## htsjdk.samtools.metrics.StringHeader # MarkDuplicates INPUT=[/project/berglandlab/DEST/dest_mapped/DESTv1/UA_Che_Uma_1_2016-09-17/UA_Che_Uma_1_2016-09-17.sorted_merged.bam] OUTPUT=/project/berglandlab/DEST/dest_mapped/DESTv1/UA_Che_Uma_1_2016-09-17/UA_Che_Uma_1_2016-09-17.dedup.bam METRICS_FILE=/project/berglandlab/DEST/dest_mapped/DESTv1/UA_Che_Uma_1_2016-09-17/UA_Che_Uma_1_2016-09-17.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 08:43:23 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 19441893 7897130 0 0 3853843 661795 0 0.146935 44446925 ## HISTOGRAM java.lang.Double BIN VALUE all_sets non_optical_sets 1.0 1 6545986 6545986 2.0 1.837214 431091 431091 3.0 2.538141 33177 33177 4.0 3.124968 4191 4191 5.0 3.616267 1405 1405 6.0 4.027589 836 836 7.0 4.371954 621 621 8.0 4.660262 471 471 9.0 4.901637 364 364 10.0 5.103719 259 259 11.0 5.272905 236 236 12.0 5.41455 234 234 13.0 5.533138 184 184 14.0 5.632421 160 160 15.0 5.715542 121 121 16.0 5.785132 149 149 17.0 5.843394 133 133 18.0 5.892171 124 124 19.0 5.933008 112 112 20.0 5.967198 89 89 21.0 5.995822 91 91 22.0 6.019786 86 86 23.0 6.03985 83 83 24.0 6.056647 76 76 25.0 6.07071 67 67 26.0 6.082484 56 56 27.0 6.092341 66 66 28.0 6.100593 47 47 29.0 6.107502 55 55 30.0 6.113287 58 58 31.0 6.11813 50 50 32.0 6.122184 44 44 33.0 6.125578 31 31 34.0 6.12842 46 46 35.0 6.1308 28 28 36.0 6.132792 33 33 37.0 6.134459 32 32 38.0 6.135855 23 23 39.0 6.137024 29 29 40.0 6.138003 28 28 41.0 6.138822 20 20 42.0 6.139508 29 29 43.0 6.140083 21 21 44.0 6.140563 22 22 45.0 6.140966 15 15 46.0 6.141303 14 14 47.0 6.141585 19 19 48.0 6.141821 17 17 49.0 6.142019 20 20 50.0 6.142185 24 24 51.0 6.142323 21 21 52.0 6.142439 10 10 53.0 6.142537 17 17 54.0 6.142618 22 22 55.0 6.142686 17 17 56.0 6.142743 15 15 57.0 6.142791 10 10 58.0 6.142831 14 14 59.0 6.142864 12 12 60.0 6.142892 9 9 61.0 6.142916 12 12 62.0 6.142935 15 15 63.0 6.142952 7 7 64.0 6.142965 13 13 65.0 6.142977 13 13 66.0 6.142987 10 10 67.0 6.142995 6 6 68.0 6.143001 10 10 69.0 6.143007 9 9 70.0 6.143012 11 11 71.0 6.143016 11 11 72.0 6.143019 8 8 73.0 6.143022 12 12 74.0 6.143024 9 9 75.0 6.143026 5 5 76.0 6.143028 8 8 77.0 6.143029 11 11 78.0 6.14303 9 9 79.0 6.143031 7 7 80.0 6.143032 13 13 81.0 6.143033 14 14 82.0 6.143033 6 6 83.0 6.143034 5 5 84.0 6.143034 3 3 85.0 6.143035 8 8 86.0 6.143035 6 6 87.0 6.143035 7 7 88.0 6.143035 7 7 89.0 6.143035 10 10 90.0 6.143036 3 3 91.0 6.143036 4 4 92.0 6.143036 9 9 93.0 6.143036 11 11 94.0 6.143036 5 5 95.0 6.143036 5 5 96.0 6.143036 5 5 97.0 6.143036 3 3 98.0 6.143036 3 3 99.0 6.143036 5 5 100.0 6.143036 6 6 101.0 0 2 2 102.0 0 5 5 103.0 0 1 1 104.0 0 3 3 105.0 0 4 4 106.0 0 3 3 107.0 0 6 6 108.0 0 3 3 109.0 0 2 2 110.0 0 3 3 111.0 0 5 5 112.0 0 6 6 113.0 0 2 2 114.0 0 2 2 115.0 0 4 4 116.0 0 4 4 117.0 0 2 2 119.0 0 2 2 120.0 0 3 3 122.0 0 2 2 123.0 0 2 2 124.0 0 4 4 125.0 0 1 1 127.0 0 1 1 128.0 0 2 2 129.0 0 4 4 130.0 0 1 1 131.0 0 2 2 132.0 0 3 3 133.0 0 1 1 134.0 0 1 1 135.0 0 3 3 136.0 0 4 4 137.0 0 1 1 139.0 0 1 1 140.0 0 3 3 141.0 0 2 2 143.0 0 2 2 144.0 0 4 4 145.0 0 1 1 146.0 0 1 1 147.0 0 2 2 150.0 0 1 1 151.0 0 1 1 152.0 0 1 1 153.0 0 2 2 154.0 0 3 3 155.0 0 2 2 156.0 0 2 2 158.0 0 1 1 159.0 0 1 1 161.0 0 1 1 167.0 0 1 1 168.0 0 3 3 169.0 0 1 1 170.0 0 1 1 171.0 0 1 1 173.0 0 2 2 175.0 0 1 1 182.0 0 2 2 183.0 0 1 1 184.0 0 2 2 185.0 0 1 1 187.0 0 1 1 188.0 0 2 2 189.0 0 2 2 191.0 0 2 2 197.0 0 1 1 201.0 0 2 2 207.0 0 1 1 209.0 0 1 1 212.0 0 1 1 213.0 0 2 2 215.0 0 1 1 216.0 0 1 1 219.0 0 1 1 223.0 0 1 1 224.0 0 1 1 227.0 0 1 1 230.0 0 2 2 237.0 0 1 1 240.0 0 1 1 245.0 0 1 1 247.0 0 2 2 249.0 0 1 1 250.0 0 1 1 251.0 0 1 1 252.0 0 1 1 257.0 0 1 1 260.0 0 1 1 261.0 0 1 1 263.0 0 1 1 267.0 0 1 1 273.0 0 2 2 283.0 0 2 2 284.0 0 1 1 286.0 0 1 1 291.0 0 1 1 297.0 0 1 1 300.0 0 1 1 305.0 0 1 1 309.0 0 1 1 310.0 0 1 1 312.0 0 1 1 322.0 0 1 1 325.0 0 1 1 348.0 0 1 1 359.0 0 1 1 378.0 0 1 1 398.0 0 1 1 412.0 0 1 1 431.0 0 1 1 483.0 0 1 1 524.0 0 1 1 574.0 0 2 2 600.0 0 1 1 1070.0 0 1 1 1801.0 0 1 1