## 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-GSM1606364.samtools-coordinate-unsieved.bam] OUTPUT=/ceph/rimlsfnwi/data/moldevbio/heeringen/siebrenf/xt_rna/results/star/Xenopus_tropicalis_v9.1-GSM1606364.samtools-coordinate-dupmarked.bam METRICS_FILE=/ceph/rimlsfnwi/data/moldevbio/heeringen/siebrenf/xt_rna/results/qc/markdup/Xenopus_tropicalis_v9.1-GSM1606364.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: Tue Nov 02 13:52:18 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 29033751 3739872 0 0 6623210 0 0.228121 53537872 ## HISTOGRAM java.lang.Double BIN CoverageMult all_sets non_optical_sets 1.0 1 19459557 19459557 2.0 1.581408 1905908 1905908 3.0 1.919443 473773 473773 4.0 2.115979 201931 201931 5.0 2.230246 108480 108480 6.0 2.296682 66093 66093 7.0 2.335309 43634 43634 8.0 2.357767 30545 30545 9.0 2.370824 21966 21966 10.0 2.378415 16514 16514 11.0 2.382829 12402 12402 12.0 2.385395 9969 9969 13.0 2.386887 8273 8273 14.0 2.387755 6575 6575 15.0 2.388259 5512 5512 16.0 2.388552 4649 4649 17.0 2.388723 3740 3740 18.0 2.388822 3330 3330 19.0 2.388879 2721 2721 20.0 2.388913 2411 2411 21.0 2.388932 2024 2024 22.0 2.388944 1755 1755 23.0 2.38895 1647 1647 24.0 2.388954 1418 1418 25.0 2.388956 1216 1216 26.0 2.388958 1183 1183 27.0 2.388958 976 976 28.0 2.388959 900 900 29.0 2.388959 816 816 30.0 2.388959 693 693 31.0 2.388959 693 693 32.0 2.388959 590 590 33.0 2.388959 580 580 34.0 2.388959 541 541 35.0 2.388959 500 500 36.0 2.388959 405 405 37.0 2.388959 400 400 38.0 2.388959 334 334 39.0 2.388959 302 302 40.0 2.388959 317 317 41.0 2.388959 266 266 42.0 2.388959 241 241 43.0 2.388959 227 227 44.0 2.388959 222 222 45.0 2.388959 214 214 46.0 2.388959 199 199 47.0 2.388959 181 181 48.0 2.388959 176 176 49.0 2.388959 176 176 50.0 2.388959 145 145 51.0 2.388959 152 152 52.0 2.388959 134 134 53.0 2.388959 112 112 54.0 2.388959 121 121 55.0 2.388959 113 113 56.0 2.388959 110 110 57.0 2.388959 95 95 58.0 2.388959 105 105 59.0 2.388959 71 71 60.0 2.388959 85 85 61.0 2.388959 88 88 62.0 2.388959 76 76 63.0 2.388959 72 72 64.0 2.388959 71 71 65.0 2.388959 83 83 66.0 2.388959 66 66 67.0 2.388959 64 64 68.0 2.388959 49 49 69.0 2.388959 53 53 70.0 2.388959 57 57 71.0 2.388959 63 63 72.0 2.388959 46 46 73.0 2.388959 47 47 74.0 2.388959 43 43 75.0 2.388959 36 36 76.0 2.388959 39 39 77.0 2.388959 45 45 78.0 2.388959 37 37 79.0 2.388959 32 32 80.0 2.388959 23 23 81.0 2.388959 34 34 82.0 2.388959 30 30 83.0 2.388959 24 24 84.0 2.388959 27 27 85.0 2.388959 24 24 86.0 2.388959 20 20 87.0 2.388959 30 30 88.0 2.388959 14 14 89.0 2.388959 14 14 90.0 2.388959 17 17 91.0 2.388959 29 29 92.0 2.388959 25 25 93.0 2.388959 21 21 94.0 2.388959 15 15 95.0 2.388959 18 18 96.0 2.388959 23 23 97.0 2.388959 13 13 98.0 2.388959 17 17 99.0 2.388959 18 18 100.0 2.388959 9 9 101.0 0 12 12 102.0 0 15 15 103.0 0 13 13 104.0 0 13 13 105.0 0 17 17 106.0 0 13 13 107.0 0 16 16 108.0 0 14 14 109.0 0 12 12 110.0 0 9 9 111.0 0 18 18 112.0 0 7 7 113.0 0 18 18 114.0 0 10 10 115.0 0 14 14 116.0 0 7 7 117.0 0 9 9 118.0 0 10 10 119.0 0 8 8 120.0 0 7 7 121.0 0 5 5 122.0 0 7 7 123.0 0 1 1 124.0 0 7 7 125.0 0 7 7 126.0 0 5 5 127.0 0 12 12 128.0 0 13 13 129.0 0 7 7 130.0 0 4 4 131.0 0 6 6 132.0 0 7 7 133.0 0 3 3 134.0 0 4 4 135.0 0 5 5 136.0 0 11 11 137.0 0 7 7 138.0 0 6 6 139.0 0 8 8 140.0 0 8 8 141.0 0 9 9 142.0 0 9 9 143.0 0 9 9 144.0 0 4 4 145.0 0 4 4 146.0 0 3 3 147.0 0 4 4 148.0 0 5 5 149.0 0 3 3 150.0 0 1 1 151.0 0 2 2 152.0 0 5 5 153.0 0 1 1 154.0 0 5 5 155.0 0 2 2 156.0 0 3 3 157.0 0 2 2 158.0 0 1 1 159.0 0 6 6 160.0 0 1 1 161.0 0 6 6 162.0 0 1 1 163.0 0 5 5 165.0 0 3 3 167.0 0 1 1 169.0 0 2 2 170.0 0 1 1 171.0 0 3 3 172.0 0 2 2 173.0 0 2 2 175.0 0 2 2 176.0 0 3 3 177.0 0 4 4 178.0 0 4 4 179.0 0 3 3 180.0 0 2 2 181.0 0 3 3 182.0 0 2 2 183.0 0 4 4 184.0 0 3 3 185.0 0 1 1 186.0 0 2 2 187.0 0 1 1 188.0 0 2 2 191.0 0 3 3 192.0 0 2 2 195.0 0 2 2 196.0 0 1 1 197.0 0 1 1 198.0 0 1 1 200.0 0 3 3 201.0 0 1 1 202.0 0 1 1 203.0 0 1 1 204.0 0 1 1 205.0 0 1 1 206.0 0 3 3 207.0 0 1 1 208.0 0 3 3 209.0 0 1 1 210.0 0 3 3 211.0 0 2 2 212.0 0 1 1 214.0 0 1 1 217.0 0 2 2 218.0 0 2 2 219.0 0 1 1 221.0 0 1 1 222.0 0 3 3 223.0 0 1 1 226.0 0 1 1 229.0 0 2 2 230.0 0 1 1 231.0 0 1 1 233.0 0 1 1 235.0 0 1 1 238.0 0 1 1 239.0 0 1 1 242.0 0 1 1 245.0 0 1 1 247.0 0 2 2 256.0 0 2 2 258.0 0 1 1 260.0 0 1 1 261.0 0 1 1 266.0 0 1 1 270.0 0 1 1 280.0 0 1 1 283.0 0 1 1 289.0 0 2 2 290.0 0 2 2 291.0 0 2 2 292.0 0 1 1 299.0 0 1 1 309.0 0 1 1 312.0 0 1 1 315.0 0 1 1 317.0 0 1 1 325.0 0 2 2 339.0 0 1 1 373.0 0 1 1 377.0 0 1 1 385.0 0 1 1 397.0 0 1 1 398.0 0 1 1 409.0 0 1 1 419.0 0 1 1 444.0 0 1 1 454.0 0 1 1 516.0 0 1 1 557.0 0 1 1 736.0 0 1 1 932.0 0 1 1 968.0 0 1 1 15573.0 0 1 1