## htsjdk.samtools.metrics.StringHeader # MarkDuplicates INPUT=[ctenidia.sorted.bam] OUTPUT=ctenidia.markdup.sorted.bam METRICS_FILE=ctenidia.markdup.sorted.MarkDuplicates.metrics.txt REMOVE_DUPLICATES=false ASSUME_SORTED=true TMP_DIR=[tmp] VALIDATION_STRINGENCY=LENIENT 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 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 Mar 25 11:10:37 GMT 2022 ## 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 Unknown Library 83149 36685637 7098706 0 59168 23560591 0 0.642308 14196274 ## HISTOGRAM java.lang.Double BIN CoverageMult all_sets non_optical_sets 1.0 1 4202192 4202192 2.0 1.075458 3253855 3253855 3.0 1.081152 2312832 2312832 4.0 1.081582 1449808 1449808 5.0 1.081614 829461 829461 6.0 1.081617 447791 447791 7.0 1.081617 238739 238739 8.0 1.081617 130486 130486 9.0 1.081617 74700 74700 10.0 1.081617 45320 45320 11.0 1.081617 29621 29621 12.0 1.081617 20396 20396 13.0 1.081617 14807 14807 14.0 1.081617 11384 11384 15.0 1.081617 8821 8821 16.0 1.081617 7054 7054 17.0 1.081617 5806 5806 18.0 1.081617 4855 4855 19.0 1.081617 4068 4068 20.0 1.081617 3352 3352 21.0 1.081617 2991 2991 22.0 1.081617 2491 2491 23.0 1.081617 2182 2182 24.0 1.081617 1965 1965 25.0 1.081617 1699 1699 26.0 1.081617 1480 1480 27.0 1.081617 1327 1327 28.0 1.081617 1181 1181 29.0 1.081617 1003 1003 30.0 1.081617 972 972 31.0 1.081617 862 862 32.0 1.081617 781 781 33.0 1.081617 649 649 34.0 1.081617 663 663 35.0 1.081617 632 632 36.0 1.081617 561 561 37.0 1.081617 479 479 38.0 1.081617 445 445 39.0 1.081617 430 430 40.0 1.081617 383 383 41.0 1.081617 375 375 42.0 1.081617 351 351 43.0 1.081617 296 296 44.0 1.081617 301 301 45.0 1.081617 261 261 46.0 1.081617 252 252 47.0 1.081617 263 263 48.0 1.081617 228 228 49.0 1.081617 179 179 50.0 1.081617 172 172 51.0 1.081617 178 178 52.0 1.081617 184 184 53.0 1.081617 152 152 54.0 1.081617 135 135 55.0 1.081617 133 133 56.0 1.081617 121 121 57.0 1.081617 124 124 58.0 1.081617 98 98 59.0 1.081617 106 106 60.0 1.081617 108 108 61.0 1.081617 97 97 62.0 1.081617 79 79 63.0 1.081617 103 103 64.0 1.081617 90 90 65.0 1.081617 78 78 66.0 1.081617 76 76 67.0 1.081617 67 67 68.0 1.081617 79 79 69.0 1.081617 83 83 70.0 1.081617 46 46 71.0 1.081617 55 55 72.0 1.081617 58 58 73.0 1.081617 50 50 74.0 1.081617 44 44 75.0 1.081617 50 50 76.0 1.081617 41 41 77.0 1.081617 53 53 78.0 1.081617 48 48 79.0 1.081617 38 38 80.0 1.081617 29 29 81.0 1.081617 45 45 82.0 1.081617 37 37 83.0 1.081617 31 31 84.0 1.081617 24 24 85.0 1.081617 30 30 86.0 1.081617 36 36 87.0 1.081617 32 32 88.0 1.081617 40 40 89.0 1.081617 18 18 90.0 1.081617 26 26 91.0 1.081617 29 29 92.0 1.081617 22 22 93.0 1.081617 33 33 94.0 1.081617 21 21 95.0 1.081617 24 24 96.0 1.081617 24 24 97.0 1.081617 17 17 98.0 1.081617 16 16 99.0 1.081617 18 18 100.0 1.081617 22 22 101.0 0 19 19 102.0 0 13 13 103.0 0 21 21 104.0 0 16 16 105.0 0 20 20 106.0 0 21 21 107.0 0 16 16 108.0 0 9 9 109.0 0 9 9 110.0 0 18 18 111.0 0 10 10 112.0 0 15 15 113.0 0 15 15 114.0 0 10 10 115.0 0 8 8 116.0 0 7 7 117.0 0 5 5 118.0 0 9 9 119.0 0 13 13 120.0 0 11 11 121.0 0 11 11 122.0 0 7 7 123.0 0 15 15 124.0 0 7 7 125.0 0 8 8 126.0 0 5 5 127.0 0 6 6 128.0 0 12 12 129.0 0 6 6 130.0 0 6 6 131.0 0 9 9 132.0 0 12 12 133.0 0 9 9 134.0 0 5 5 135.0 0 7 7 136.0 0 5 5 137.0 0 8 8 138.0 0 8 8 139.0 0 4 4 140.0 0 8 8 141.0 0 3 3 142.0 0 5 5 143.0 0 2 2 144.0 0 6 6 145.0 0 9 9 146.0 0 1 1 147.0 0 4 4 148.0 0 6 6 149.0 0 5 5 150.0 0 5 5 151.0 0 6 6 152.0 0 4 4 153.0 0 7 7 154.0 0 4 4 155.0 0 7 7 156.0 0 4 4 157.0 0 2 2 158.0 0 3 3 159.0 0 1 1 160.0 0 2 2 161.0 0 2 2 162.0 0 4 4 163.0 0 2 2 165.0 0 3 3 166.0 0 2 2 167.0 0 2 2 168.0 0 1 1 169.0 0 3 3 170.0 0 2 2 171.0 0 9 9 172.0 0 3 3 173.0 0 3 3 174.0 0 4 4 175.0 0 1 1 176.0 0 1 1 177.0 0 1 1 178.0 0 2 2 179.0 0 3 3 180.0 0 2 2 181.0 0 1 1 182.0 0 5 5 183.0 0 3 3 186.0 0 4 4 187.0 0 2 2 189.0 0 2 2 190.0 0 3 3 192.0 0 2 2 193.0 0 2 2 194.0 0 3 3 195.0 0 4 4 196.0 0 1 1 198.0 0 4 4 199.0 0 1 1 200.0 0 2 2 201.0 0 2 2 202.0 0 2 2 203.0 0 1 1 205.0 0 2 2 206.0 0 1 1 209.0 0 2 2 212.0 0 2 2 213.0 0 1 1 215.0 0 1 1 216.0 0 2 2 217.0 0 1 1 218.0 0 1 1 220.0 0 1 1 222.0 0 1 1 223.0 0 1 1 224.0 0 2 2 225.0 0 1 1 226.0 0 1 1 227.0 0 2 2 228.0 0 1 1 230.0 0 2 2 232.0 0 2 2 234.0 0 1 1 235.0 0 2 2 236.0 0 1 1 238.0 0 1 1 243.0 0 2 2 245.0 0 2 2 248.0 0 1 1 249.0 0 1 1 251.0 0 1 1 254.0 0 1 1 255.0 0 1 1 258.0 0 1 1 261.0 0 1 1 262.0 0 1 1 264.0 0 1 1 266.0 0 1 1 267.0 0 1 1 268.0 0 2 2 269.0 0 2 2 270.0 0 1 1 272.0 0 1 1 273.0 0 1 1 276.0 0 3 3 283.0 0 1 1 284.0 0 1 1 288.0 0 1 1 290.0 0 2 2 292.0 0 1 1 293.0 0 2 2 295.0 0 1 1 296.0 0 1 1 299.0 0 2 2 303.0 0 1 1 304.0 0 2 2 306.0 0 1 1 312.0 0 2 2 335.0 0 2 2 340.0 0 1 1 347.0 0 1 1 349.0 0 1 1 391.0 0 1 1 425.0 0 1 1 455.0 0 1 1 462.0 0 1 1 507.0 0 1 1 533.0 0 1 1 558.0 0 1 1 608.0 0 1 1 670.0 0 1 1 722.0 0 1 1 805.0 0 1 1 1059.0 0 1 1 1157.0 0 1 1