## 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-GSM1606235.samtools-coordinate-unsieved.bam] OUTPUT=/ceph/rimlsfnwi/data/moldevbio/heeringen/siebrenf/xt_rna/results/star/Xenopus_tropicalis_v9.1-GSM1606235.samtools-coordinate-dupmarked.bam METRICS_FILE=/ceph/rimlsfnwi/data/moldevbio/heeringen/siebrenf/xt_rna/results/qc/markdup/Xenopus_tropicalis_v9.1-GSM1606235.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 22:03:04 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 39454944 5386392 0 0 6718099 0 0.170273 102294942 ## HISTOGRAM java.lang.Double BIN CoverageMult all_sets non_optical_sets 1.0 1 29656700 29656700 2.0 1.679976 2008312 2008312 3.0 2.142343 493090 493090 4.0 2.456742 208711 208711 5.0 2.670525 111112 111112 6.0 2.815893 66718 66718 7.0 2.914739 43852 43852 8.0 2.981953 30451 30451 9.0 3.027656 21939 21939 10.0 3.058733 16336 16336 11.0 3.079865 12601 12601 12.0 3.094234 9814 9814 13.0 3.104005 7943 7943 14.0 3.110648 6454 6454 15.0 3.115166 5131 5131 16.0 3.118238 4472 4472 17.0 3.120327 3713 3713 18.0 3.121747 3146 3146 19.0 3.122713 2710 2710 20.0 3.123369 2299 2299 21.0 3.123816 1940 1940 22.0 3.12412 1785 1785 23.0 3.124326 1562 1562 24.0 3.124467 1351 1351 25.0 3.124562 1176 1176 26.0 3.124627 1040 1040 27.0 3.124671 926 926 28.0 3.124701 876 876 29.0 3.124721 734 734 30.0 3.124735 677 677 31.0 3.124745 627 627 32.0 3.124751 574 574 33.0 3.124756 505 505 34.0 3.124759 456 456 35.0 3.124761 451 451 36.0 3.124762 387 387 37.0 3.124763 362 362 38.0 3.124763 368 368 39.0 3.124764 301 301 40.0 3.124764 276 276 41.0 3.124764 268 268 42.0 3.124765 292 292 43.0 3.124765 239 239 44.0 3.124765 231 231 45.0 3.124765 179 179 46.0 3.124765 163 163 47.0 3.124765 175 175 48.0 3.124765 162 162 49.0 3.124765 180 180 50.0 3.124765 127 127 51.0 3.124765 124 124 52.0 3.124765 121 121 53.0 3.124765 124 124 54.0 3.124765 126 126 55.0 3.124765 90 90 56.0 3.124765 93 93 57.0 3.124765 94 94 58.0 3.124765 84 84 59.0 3.124765 87 87 60.0 3.124765 86 86 61.0 3.124765 103 103 62.0 3.124765 80 80 63.0 3.124765 62 62 64.0 3.124765 60 60 65.0 3.124765 56 56 66.0 3.124765 42 42 67.0 3.124765 46 46 68.0 3.124765 57 57 69.0 3.124765 48 48 70.0 3.124765 48 48 71.0 3.124765 39 39 72.0 3.124765 36 36 73.0 3.124765 28 28 74.0 3.124765 40 40 75.0 3.124765 42 42 76.0 3.124765 35 35 77.0 3.124765 44 44 78.0 3.124765 29 29 79.0 3.124765 26 26 80.0 3.124765 32 32 81.0 3.124765 31 31 82.0 3.124765 34 34 83.0 3.124765 27 27 84.0 3.124765 19 19 85.0 3.124765 36 36 86.0 3.124765 28 28 87.0 3.124765 25 25 88.0 3.124765 18 18 89.0 3.124765 16 16 90.0 3.124765 14 14 91.0 3.124765 12 12 92.0 3.124765 26 26 93.0 3.124765 22 22 94.0 3.124765 14 14 95.0 3.124765 13 13 96.0 3.124765 14 14 97.0 3.124765 15 15 98.0 3.124765 11 11 99.0 3.124765 17 17 100.0 3.124765 12 12 101.0 0 12 12 102.0 0 10 10 103.0 0 14 14 104.0 0 11 11 105.0 0 13 13 106.0 0 13 13 107.0 0 15 15 108.0 0 13 13 109.0 0 14 14 110.0 0 7 7 111.0 0 10 10 112.0 0 10 10 113.0 0 9 9 114.0 0 7 7 115.0 0 10 10 116.0 0 13 13 117.0 0 10 10 118.0 0 11 11 119.0 0 8 8 120.0 0 6 6 121.0 0 7 7 122.0 0 8 8 123.0 0 6 6 124.0 0 6 6 125.0 0 6 6 126.0 0 6 6 127.0 0 12 12 128.0 0 4 4 129.0 0 7 7 130.0 0 3 3 131.0 0 7 7 132.0 0 6 6 133.0 0 5 5 134.0 0 4 4 135.0 0 6 6 136.0 0 8 8 137.0 0 2 2 138.0 0 2 2 139.0 0 2 2 140.0 0 4 4 141.0 0 7 7 142.0 0 4 4 143.0 0 3 3 144.0 0 5 5 145.0 0 4 4 146.0 0 8 8 147.0 0 2 2 148.0 0 5 5 149.0 0 2 2 150.0 0 4 4 151.0 0 5 5 152.0 0 5 5 153.0 0 7 7 154.0 0 3 3 155.0 0 4 4 156.0 0 2 2 157.0 0 3 3 158.0 0 1 1 159.0 0 2 2 160.0 0 3 3 161.0 0 1 1 162.0 0 3 3 163.0 0 7 7 166.0 0 3 3 167.0 0 4 4 168.0 0 3 3 169.0 0 2 2 170.0 0 2 2 171.0 0 2 2 172.0 0 4 4 173.0 0 1 1 174.0 0 1 1 176.0 0 2 2 177.0 0 2 2 178.0 0 1 1 179.0 0 4 4 180.0 0 2 2 181.0 0 1 1 184.0 0 2 2 185.0 0 4 4 186.0 0 3 3 187.0 0 1 1 188.0 0 1 1 189.0 0 2 2 190.0 0 2 2 191.0 0 1 1 193.0 0 1 1 195.0 0 1 1 196.0 0 3 3 198.0 0 1 1 199.0 0 1 1 202.0 0 3 3 203.0 0 1 1 204.0 0 2 2 207.0 0 1 1 208.0 0 1 1 209.0 0 1 1 212.0 0 2 2 214.0 0 2 2 215.0 0 1 1 216.0 0 1 1 218.0 0 2 2 221.0 0 1 1 222.0 0 1 1 223.0 0 2 2 224.0 0 1 1 225.0 0 1 1 226.0 0 1 1 228.0 0 1 1 232.0 0 2 2 233.0 0 2 2 235.0 0 2 2 237.0 0 2 2 240.0 0 2 2 245.0 0 3 3 246.0 0 1 1 247.0 0 1 1 248.0 0 1 1 249.0 0 2 2 250.0 0 2 2 251.0 0 1 1 252.0 0 1 1 254.0 0 2 2 255.0 0 1 1 256.0 0 2 2 257.0 0 1 1 262.0 0 1 1 265.0 0 1 1 271.0 0 1 1 273.0 0 1 1 278.0 0 1 1 280.0 0 1 1 282.0 0 1 1 284.0 0 2 2 290.0 0 1 1 292.0 0 1 1 295.0 0 1 1 298.0 0 1 1 302.0 0 1 1 304.0 0 1 1 310.0 0 1 1 323.0 0 1 1 325.0 0 1 1 338.0 0 1 1 339.0 0 1 1 350.0 0 1 1 368.0 0 1 1 370.0 0 1 1 410.0 0 1 1 411.0 0 1 1 413.0 0 1 1 426.0 0 1 1 447.0 0 1 1 460.0 0 1 1 534.0 0 1 1 540.0 0 1 1 551.0 0 1 1 574.0 0 1 1 605.0 0 1 1 610.0 0 1 1 631.0 0 1 1 971.0 0 1 1 1669.0 0 1 1