## htsjdk.samtools.metrics.StringHeader # MarkDuplicates INPUT=[/project/berglandlab/DEST/dest_mapped/DESTv1/US_Pen_Sta_1_2014-10-16/US_Pen_Sta_1_2014-10-16.sorted_merged.bam] OUTPUT=/project/berglandlab/DEST/dest_mapped/DESTv1/US_Pen_Sta_1_2014-10-16/US_Pen_Sta_1_2014-10-16.dedup.bam METRICS_FILE=/project/berglandlab/DEST/dest_mapped/DESTv1/US_Pen_Sta_1_2014-10-16/US_Pen_Sta_1_2014-10-16.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 22:19:44 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 772458 60398088 0 0 444962 24540699 0 0.407394 52417148 ## HISTOGRAM java.lang.Double BIN VALUE all_sets non_optical_sets 1.0 1 19016584 19016584 2.0 1.315923 9603248 9603248 3.0 1.41573 3958068 3958068 4.0 1.447261 1388330 1388330 5.0 1.457222 433014 433014 6.0 1.460369 124631 124631 7.0 1.461364 35234 35234 8.0 1.461678 10268 10268 9.0 1.461777 3567 3567 10.0 1.461808 1638 1638 11.0 1.461818 1000 1000 12.0 1.461821 696 696 13.0 1.461822 477 477 14.0 1.461823 404 404 15.0 1.461823 311 311 16.0 1.461823 300 300 17.0 1.461823 227 227 18.0 1.461823 213 213 19.0 1.461823 189 189 20.0 1.461823 147 147 21.0 1.461823 134 134 22.0 1.461823 127 127 23.0 1.461823 123 123 24.0 1.461823 109 109 25.0 1.461823 90 90 26.0 1.461823 80 80 27.0 1.461823 78 78 28.0 1.461823 68 68 29.0 1.461823 55 55 30.0 1.461823 55 55 31.0 1.461823 55 55 32.0 1.461823 49 49 33.0 1.461823 42 42 34.0 1.461823 57 57 35.0 1.461823 46 46 36.0 1.461823 38 38 37.0 1.461823 40 40 38.0 1.461823 36 36 39.0 1.461823 21 21 40.0 1.461823 30 30 41.0 1.461823 38 38 42.0 1.461823 31 31 43.0 1.461823 24 24 44.0 1.461823 21 21 45.0 1.461823 21 21 46.0 1.461823 15 15 47.0 1.461823 18 18 48.0 1.461823 13 13 49.0 1.461823 27 27 50.0 1.461823 18 18 51.0 1.461823 24 24 52.0 1.461823 17 17 53.0 1.461823 14 14 54.0 1.461823 16 16 55.0 1.461823 13 13 56.0 1.461823 22 22 57.0 1.461823 19 19 58.0 1.461823 8 8 59.0 1.461823 13 13 60.0 1.461823 11 11 61.0 1.461823 12 12 62.0 1.461823 18 18 63.0 1.461823 9 9 64.0 1.461823 9 9 65.0 1.461823 19 19 66.0 1.461823 9 9 67.0 1.461823 12 12 68.0 1.461823 16 16 69.0 1.461823 9 9 70.0 1.461823 16 16 71.0 1.461823 7 7 72.0 1.461823 5 5 73.0 1.461823 7 7 74.0 1.461823 4 4 75.0 1.461823 7 7 76.0 1.461823 3 3 77.0 1.461823 9 9 78.0 1.461823 6 6 79.0 1.461823 5 5 80.0 1.461823 5 5 81.0 1.461823 3 3 82.0 1.461823 6 6 83.0 1.461823 3 3 84.0 1.461823 4 4 85.0 1.461823 4 4 86.0 1.461823 8 8 87.0 1.461823 6 6 88.0 1.461823 3 3 89.0 1.461823 5 5 90.0 1.461823 5 5 91.0 1.461823 4 4 92.0 1.461823 4 4 93.0 1.461823 4 4 94.0 1.461823 7 7 95.0 1.461823 3 3 96.0 1.461823 3 3 97.0 1.461823 4 4 98.0 1.461823 4 4 99.0 1.461823 3 3 100.0 1.461823 3 3 101.0 0 1 1 103.0 0 4 4 104.0 0 4 4 105.0 0 2 2 106.0 0 5 5 107.0 0 4 4 108.0 0 2 2 109.0 0 3 3 110.0 0 1 1 111.0 0 6 6 112.0 0 5 5 113.0 0 2 2 114.0 0 5 5 115.0 0 4 4 116.0 0 1 1 120.0 0 1 1 121.0 0 4 4 122.0 0 2 2 124.0 0 3 3 125.0 0 3 3 127.0 0 1 1 128.0 0 6 6 130.0 0 3 3 131.0 0 2 2 132.0 0 2 2 133.0 0 3 3 134.0 0 3 3 135.0 0 1 1 136.0 0 1 1 137.0 0 1 1 138.0 0 3 3 139.0 0 2 2 140.0 0 1 1 143.0 0 2 2 144.0 0 1 1 145.0 0 1 1 146.0 0 1 1 148.0 0 1 1 151.0 0 1 1 152.0 0 5 5 153.0 0 1 1 154.0 0 1 1 157.0 0 1 1 158.0 0 1 1 160.0 0 1 1 161.0 0 2 2 162.0 0 2 2 164.0 0 1 1 165.0 0 2 2 166.0 0 1 1 167.0 0 3 3 168.0 0 2 2 169.0 0 1 1 173.0 0 1 1 174.0 0 1 1 178.0 0 1 1 180.0 0 4 4 181.0 0 1 1 182.0 0 1 1 185.0 0 3 3 188.0 0 2 2 193.0 0 1 1 194.0 0 2 2 196.0 0 3 3 197.0 0 1 1 198.0 0 2 2 201.0 0 2 2 204.0 0 1 1 208.0 0 1 1 211.0 0 3 3 213.0 0 2 2 214.0 0 2 2 215.0 0 1 1 217.0 0 2 2 218.0 0 1 1 222.0 0 2 2 229.0 0 2 2 230.0 0 1 1 231.0 0 1 1 238.0 0 1 1 240.0 0 1 1 241.0 0 1 1 242.0 0 1 1 245.0 0 1 1 249.0 0 1 1 250.0 0 2 2 260.0 0 2 2 262.0 0 1 1 272.0 0 1 1 274.0 0 1 1 276.0 0 1 1 281.0 0 1 1 282.0 0 1 1 285.0 0 1 1 288.0 0 1 1 291.0 0 1 1 295.0 0 1 1 297.0 0 2 2 298.0 0 2 2 303.0 0 1 1 306.0 0 1 1 307.0 0 1 1 308.0 0 1 1 310.0 0 1 1 311.0 0 1 1 316.0 0 1 1 319.0 0 1 1 320.0 0 1 1 333.0 0 1 1 335.0 0 1 1 337.0 0 1 1 344.0 0 1 1 348.0 0 1 1 352.0 0 1 1 357.0 0 2 2 361.0 0 1 1 363.0 0 1 1 366.0 0 1 1 367.0 0 1 1 370.0 0 1 1 373.0 0 1 1 380.0 0 1 1 383.0 0 1 1 385.0 0 1 1 390.0 0 1 1 391.0 0 2 2 395.0 0 1 1 423.0 0 1 1 424.0 0 1 1 427.0 0 1 1 428.0 0 1 1 437.0 0 1 1 438.0 0 1 1 439.0 0 1 1 448.0 0 2 2 466.0 0 1 1 471.0 0 1 1 473.0 0 1 1 477.0 0 1 1 504.0 0 1 1 507.0 0 1 1 579.0 0 1 1 583.0 0 1 1