## 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-GSM919953.samtools-coordinate-unsieved.bam] OUTPUT=/ceph/rimlsfnwi/data/moldevbio/heeringen/siebrenf/xt_rna/results/star/Xenopus_tropicalis_v9.1-GSM919953.samtools-coordinate-dupmarked.bam METRICS_FILE=/ceph/rimlsfnwi/data/moldevbio/heeringen/siebrenf/xt_rna/results/qc/markdup/Xenopus_tropicalis_v9.1-GSM919953.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 15:51:00 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 9350598 1865672 0 0 2133569 0 0.228175 17237539 ## HISTOGRAM java.lang.Double BIN CoverageMult all_sets non_optical_sets 1.0 1 6335598 6335598 2.0 1.581319 563760 563760 3.0 1.919251 140364 140364 4.0 2.115697 60923 60923 5.0 2.229895 32947 32947 6.0 2.296281 20380 20380 7.0 2.334872 13407 13407 8.0 2.357305 9505 9505 9.0 2.370347 6954 6954 10.0 2.377928 5171 5171 11.0 2.382335 4039 4039 12.0 2.384897 3264 3264 13.0 2.386386 2596 2596 14.0 2.387252 2104 2104 15.0 2.387755 1743 1743 16.0 2.388047 1501 1501 17.0 2.388217 1287 1287 18.0 2.388316 1089 1089 19.0 2.388374 920 920 20.0 2.388407 874 874 21.0 2.388427 741 741 22.0 2.388438 619 619 23.0 2.388445 569 569 24.0 2.388448 464 464 25.0 2.388451 463 463 26.0 2.388452 405 405 27.0 2.388453 349 349 28.0 2.388453 319 319 29.0 2.388453 271 271 30.0 2.388453 254 254 31.0 2.388453 241 241 32.0 2.388454 211 211 33.0 2.388454 219 219 34.0 2.388454 167 167 35.0 2.388454 186 186 36.0 2.388454 155 155 37.0 2.388454 157 157 38.0 2.388454 143 143 39.0 2.388454 125 125 40.0 2.388454 108 108 41.0 2.388454 132 132 42.0 2.388454 99 99 43.0 2.388454 105 105 44.0 2.388454 91 91 45.0 2.388454 77 77 46.0 2.388454 89 89 47.0 2.388454 85 85 48.0 2.388454 71 71 49.0 2.388454 78 78 50.0 2.388454 60 60 51.0 2.388454 59 59 52.0 2.388454 59 59 53.0 2.388454 42 42 54.0 2.388454 55 55 55.0 2.388454 40 40 56.0 2.388454 47 47 57.0 2.388454 50 50 58.0 2.388454 29 29 59.0 2.388454 34 34 60.0 2.388454 30 30 61.0 2.388454 40 40 62.0 2.388454 25 25 63.0 2.388454 42 42 64.0 2.388454 31 31 65.0 2.388454 25 25 66.0 2.388454 34 34 67.0 2.388454 33 33 68.0 2.388454 31 31 69.0 2.388454 23 23 70.0 2.388454 18 18 71.0 2.388454 21 21 72.0 2.388454 20 20 73.0 2.388454 20 20 74.0 2.388454 21 21 75.0 2.388454 19 19 76.0 2.388454 27 27 77.0 2.388454 19 19 78.0 2.388454 10 10 79.0 2.388454 17 17 80.0 2.388454 18 18 81.0 2.388454 16 16 82.0 2.388454 16 16 83.0 2.388454 17 17 84.0 2.388454 7 7 85.0 2.388454 9 9 86.0 2.388454 12 12 87.0 2.388454 11 11 88.0 2.388454 15 15 89.0 2.388454 10 10 90.0 2.388454 5 5 91.0 2.388454 12 12 92.0 2.388454 11 11 93.0 2.388454 5 5 94.0 2.388454 10 10 95.0 2.388454 5 5 96.0 2.388454 8 8 97.0 2.388454 13 13 98.0 2.388454 5 5 99.0 2.388454 4 4 100.0 2.388454 9 9 101.0 0 11 11 102.0 0 4 4 103.0 0 4 4 104.0 0 6 6 105.0 0 5 5 106.0 0 9 9 107.0 0 2 2 108.0 0 7 7 109.0 0 6 6 110.0 0 7 7 111.0 0 5 5 112.0 0 5 5 113.0 0 7 7 114.0 0 6 6 115.0 0 4 4 116.0 0 9 9 117.0 0 1 1 118.0 0 9 9 119.0 0 2 2 120.0 0 9 9 121.0 0 2 2 122.0 0 5 5 123.0 0 4 4 124.0 0 10 10 125.0 0 4 4 126.0 0 4 4 127.0 0 5 5 128.0 0 3 3 129.0 0 5 5 130.0 0 3 3 131.0 0 2 2 132.0 0 2 2 133.0 0 5 5 134.0 0 6 6 135.0 0 2 2 136.0 0 2 2 137.0 0 5 5 138.0 0 2 2 139.0 0 2 2 141.0 0 4 4 142.0 0 2 2 143.0 0 1 1 144.0 0 5 5 145.0 0 2 2 146.0 0 2 2 147.0 0 2 2 148.0 0 3 3 149.0 0 6 6 150.0 0 2 2 151.0 0 3 3 152.0 0 1 1 153.0 0 2 2 154.0 0 2 2 155.0 0 2 2 156.0 0 2 2 157.0 0 2 2 158.0 0 2 2 159.0 0 2 2 160.0 0 3 3 161.0 0 2 2 162.0 0 3 3 163.0 0 3 3 165.0 0 2 2 167.0 0 3 3 169.0 0 2 2 170.0 0 4 4 172.0 0 1 1 173.0 0 1 1 174.0 0 4 4 175.0 0 4 4 176.0 0 2 2 177.0 0 2 2 179.0 0 1 1 181.0 0 2 2 182.0 0 1 1 184.0 0 1 1 185.0 0 4 4 186.0 0 1 1 187.0 0 1 1 188.0 0 3 3 189.0 0 1 1 190.0 0 2 2 191.0 0 1 1 192.0 0 1 1 193.0 0 2 2 194.0 0 1 1 195.0 0 1 1 196.0 0 3 3 197.0 0 1 1 199.0 0 3 3 200.0 0 1 1 202.0 0 1 1 203.0 0 1 1 204.0 0 1 1 206.0 0 3 3 208.0 0 1 1 211.0 0 1 1 212.0 0 1 1 213.0 0 2 2 215.0 0 1 1 217.0 0 1 1 219.0 0 1 1 220.0 0 1 1 222.0 0 1 1 223.0 0 1 1 225.0 0 2 2 227.0 0 2 2 228.0 0 1 1 232.0 0 1 1 233.0 0 1 1 234.0 0 1 1 235.0 0 1 1 237.0 0 1 1 239.0 0 1 1 243.0 0 1 1 244.0 0 1 1 246.0 0 1 1 251.0 0 1 1 254.0 0 1 1 256.0 0 1 1 258.0 0 1 1 261.0 0 1 1 263.0 0 2 2 265.0 0 1 1 266.0 0 1 1 267.0 0 1 1 284.0 0 1 1 287.0 0 1 1 289.0 0 1 1 290.0 0 1 1 292.0 0 2 2 298.0 0 1 1 300.0 0 1 1 301.0 0 1 1 303.0 0 1 1 308.0 0 1 1 310.0 0 1 1 312.0 0 1 1 318.0 0 1 1 319.0 0 1 1 322.0 0 1 1 323.0 0 1 1 328.0 0 1 1 334.0 0 1 1 335.0 0 2 2 341.0 0 1 1 354.0 0 1 1 356.0 0 1 1 382.0 0 1 1 383.0 0 1 1 389.0 0 2 2 391.0 0 1 1 396.0 0 1 1 398.0 0 1 1 399.0 0 1 1 400.0 0 1 1 401.0 0 1 1 447.0 0 1 1 454.0 0 1 1 473.0 0 1 1 476.0 0 1 1 477.0 0 1 1 493.0 0 1 1 512.0 0 2 2 582.0 0 1 1 606.0 0 1 1 610.0 0 1 1 615.0 0 1 1 635.0 0 1 1 650.0 0 1 1 674.0 0 1 1 677.0 0 1 1 761.0 0 1 1 781.0 0 1 1 850.0 0 1 1 955.0 0 1 1 974.0 0 1 1 981.0 0 1 1 1009.0 0 1 1 1021.0 0 1 1 1063.0 0 1 1 1087.0 0 1 1 1183.0 0 1 1 1689.0 0 1 1 1752.0 0 1 1 2981.0 0 1 1 4522.0 0 1 1