## htsjdk.samtools.metrics.StringHeader # MarkDuplicates INPUT=[/project/berglandlab/DEST/dest_mapped/DESTv1/UA_Kie_Cho_1_2015-08-26/UA_Kie_Cho_1_2015-08-26.sorted_merged.bam] OUTPUT=/project/berglandlab/DEST/dest_mapped/DESTv1/UA_Kie_Cho_1_2015-08-26/UA_Kie_Cho_1_2015-08-26.dedup.bam METRICS_FILE=/project/berglandlab/DEST/dest_mapped/DESTv1/UA_Kie_Cho_1_2015-08-26/UA_Kie_Cho_1_2015-08-26.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 08:49:01 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 30074923 9048824 0 0 7213152 776178 0 0.181961 49684927 ## HISTOGRAM java.lang.Double BIN VALUE all_sets non_optical_sets 1.0 1 7486154 7486154 2.0 1.833498 479087 479087 3.0 2.528217 37562 37562 4.0 3.107263 4828 4828 5.0 3.589897 1722 1722 6.0 3.992172 1085 1085 7.0 4.327467 717 717 8.0 4.606934 500 500 9.0 4.83987 423 423 10.0 5.034021 356 356 11.0 5.195846 270 270 12.0 5.330727 216 216 13.0 5.443149 188 188 14.0 5.536853 180 180 15.0 5.614955 149 149 16.0 5.680053 149 149 17.0 5.734312 132 132 18.0 5.779537 120 120 19.0 5.817232 119 119 20.0 5.848651 95 95 21.0 5.874838 106 106 22.0 5.896665 114 114 23.0 5.914858 106 106 24.0 5.930021 86 86 25.0 5.94266 83 83 26.0 5.953195 79 79 27.0 5.961975 75 75 28.0 5.969293 69 69 29.0 5.975393 65 65 30.0 5.980478 52 52 31.0 5.984715 60 60 32.0 5.988248 48 48 33.0 5.991192 51 51 34.0 5.993645 33 33 35.0 5.995691 43 43 36.0 5.997396 35 35 37.0 5.998816 35 35 38.0 6.000001 24 24 39.0 6.000988 30 30 40.0 6.001811 30 30 41.0 6.002496 29 29 42.0 6.003068 30 30 43.0 6.003544 32 32 44.0 6.003941 20 20 45.0 6.004272 20 20 46.0 6.004548 28 28 47.0 6.004778 18 18 48.0 6.00497 28 28 49.0 6.00513 21 21 50.0 6.005263 17 17 51.0 6.005374 16 16 52.0 6.005466 13 13 53.0 6.005543 25 25 54.0 6.005608 16 16 55.0 6.005661 13 13 56.0 6.005706 14 14 57.0 6.005743 21 21 58.0 6.005774 20 20 59.0 6.0058 9 9 60.0 6.005821 15 15 61.0 6.005839 11 11 62.0 6.005854 15 15 63.0 6.005867 16 16 64.0 6.005877 12 12 65.0 6.005886 8 8 66.0 6.005893 7 7 67.0 6.005899 19 19 68.0 6.005904 10 10 69.0 6.005908 15 15 70.0 6.005912 9 9 71.0 6.005915 12 12 72.0 6.005917 10 10 73.0 6.005919 13 13 74.0 6.005921 13 13 75.0 6.005922 4 4 76.0 6.005923 16 16 77.0 6.005924 8 8 78.0 6.005925 13 13 79.0 6.005926 7 7 80.0 6.005926 10 10 81.0 6.005927 11 11 82.0 6.005927 5 5 83.0 6.005928 9 9 84.0 6.005928 9 9 85.0 6.005928 9 9 86.0 6.005928 12 12 87.0 6.005929 6 6 88.0 6.005929 7 7 89.0 6.005929 14 14 90.0 6.005929 5 5 91.0 6.005929 12 12 92.0 6.005929 7 7 93.0 6.005929 4 4 94.0 6.005929 10 10 95.0 6.005929 5 5 96.0 6.005929 6 6 97.0 6.005929 7 7 98.0 6.005929 5 5 99.0 6.005929 4 4 100.0 6.005929 8 8 101.0 0 7 7 102.0 0 8 8 103.0 0 7 7 104.0 0 9 9 105.0 0 2 2 106.0 0 6 6 107.0 0 4 4 108.0 0 5 5 109.0 0 4 4 110.0 0 3 3 112.0 0 4 4 113.0 0 1 1 114.0 0 7 7 115.0 0 7 7 116.0 0 1 1 117.0 0 5 5 118.0 0 5 5 119.0 0 1 1 120.0 0 3 3 121.0 0 5 5 122.0 0 4 4 123.0 0 1 1 124.0 0 7 7 125.0 0 3 3 126.0 0 5 5 127.0 0 2 2 128.0 0 3 3 129.0 0 1 1 130.0 0 3 3 131.0 0 2 2 132.0 0 2 2 133.0 0 3 3 134.0 0 4 4 135.0 0 5 5 136.0 0 3 3 137.0 0 2 2 139.0 0 8 8 140.0 0 4 4 141.0 0 4 4 142.0 0 3 3 143.0 0 3 3 144.0 0 2 2 145.0 0 1 1 146.0 0 2 2 147.0 0 4 4 148.0 0 7 7 149.0 0 3 3 150.0 0 2 2 151.0 0 1 1 152.0 0 3 3 153.0 0 4 4 155.0 0 1 1 156.0 0 3 3 158.0 0 4 4 161.0 0 1 1 163.0 0 2 2 164.0 0 1 1 168.0 0 2 2 170.0 0 3 3 171.0 0 3 3 172.0 0 1 1 173.0 0 3 3 174.0 0 2 2 175.0 0 2 2 177.0 0 1 1 178.0 0 2 2 179.0 0 1 1 185.0 0 1 1 186.0 0 3 3 187.0 0 1 1 190.0 0 1 1 191.0 0 1 1 192.0 0 1 1 193.0 0 1 1 194.0 0 1 1 198.0 0 2 2 201.0 0 1 1 202.0 0 1 1 203.0 0 1 1 204.0 0 2 2 205.0 0 3 3 210.0 0 1 1 211.0 0 1 1 212.0 0 2 2 213.0 0 3 3 214.0 0 1 1 216.0 0 1 1 217.0 0 2 2 218.0 0 2 2 221.0 0 1 1 223.0 0 1 1 225.0 0 1 1 229.0 0 1 1 230.0 0 2 2 231.0 0 1 1 233.0 0 1 1 235.0 0 2 2 237.0 0 1 1 238.0 0 1 1 244.0 0 1 1 245.0 0 2 2 246.0 0 2 2 248.0 0 1 1 249.0 0 1 1 251.0 0 1 1 252.0 0 1 1 254.0 0 1 1 257.0 0 1 1 261.0 0 2 2 262.0 0 1 1 264.0 0 1 1 267.0 0 1 1 271.0 0 1 1 273.0 0 1 1 274.0 0 1 1 278.0 0 1 1 283.0 0 1 1 284.0 0 3 3 290.0 0 2 2 293.0 0 1 1 294.0 0 1 1 300.0 0 1 1 301.0 0 1 1 302.0 0 2 2 303.0 0 1 1 304.0 0 1 1 305.0 0 1 1 307.0 0 1 1 311.0 0 1 1 312.0 0 1 1 314.0 0 1 1 315.0 0 1 1 318.0 0 1 1 331.0 0 1 1 338.0 0 1 1 340.0 0 1 1 343.0 0 1 1 345.0 0 1 1 346.0 0 1 1 351.0 0 1 1 353.0 0 1 1 356.0 0 1 1 360.0 0 1 1 364.0 0 1 1 366.0 0 1 1 377.0 0 1 1 381.0 0 1 1 387.0 0 1 1 404.0 0 1 1 427.0 0 2 2 433.0 0 1 1 434.0 0 1 1 436.0 0 1 1 445.0 0 1 1 486.0 0 1 1 500.0 0 1 1 510.0 0 1 1 549.0 0 1 1 552.0 0 1 1 574.0 0 1 1 625.0 0 1 1 632.0 0 1 1 652.0 0 1 1 655.0 0 1 1 663.0 0 2 2 760.0 0 1 1 788.0 0 1 1 908.0 0 1 1 931.0 0 1 1 1137.0 0 1 1 1284.0 0 1 1 1708.0 0 1 1 3596.0 0 1 1