## htsjdk.samtools.metrics.StringHeader # MarkDuplicates INPUT=[/project/berglandlab/DEST/dest_mapped/DESTv1/AT_Nie_Mau_1_2015-10-19/AT_Nie_Mau_1_2015-10-19.sorted_merged.bam] OUTPUT=/project/berglandlab/DEST/dest_mapped/DESTv1/AT_Nie_Mau_1_2015-10-19/AT_Nie_Mau_1_2015-10-19.dedup.bam METRICS_FILE=/project/berglandlab/DEST/dest_mapped/DESTv1/AT_Nie_Mau_1_2015-10-19/AT_Nie_Mau_1_2015-10-19.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 09:24:29 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 10312266 35833410 0 0 4089601 4090937 0 0.14969 144749595 ## HISTOGRAM java.lang.Double BIN VALUE all_sets non_optical_sets 1.0 1 27787496 27787496 2.0 1.780708 3219550 3219550 3.0 2.390212 337054 337054 4.0 2.866057 34287 34287 5.0 3.237553 4064 4064 6.0 3.527582 814 814 7.0 3.754011 405 405 8.0 3.930785 280 280 9.0 4.068794 225 225 10.0 4.176539 210 210 11.0 4.260656 187 187 12.0 4.326327 142 142 13.0 4.377597 135 135 14.0 4.417623 125 125 15.0 4.448873 112 112 16.0 4.473269 83 83 17.0 4.492316 99 99 18.0 4.507185 83 83 19.0 4.518794 78 78 20.0 4.527857 76 76 21.0 4.534933 63 63 22.0 4.540457 79 79 23.0 4.54477 52 52 24.0 4.548137 56 56 25.0 4.550765 58 58 26.0 4.552817 50 50 27.0 4.55442 33 33 28.0 4.55567 38 38 29.0 4.556647 40 40 30.0 4.557409 37 37 31.0 4.558004 33 33 32.0 4.558469 30 30 33.0 4.558832 31 31 34.0 4.559115 27 27 35.0 4.559336 26 26 36.0 4.559509 27 27 37.0 4.559644 18 18 38.0 4.559749 21 21 39.0 4.559831 15 15 40.0 4.559895 13 13 41.0 4.559945 19 19 42.0 4.559984 13 13 43.0 4.560015 15 15 44.0 4.560039 18 18 45.0 4.560057 17 17 46.0 4.560072 16 16 47.0 4.560083 11 11 48.0 4.560092 12 12 49.0 4.560099 8 8 50.0 4.560104 13 13 51.0 4.560108 7 7 52.0 4.560112 8 8 53.0 4.560114 14 14 54.0 4.560116 9 9 55.0 4.560118 5 5 56.0 4.560119 14 14 57.0 4.56012 8 8 58.0 4.560121 5 5 59.0 4.560121 6 6 60.0 4.560122 5 5 61.0 4.560122 10 10 62.0 4.560122 3 3 63.0 4.560123 9 9 64.0 4.560123 4 4 65.0 4.560123 9 9 66.0 4.560123 3 3 67.0 4.560123 5 5 68.0 4.560123 4 4 69.0 4.560123 6 6 70.0 4.560123 8 8 71.0 4.560123 7 7 72.0 4.560123 1 1 73.0 4.560123 4 4 74.0 4.560123 2 2 75.0 4.560123 2 2 76.0 4.560123 7 7 77.0 4.560123 3 3 78.0 4.560123 3 3 79.0 4.560123 6 6 80.0 4.560123 7 7 81.0 4.560123 1 1 82.0 4.560123 2 2 83.0 4.560123 2 2 84.0 4.560123 2 2 85.0 4.560123 1 1 86.0 4.560123 2 2 87.0 4.560123 5 5 88.0 4.560123 3 3 89.0 4.560123 3 3 90.0 4.560123 3 3 91.0 4.560123 2 2 92.0 4.560123 3 3 93.0 4.560123 4 4 94.0 4.560123 2 2 95.0 4.560123 4 4 96.0 4.560123 5 5 97.0 4.560123 4 4 98.0 4.560123 0 0 99.0 4.560123 5 5 100.0 4.560123 1 1 101.0 0 1 1 102.0 0 3 3 103.0 0 2 2 104.0 0 1 1 105.0 0 1 1 106.0 0 1 1 107.0 0 4 4 108.0 0 5 5 109.0 0 1 1 110.0 0 1 1 113.0 0 1 1 114.0 0 1 1 120.0 0 1 1 122.0 0 2 2 123.0 0 1 1 127.0 0 1 1 128.0 0 2 2 130.0 0 1 1 131.0 0 1 1 135.0 0 1 1 136.0 0 1 1 138.0 0 1 1 146.0 0 1 1 148.0 0 1 1 149.0 0 1 1 150.0 0 1 1 153.0 0 1 1 155.0 0 1 1 168.0 0 1 1 175.0 0 2 2 192.0 0 1 1 202.0 0 1 1 206.0 0 1 1 218.0 0 1 1 252.0 0 1 1 254.0 0 1 1 273.0 0 1 1 289.0 0 1 1 305.0 0 1 1 452.0 0 1 1