## htsjdk.samtools.metrics.StringHeader # MarkDuplicates INPUT=[/project/berglandlab/DEST/dest_mapped/DESTv1/ES_Ler_Gim_1_2015-10-22/ES_Ler_Gim_1_2015-10-22.sorted_merged.bam] OUTPUT=/project/berglandlab/DEST/dest_mapped/DESTv1/ES_Ler_Gim_1_2015-10-22/ES_Ler_Gim_1_2015-10-22.dedup.bam METRICS_FILE=/project/berglandlab/DEST/dest_mapped/DESTv1/ES_Ler_Gim_1_2015-10-22/ES_Ler_Gim_1_2015-10-22.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 09:04:04 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 4980492 28192571 0 0 2201929 2680836 0 0.123255 138686741 ## HISTOGRAM java.lang.Double BIN VALUE all_sets non_optical_sets 1.0 1 22676263 22676263 2.0 1.816048 2066608 2066608 3.0 2.481982 168024 168024 4.0 3.025416 16428 16428 5.0 3.468884 3066 3066 6.0 3.830775 1341 1341 7.0 4.126095 842 842 8.0 4.367091 617 617 9.0 4.563755 454 454 10.0 4.724242 366 366 11.0 4.855207 280 280 12.0 4.962081 264 264 13.0 5.049295 221 221 14.0 5.120466 193 193 15.0 5.178545 186 186 16.0 5.22594 146 146 17.0 5.264617 152 152 18.0 5.296179 154 154 19.0 5.321935 117 117 20.0 5.342953 104 104 21.0 5.360105 99 99 22.0 5.374102 88 88 23.0 5.385524 99 99 24.0 5.394845 91 91 25.0 5.402451 88 88 26.0 5.408658 70 70 27.0 5.413723 67 67 28.0 5.417857 70 70 29.0 5.42123 56 56 30.0 5.423983 74 74 31.0 5.426229 53 53 32.0 5.428062 61 61 33.0 5.429558 46 46 34.0 5.430779 46 46 35.0 5.431775 47 47 36.0 5.432588 43 43 37.0 5.433251 40 40 38.0 5.433792 34 34 39.0 5.434234 44 44 40.0 5.434595 39 39 41.0 5.434889 44 44 42.0 5.435129 35 35 43.0 5.435325 28 28 44.0 5.435485 26 26 45.0 5.435615 34 34 46.0 5.435722 24 24 47.0 5.435809 24 24 48.0 5.435879 22 22 49.0 5.435937 22 22 50.0 5.435985 23 23 51.0 5.436023 24 24 52.0 5.436055 36 36 53.0 5.43608 29 29 54.0 5.436101 17 17 55.0 5.436118 26 26 56.0 5.436132 24 24 57.0 5.436144 21 21 58.0 5.436153 19 19 59.0 5.43616 20 20 60.0 5.436167 15 15 61.0 5.436172 13 13 62.0 5.436176 19 19 63.0 5.436179 17 17 64.0 5.436182 17 17 65.0 5.436184 13 13 66.0 5.436186 18 18 67.0 5.436187 14 14 68.0 5.436189 20 20 69.0 5.43619 17 17 70.0 5.43619 12 12 71.0 5.436191 5 5 72.0 5.436192 16 16 73.0 5.436192 9 9 74.0 5.436192 12 12 75.0 5.436193 16 16 76.0 5.436193 9 9 77.0 5.436193 16 16 78.0 5.436193 9 9 79.0 5.436193 12 12 80.0 5.436194 7 7 81.0 5.436194 14 14 82.0 5.436194 16 16 83.0 5.436194 6 6 84.0 5.436194 12 12 85.0 5.436194 12 12 86.0 5.436194 11 11 87.0 5.436194 12 12 88.0 5.436194 9 9 89.0 5.436194 8 8 90.0 5.436194 5 5 91.0 5.436194 4 4 92.0 5.436194 9 9 93.0 5.436194 9 9 94.0 5.436194 11 11 95.0 5.436194 4 4 96.0 5.436194 7 7 97.0 5.436194 5 5 98.0 5.436194 12 12 99.0 5.436194 11 11 100.0 5.436194 2 2 101.0 0 12 12 102.0 0 5 5 103.0 0 6 6 104.0 0 12 12 105.0 0 9 9 106.0 0 6 6 107.0 0 2 2 108.0 0 2 2 109.0 0 5 5 110.0 0 4 4 111.0 0 2 2 112.0 0 7 7 113.0 0 4 4 114.0 0 11 11 115.0 0 5 5 116.0 0 7 7 117.0 0 6 6 118.0 0 5 5 119.0 0 2 2 120.0 0 4 4 121.0 0 3 3 122.0 0 4 4 123.0 0 5 5 124.0 0 3 3 125.0 0 2 2 126.0 0 4 4 127.0 0 4 4 128.0 0 4 4 129.0 0 6 6 130.0 0 8 8 131.0 0 1 1 132.0 0 3 3 133.0 0 4 4 134.0 0 6 6 135.0 0 3 3 136.0 0 4 4 137.0 0 1 1 138.0 0 2 2 139.0 0 7 7 140.0 0 3 3 141.0 0 3 3 142.0 0 2 2 143.0 0 2 2 144.0 0 2 2 146.0 0 1 1 147.0 0 5 5 148.0 0 4 4 149.0 0 2 2 150.0 0 4 4 152.0 0 4 4 153.0 0 5 5 154.0 0 5 5 155.0 0 2 2 156.0 0 3 3 157.0 0 2 2 158.0 0 3 3 159.0 0 2 2 160.0 0 3 3 161.0 0 1 1 162.0 0 2 2 163.0 0 1 1 164.0 0 5 5 165.0 0 2 2 166.0 0 3 3 167.0 0 2 2 168.0 0 2 2 169.0 0 2 2 170.0 0 1 1 172.0 0 1 1 174.0 0 2 2 176.0 0 2 2 177.0 0 2 2 178.0 0 1 1 180.0 0 1 1 181.0 0 2 2 182.0 0 2 2 185.0 0 2 2 186.0 0 1 1 187.0 0 1 1 188.0 0 4 4 189.0 0 1 1 190.0 0 1 1 191.0 0 1 1 193.0 0 1 1 194.0 0 2 2 195.0 0 2 2 197.0 0 5 5 198.0 0 2 2 199.0 0 2 2 200.0 0 2 2 201.0 0 2 2 202.0 0 3 3 203.0 0 2 2 206.0 0 1 1 208.0 0 3 3 209.0 0 1 1 210.0 0 2 2 211.0 0 1 1 214.0 0 3 3 215.0 0 1 1 216.0 0 1 1 218.0 0 2 2 220.0 0 1 1 221.0 0 1 1 225.0 0 2 2 228.0 0 1 1 229.0 0 2 2 230.0 0 1 1 231.0 0 1 1 233.0 0 1 1 234.0 0 1 1 235.0 0 1 1 236.0 0 1 1 239.0 0 1 1 240.0 0 2 2 242.0 0 1 1 243.0 0 1 1 245.0 0 1 1 246.0 0 1 1 247.0 0 1 1 248.0 0 2 2 256.0 0 1 1 258.0 0 1 1 259.0 0 1 1 263.0 0 1 1 266.0 0 2 2 267.0 0 3 3 270.0 0 1 1 271.0 0 1 1 272.0 0 1 1 274.0 0 1 1 280.0 0 1 1 282.0 0 1 1 283.0 0 1 1 289.0 0 1 1 294.0 0 1 1 296.0 0 1 1 298.0 0 1 1 301.0 0 1 1 304.0 0 1 1 306.0 0 1 1 307.0 0 1 1 309.0 0 2 2 314.0 0 1 1 315.0 0 2 2 318.0 0 1 1 325.0 0 1 1 328.0 0 1 1 329.0 0 1 1 332.0 0 2 2 342.0 0 1 1 348.0 0 1 1 353.0 0 1 1 360.0 0 1 1 365.0 0 1 1 367.0 0 1 1 378.0 0 1 1 381.0 0 1 1 406.0 0 1 1 419.0 0 1 1 423.0 0 1 1 427.0 0 1 1 432.0 0 2 2 436.0 0 1 1 440.0 0 1 1 452.0 0 1 1 456.0 0 1 1 468.0 0 1 1 472.0 0 1 1 488.0 0 1 1 493.0 0 1 1 537.0 0 1 1 590.0 0 1 1 624.0 0 1 1 677.0 0 1 1 713.0 0 1 1 838.0 0 1 1