 5.980517 14 14 57.0 5.980553 18 18 58.0 5.980582 15 15 59.0 5.980607 12 12 60.0 5.980627 17 17 61.0 5.980644 13 13 62.0 5.980659 15 15 63.0 5.980671 14 14 64.0 5.98068 11 11 65.0 5.980689 12 12 66.0 5.980695 15 15 67.0 5.980701 19 19 68.0 5.980706 12 12 69.0 5.98071 11 11 70.0 5.980713 15 15 71.0 5.980716 9 9 72.0 5.980718 11 11 73.0 5.98072 13 13 74.0 5.980722 15 15 75.0 5.980723 9 9 76.0 5.980724 5 5 77.0 5.980725 10 10 78.0 5.980726 10 10 79.0 5.980726 8 8 80.0 5.980727 11 11 81.0 5.980727 8 8 82.0 5.980728 8 8 83.0 5.980728 14 14 84.0 5.980728 10 10 85.0 5.980728 9 9 86.0 5.980729 6 6 87.0 5.980729 5 5 88.0 5.980729 7 7 89.0 5.980729 5 5 90.0 5.980729 9 9 91.0 5.980729 10 10 92.0 5.980729 4 4 93.0 5.980729 8 8 94.0 5.980729 6 6 95.0 5.980729 10 10 96.0 5.980729 10 10 97.0 5.980729 9 9 98.0 5.980729 11 11 99.0 5.980729 4 4 100.0 5.980729 4 4 101.0 0 7 7 102.0 0 10 10 103.0 0 7 7 104.0 0 5 5 105.0 0 8 8 106.0 0 4 4 107.0 0 6 6 108.0 0 5 5 109.0 0 4 4 110.0 0 4 4 111.0 0 6 6 112.0 0 7 7 113.0 0 3 3 114.0 0 2 2 115.0 0 1 1 116.0 0 5 5 117.0 0 5 5 118.0 0 3 3 119.0 0 6 6 120.0 0 4 4 121.0 0 7 7 122.0 0 6 6 123.0 0 2 2 124.0 0 7 7 125.0 0 2 2 126.0 0 3 3 127.0 0 6 6 128.0 0 3 3 129.0 0 5 5 130.0 0 2 2 131.0 0 1 1 132.0 0 2 2 133.0 0 4 4 134.0 0 3 3 135.0 0 5 5 136.0 0 5 5 137.0 0 5 5 138.0 0 2 2 139.0 0 4 4 141.0 0 1 1 142.0 0 6 6 143.0 0 5 5 144.0 0 2 2 145.0 0 1 1 146.0 0 2 2 147.0 0 3 3 148.0 0 3 3 149.0 0 5 5 150.0 0 3 3 151.0 0 3 3 152.0 0 3 3 153.0 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 2 2 161.0 0 1 1 162.0 0 2 2 163.0 0 1 1 164.0 0 1 1 165.0 0 1 1 167.0 0 1 1 168.0 0 1 1 170.0 0 2 2 171.0 0 2 2 173.0 0 1 1 174.0 0 1 1 175.0 0 2 2 177.0 0 2 2 178.0 0 3 3 179.0 0 1 1 180.0 0 1 1 182.0 0 2 2 183.0 0 1 1 184.0 0 3 3 187.0 0 1 1 192.0 0 1 1 193.0 0 1 1 194.0 0 1 1 196.0 0 1 1 197.0 0 3 3 198.0 0 2 2 201.0 0 1 1 202.0 0 1 1 205.0 0 1 1 208.0 0 2 2 212.0 0 3 3 213.0 0 2 2 214.0 0 2 2 215.0 0 1 1 216.0 0 1 1 218.0 0 1 1 219.0 0 4 4 223.0 0 2 2 224.0 0 1 1 225.0 0 1 1 229.0 0 1 1 233.0 0 1 1 234.0 0 2 2 237.0 0 1 1 238.0 0 2 2 239.0 0 1 1 240.0 0 1 1 241.0 0 2 2 242.0 0 2 2 243.0 0 1 1 244.0 0 1 1 256.0 0 2 2 258.0 0 1 1 259.0 0 1 1 263.0 0 1 1 265.0 0 1 1 266.0 0 3 3 269.0 0 1 1 271.0 0 1 1 272.0 0 1 1 276.0 0 1 1 278.0 0 1 1 282.0 0 2 2 283.0 0 1 1 287.0 0 1 1 288.0 0 3 3 289.0 0 1 1 292.0 0 2 2 295.0 0 2 2 302.0 0 1 1 305.0 0 1 1 306.0 0 3 3 311.0 0 1 1 313.0 0 1 1 314.0 0 1 1 319.0 0 2 2 324.0 0 1 1 327.0 0 1 1 328.0 0 1 1 330.0 0 2 2 331.0 0 1 1 332.0 0 1 1 339.0 0 1 1 341.0 0 1 1 346.0 0 1 1 355.0 0 1 1 361.0 0 1 1 372.0 0 1 1 381.0 0 1 1 387.0 0 1 1 389.0 0 1 1 396.0 0 1 1 409.0 0 1 1 419.0 0 1 1 433.0 0 1 1 434.0 0 1 1 454.0 0 1 1 460.0 0 1 1 471.0 0 1 1 473.0 0 2 2 484.0 0 1 1 500.0 0 1 1 510.0 0 1 1 520.0 0 1 1 567.0 0 1 1 574.0 0 1 1 576.0 0 1 1 595.0 0 1 1 609.0 0 1 1 643.0 0 1 1 677.0 0 1 1 828.0 0 1 1 896.0 0 1 1 911.0 0 1 1 979.0 0 1 1 1827.0 0 1 1 3394.0 0 1 1