## htsjdk.samtools.metrics.StringHeader # MarkDuplicates INPUT=[/project/berglandlab/DEST/dest_mapped/DESTv1/AT_Nie_Mau_1_2014-10-19/AT_Nie_Mau_1_2014-10-19.sorted_merged.bam] OUTPUT=/project/berglandlab/DEST/dest_mapped/DESTv1/AT_Nie_Mau_1_2014-10-19/AT_Nie_Mau_1_2014-10-19.dedup.bam METRICS_FILE=/project/berglandlab/DEST/dest_mapped/DESTv1/AT_Nie_Mau_1_2014-10-19/AT_Nie_Mau_1_2014-10-19.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 09:11:47 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 3816570 25799601 0 0 1067497 996855 0 0.055241 325203275 ## HISTOGRAM java.lang.Double BIN VALUE all_sets non_optical_sets 1.0 1 23342140 23342140 2.0 1.923732 788063 788063 3.0 2.777012 25274 25274 4.0 3.565213 1617 1617 5.0 4.2933 477 477 6.0 4.965857 362 362 7.0 5.587119 214 214 8.0 6.160998 203 203 9.0 6.691108 154 154 10.0 7.180788 138 138 11.0 7.63312 115 115 12.0 8.050954 101 101 13.0 8.43692 86 86 14.0 8.79345 89 89 15.0 9.122787 85 85 16.0 9.427006 79 79 17.0 9.708023 68 68 18.0 9.967607 65 65 19.0 10.207394 60 60 20.0 10.428892 55 55 21.0 10.633496 50 50 22.0 10.822496 45 45 23.0 10.997081 46 46 24.0 11.158351 39 39 25.0 11.307321 34 34 26.0 11.444929 34 34 27.0 11.572042 20 20 28.0 11.689461 31 31 29.0 11.797924 29 29 30.0 11.898115 27 27 31.0 11.990664 27 27 32.0 12.076155 21 21 33.0 12.155125 26 26 34.0 12.228073 23 23 35.0 12.295457 27 27 36.0 12.357702 31 31 37.0 12.415199 22 22 38.0 12.468311 19 19 39.0 12.517373 15 15 40.0 12.562692 15 15 41.0 12.604555 27 27 42.0 12.643225 21 21 43.0 12.678946 17 17 44.0 12.711943 13 13 45.0 12.742423 14 14 46.0 12.770578 16 16 47.0 12.796586 14 14 48.0 12.82061 20 20 49.0 12.842803 16 16 50.0 12.863302 20 20 51.0 12.882238 12 12 52.0 12.89973 14 14 53.0 12.915888 10 10 54.0 12.930813 11 11 55.0 12.9446 13 13 56.0 12.957336 14 14 57.0 12.9691 12 12 58.0 12.979967 16 16 59.0 12.990005 12 12 60.0 12.999278 11 11 61.0 13.007843 9 9 62.0 13.015755 10 10 63.0 13.023064 9 9 64.0 13.029815 13 13 65.0 13.036051 11 11 66.0 13.041812 8 8 67.0 13.047134 5 5 68.0 13.052049 10 10 69.0 13.05659 3 3 70.0 13.060784 6 6 71.0 13.064658 10 10 72.0 13.068237 5 5 73.0 13.071543 8 8 74.0 13.074597 6 6 75.0 13.077418 5 5 76.0 13.080024 5 5 77.0 13.082431 9 9 78.0 13.084654 4 4 79.0 13.086708 10 10 80.0 13.088605 4 4 81.0 13.090358 6 6 82.0 13.091977 3 3 83.0 13.093472 9 9 84.0 13.094853 5 5 85.0 13.096129 2 2 86.0 13.097308 5 5 87.0 13.098397 2 2 88.0 13.099402 2 2 89.0 13.100331 6 6 90.0 13.10119 3 3 91.0 13.101982 6 6 92.0 13.102715 5 5 93.0 13.103391 6 6 94.0 13.104016 5 5 95.0 13.104593 7 7 96.0 13.105126 4 4 97.0 13.105619 6 6 98.0 13.106074 5 5 99.0 13.106494 3 3 100.0 13.106882 5 5 101.0 0 5 5 102.0 0 3 3 103.0 0 2 2 104.0 0 3 3 105.0 0 4 4 106.0 0 6 6 107.0 0 6 6 108.0 0 4 4 109.0 0 5 5 110.0 0 10 10 111.0 0 2 2 112.0 0 6 6 113.0 0 1 1 114.0 0 3 3 115.0 0 8 8 116.0 0 3 3 118.0 0 5 5 119.0 0 2 2 120.0 0 4 4 121.0 0 3 3 122.0 0 3 3 123.0 0 6 6 124.0 0 4 4 125.0 0 3 3 126.0 0 2 2 127.0 0 4 4 128.0 0 2 2 129.0 0 2 2 130.0 0 2 2 131.0 0 2 2 133.0 0 4 4 134.0 0 1 1 135.0 0 4 4 136.0 0 1 1 137.0 0 2 2 138.0 0 3 3 139.0 0 3 3 140.0 0 3 3 141.0 0 1 1 142.0 0 6 6 144.0 0 4 4 145.0 0 2 2 147.0 0 3 3 148.0 0 3 3 149.0 0 4 4 150.0 0 1 1 151.0 0 6 6 152.0 0 3 3 153.0 0 1 1 154.0 0 3 3 155.0 0 3 3 156.0 0 4 4 158.0 0 2 2 159.0 0 1 1 160.0 0 4 4 161.0 0 2 2 162.0 0 2 2 163.0 0 1 1 164.0 0 2 2 165.0 0 1 1 166.0 0 1 1 167.0 0 2 2 168.0 0 1 1 169.0 0 1 1 170.0 0 1 1 172.0 0 7 7 173.0 0 1 1 175.0 0 4 4 176.0 0 2 2 177.0 0 4 4 179.0 0 1 1 181.0 0 1 1 182.0 0 1 1 184.0 0 3 3 185.0 0 2 2 186.0 0 2 2 187.0 0 3 3 188.0 0 1 1 189.0 0 2 2 191.0 0 1 1 192.0 0 1 1 193.0 0 1 1 194.0 0 1 1 195.0 0 2 2 197.0 0 1 1 199.0 0 1 1 201.0 0 2 2 202.0 0 2 2 205.0 0 1 1 206.0 0 2 2 208.0 0 2 2 209.0 0 2 2 210.0 0 2 2 213.0 0 1 1 214.0 0 1 1 215.0 0 2 2 216.0 0 1 1 218.0 0 2 2 219.0 0 2 2 220.0 0 2 2 221.0 0 2 2 224.0 0 1 1 225.0 0 1 1 226.0 0 1 1 228.0 0 2 2 230.0 0 2 2 232.0 0 3 3 236.0 0 1 1 237.0 0 1 1 238.0 0 1 1 239.0 0 2 2 240.0 0 1 1 241.0 0 2 2 242.0 0 1 1 243.0 0 2 2 245.0 0 1 1 246.0 0 2 2 247.0 0 1 1 255.0 0 1 1 256.0 0 2 2 257.0 0 1 1 258.0 0 1 1 260.0 0 1 1 262.0 0 2 2 265.0 0 1 1 269.0 0 2 2 270.0 0 1 1 272.0 0 1 1 276.0 0 1 1 278.0 0 2 2 279.0 0 1 1 281.0 0 2 2 282.0 0 1 1 286.0 0 1 1 290.0 0 1 1 291.0 0 1 1 294.0 0 1 1 297.0 0 3 3 298.0 0 1 1 299.0 0 1 1 300.0 0 1 1 302.0 0 1 1 303.0 0 1 1 304.0 0 1 1 305.0 0 2 2 308.0 0 2 2 310.0 0 1 1 311.0 0 2 2 312.0 0 1 1 313.0 0 1 1 314.0 0 1 1 315.0 0 1 1 317.0 0 1 1 320.0 0 1 1 324.0 0 1 1 326.0 0 2 2 327.0 0 1 1 329.0 0 1 1 337.0 0 1 1 339.0 0 1 1 350.0 0 1 1 377.0 0 1 1 382.0 0 1 1 383.0 0 1 1 388.0 0 2 2 389.0 0 1 1 394.0 0 1 1 401.0 0 1 1 402.0 0 2 2 407.0 0 1 1 411.0 0 1 1 418.0 0 1 1 421.0 0 1 1 426.0 0 1 1 430.0 0 1 1 435.0 0 1 1 457.0 0 1 1 460.0 0 1 1 461.0 0 1 1 463.0 0 1 1 466.0 0 1 1 467.0 0 1 1 470.0 0 1 1 474.0 0 1 1 477.0 0 1 1 480.0 0 1 1 483.0 0 1 1 492.0 0 1 1 497.0 0 1 1 501.0 0 1 1 521.0 0 1 1 523.0 0 1 1 579.0 0 1 1 589.0 0 1 1 599.0 0 1 1 613.0 0 1 1 647.0 0 1 1 655.0 0 1 1 659.0 0 1 1 717.0 0 1 1 728.0 0 1 1 777.0 0 1 1 941.0 0 1 1 1025.0 0 1 1