## htsjdk.samtools.metrics.StringHeader # MarkDuplicates MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=999 INPUT=[/ceph/rimlsfnwi/data/moldevbio/heeringen/siebrenf/xt_rna/results/star/Xenopus_tropicalis_v9.1-GSM1606350.samtools-coordinate-unsieved.bam] OUTPUT=/ceph/rimlsfnwi/data/moldevbio/heeringen/siebrenf/xt_rna/results/star/Xenopus_tropicalis_v9.1-GSM1606350.samtools-coordinate-dupmarked.bam METRICS_FILE=/ceph/rimlsfnwi/data/moldevbio/heeringen/siebrenf/xt_rna/results/qc/markdup/Xenopus_tropicalis_v9.1-GSM1606350.samtools-coordinate.metrics.txt TMP_DIR=[/scratch/siebrenf/tmp] MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 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 REMOVE_DUPLICATES=false 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 VALIDATION_STRINGENCY=STRICT 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: Mon Nov 01 22:59:07 CET 2021 ## 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 0 48960402 7007040 0 0 10034400 0 0.204949 102496794 ## HISTOGRAM java.lang.Double BIN CoverageMult all_sets non_optical_sets 1.0 1 34204533 34204533 2.0 1.620222 3173006 3173006 3.0 2.004898 737052 737052 4.0 2.243482 296581 296581 5.0 2.391458 153895 153895 6.0 2.483235 91825 91825 7.0 2.540158 59918 59918 8.0 2.575462 41408 41408 9.0 2.597359 30011 30011 10.0 2.61094 22358 22358 11.0 2.619363 17358 17358 12.0 2.624587 13509 13509 13.0 2.627827 11060 11060 14.0 2.629837 8911 8911 15.0 2.631083 7361 7361 16.0 2.631856 6295 6295 17.0 2.632336 5211 5211 18.0 2.632633 4476 4476 19.0 2.632818 3872 3872 20.0 2.632932 3285 3285 21.0 2.633003 3001 3001 22.0 2.633047 2616 2616 23.0 2.633074 2374 2374 24.0 2.633091 2103 2103 25.0 2.633102 1728 1728 26.0 2.633108 1602 1602 27.0 2.633112 1426 1426 28.0 2.633115 1363 1363 29.0 2.633116 1227 1227 30.0 2.633117 1065 1065 31.0 2.633118 971 971 32.0 2.633118 893 893 33.0 2.633119 843 843 34.0 2.633119 717 717 35.0 2.633119 718 718 36.0 2.633119 653 653 37.0 2.633119 610 610 38.0 2.633119 534 534 39.0 2.633119 540 540 40.0 2.633119 435 435 41.0 2.633119 444 444 42.0 2.633119 419 419 43.0 2.633119 407 407 44.0 2.633119 345 345 45.0 2.633119 344 344 46.0 2.633119 277 277 47.0 2.633119 280 280 48.0 2.633119 272 272 49.0 2.633119 240 240 50.0 2.633119 252 252 51.0 2.633119 230 230 52.0 2.633119 207 207 53.0 2.633119 199 199 54.0 2.633119 189 189 55.0 2.633119 191 191 56.0 2.633119 176 176 57.0 2.633119 174 174 58.0 2.633119 150 150 59.0 2.633119 149 149 60.0 2.633119 143 143 61.0 2.633119 136 136 62.0 2.633119 107 107 63.0 2.633119 99 99 64.0 2.633119 124 124 65.0 2.633119 89 89 66.0 2.633119 93 93 67.0 2.633119 94 94 68.0 2.633119 103 103 69.0 2.633119 87 87 70.0 2.633119 72 72 71.0 2.633119 99 99 72.0 2.633119 96 96 73.0 2.633119 77 77 74.0 2.633119 69 69 75.0 2.633119 57 57 76.0 2.633119 76 76 77.0 2.633119 69 69 78.0 2.633119 61 61 79.0 2.633119 56 56 80.0 2.633119 52 52 81.0 2.633119 55 55 82.0 2.633119 47 47 83.0 2.633119 43 43 84.0 2.633119 39 39 85.0 2.633119 53 53 86.0 2.633119 48 48 87.0 2.633119 44 44 88.0 2.633119 44 44 89.0 2.633119 39 39 90.0 2.633119 41 41 91.0 2.633119 30 30 92.0 2.633119 32 32 93.0 2.633119 37 37 94.0 2.633119 33 33 95.0 2.633119 32 32 96.0 2.633119 31 31 97.0 2.633119 32 32 98.0 2.633119 30 30 99.0 2.633119 31 31 100.0 2.633119 27 27 101.0 0 20 20 102.0 0 32 32 103.0 0 26 26 104.0 0 26 26 105.0 0 38 38 106.0 0 23 23 107.0 0 16 16 108.0 0 14 14 109.0 0 15 15 110.0 0 20 20 111.0 0 20 20 112.0 0 22 22 113.0 0 22 22 114.0 0 16 16 115.0 0 21 21 116.0 0 13 13 117.0 0 18 18 118.0 0 13 13 119.0 0 14 14 120.0 0 11 11 121.0 0 16 16 122.0 0 20 20 123.0 0 17 17 124.0 0 8 8 125.0 0 13 13 126.0 0 13 13 127.0 0 15 15 128.0 0 16 16 129.0 0 9 9 130.0 0 8 8 131.0 0 17 17 132.0 0 4 4 133.0 0 11 11 134.0 0 10 10 135.0 0 9 9 136.0 0 9 9 137.0 0 12 12 138.0 0 7 7 139.0 0 13 13 140.0 0 10 10 141.0 0 7 7 142.0 0 11 11 143.0 0 8 8 144.0 0 7 7 145.0 0 7 7 146.0 0 12 12 147.0 0 5 5 148.0 0 6 6 149.0 0 8 8 150.0 0 10 10 151.0 0 5 5 152.0 0 7 7 153.0 0 10 10 154.0 0 4 4 155.0 0 6 6 156.0 0 5 5 157.0 0 4 4 158.0 0 2 2 159.0 0 2 2 160.0 0 4 4 161.0 0 4 4 162.0 0 5 5 163.0 0 2 2 164.0 0 4 4 165.0 0 3 3 166.0 0 5 5 167.0 0 7 7 168.0 0 4 4 169.0 0 5 5 170.0 0 5 5 171.0 0 4 4 172.0 0 5 5 173.0 0 5 5 174.0 0 9 9 175.0 0 6 6 176.0 0 4 4 177.0 0 5 5 178.0 0 1 1 179.0 0 1 1 180.0 0 6 6 181.0 0 1 1 182.0 0 4 4 183.0 0 4 4 184.0 0 3 3 185.0 0 6 6 186.0 0 2 2 187.0 0 1 1 188.0 0 2 2 189.0 0 2 2 190.0 0 3 3 191.0 0 4 4 192.0 0 5 5 193.0 0 3 3 194.0 0 2 2 195.0 0 4 4 196.0 0 4 4 197.0 0 2 2 198.0 0 5 5 199.0 0 1 1 201.0 0 3 3 202.0 0 1 1 203.0 0 1 1 204.0 0 5 5 205.0 0 4 4 206.0 0 1 1 207.0 0 3 3 208.0 0 2 2 209.0 0 3 3 210.0 0 1 1 211.0 0 1 1 212.0 0 3 3 213.0 0 4 4 214.0 0 1 1 215.0 0 2 2 216.0 0 2 2 217.0 0 1 1 218.0 0 2 2 219.0 0 1 1 220.0 0 6 6 221.0 0 2 2 222.0 0 3 3 223.0 0 2 2 224.0 0 1 1 225.0 0 4 4 226.0 0 1 1 228.0 0 1 1 229.0 0 2 2 230.0 0 3 3 231.0 0 2 2 232.0 0 3 3 233.0 0 1 1 234.0 0 1 1 235.0 0 2 2 236.0 0 1 1 237.0 0 2 2 240.0 0 4 4 242.0 0 3 3 246.0 0 3 3 248.0 0 2 2 249.0 0 3 3 251.0 0 1 1 252.0 0 2 2 254.0 0 1 1 255.0 0 1 1 256.0 0 2 2 257.0 0 1 1 258.0 0 2 2 259.0 0 1 1 263.0 0 1 1 265.0 0 1 1 266.0 0 2 2 267.0 0 1 1 268.0 0 1 1 269.0 0 3 3 270.0 0 2 2 273.0 0 3 3 274.0 0 1 1 276.0 0 2 2 278.0 0 1 1 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