## 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-GSM1606234.samtools-coordinate-unsieved.bam] OUTPUT=/ceph/rimlsfnwi/data/moldevbio/heeringen/siebrenf/xt_rna/results/star/Xenopus_tropicalis_v9.1-GSM1606234.samtools-coordinate-dupmarked.bam METRICS_FILE=/ceph/rimlsfnwi/data/moldevbio/heeringen/siebrenf/xt_rna/results/qc/markdup/Xenopus_tropicalis_v9.1-GSM1606234.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 14:31:54 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 27594475 3914042 0 0 4021673 0 0.145742 85228097 ## HISTOGRAM java.lang.Double BIN CoverageMult all_sets non_optical_sets 1.0 1 21633389 21633389 2.0 1.723415 1286577 1286577 3.0 2.246745 307681 307681 4.0 2.625329 128965 128965 5.0 2.899203 67227 67227 6.0 3.097327 39828 39828 7.0 3.240653 25934 25934 8.0 3.344338 17712 17712 9.0 3.419344 12867 12867 10.0 3.473606 9375 9375 11.0 3.512859 7178 7178 12.0 3.541255 5469 5469 13.0 3.561798 4412 4412 14.0 3.576658 3729 3729 15.0 3.587409 2810 2810 16.0 3.595186 2401 2401 17.0 3.600812 1947 1947 18.0 3.604882 1668 1668 19.0 3.607826 1433 1433 20.0 3.609956 1284 1284 21.0 3.611497 1093 1093 22.0 3.612611 946 946 23.0 3.613418 825 825 24.0 3.614001 685 685 25.0 3.614423 656 656 26.0 3.614728 577 577 27.0 3.614949 483 483 28.0 3.615109 411 411 29.0 3.615225 383 383 30.0 3.615308 352 352 31.0 3.615369 336 336 32.0 3.615412 278 278 33.0 3.615444 260 260 34.0 3.615467 221 221 35.0 3.615483 199 199 36.0 3.615495 214 214 37.0 3.615504 146 146 38.0 3.61551 165 165 39.0 3.615515 156 156 40.0 3.615518 136 136 41.0 3.615521 145 145 42.0 3.615522 123 123 43.0 3.615524 113 113 44.0 3.615524 126 126 45.0 3.615525 119 119 46.0 3.615526 96 96 47.0 3.615526 83 83 48.0 3.615526 81 81 49.0 3.615526 79 79 50.0 3.615526 63 63 51.0 3.615527 63 63 52.0 3.615527 57 57 53.0 3.615527 57 57 54.0 3.615527 54 54 55.0 3.615527 34 34 56.0 3.615527 40 40 57.0 3.615527 41 41 58.0 3.615527 37 37 59.0 3.615527 32 32 60.0 3.615527 33 33 61.0 3.615527 38 38 62.0 3.615527 39 39 63.0 3.615527 32 32 64.0 3.615527 42 42 65.0 3.615527 25 25 66.0 3.615527 28 28 67.0 3.615527 19 19 68.0 3.615527 27 27 69.0 3.615527 20 20 70.0 3.615527 16 16 71.0 3.615527 22 22 72.0 3.615527 24 24 73.0 3.615527 21 21 74.0 3.615527 17 17 75.0 3.615527 23 23 76.0 3.615527 19 19 77.0 3.615527 21 21 78.0 3.615527 20 20 79.0 3.615527 16 16 80.0 3.615527 15 15 81.0 3.615527 10 10 82.0 3.615527 11 11 83.0 3.615527 10 10 84.0 3.615527 11 11 85.0 3.615527 7 7 86.0 3.615527 12 12 87.0 3.615527 11 11 88.0 3.615527 10 10 89.0 3.615527 9 9 90.0 3.615527 10 10 91.0 3.615527 11 11 92.0 3.615527 7 7 93.0 3.615527 9 9 94.0 3.615527 7 7 95.0 3.615527 6 6 96.0 3.615527 7 7 97.0 3.615527 10 10 98.0 3.615527 11 11 99.0 3.615527 11 11 100.0 3.615527 7 7 101.0 0 8 8 102.0 0 7 7 103.0 0 6 6 104.0 0 9 9 105.0 0 6 6 106.0 0 9 9 107.0 0 7 7 108.0 0 2 2 109.0 0 4 4 110.0 0 8 8 111.0 0 3 3 112.0 0 3 3 113.0 0 3 3 114.0 0 5 5 115.0 0 8 8 117.0 0 3 3 118.0 0 3 3 119.0 0 3 3 120.0 0 2 2 121.0 0 2 2 122.0 0 3 3 123.0 0 2 2 124.0 0 3 3 125.0 0 1 1 126.0 0 2 2 127.0 0 1 1 128.0 0 1 1 129.0 0 1 1 130.0 0 3 3 131.0 0 1 1 132.0 0 1 1 133.0 0 1 1 134.0 0 4 4 135.0 0 5 5 136.0 0 4 4 137.0 0 1 1 138.0 0 3 3 139.0 0 4 4 140.0 0 2 2 141.0 0 2 2 142.0 0 3 3 143.0 0 1 1 144.0 0 2 2 146.0 0 4 4 148.0 0 3 3 150.0 0 1 1 151.0 0 2 2 153.0 0 2 2 155.0 0 2 2 156.0 0 3 3 157.0 0 1 1 158.0 0 2 2 165.0 0 2 2 166.0 0 3 3 168.0 0 2 2 169.0 0 2 2 170.0 0 1 1 171.0 0 2 2 173.0 0 2 2 174.0 0 3 3 175.0 0 1 1 176.0 0 3 3 177.0 0 1 1 178.0 0 1 1 179.0 0 2 2 180.0 0 2 2 185.0 0 1 1 186.0 0 2 2 187.0 0 3 3 188.0 0 1 1 190.0 0 1 1 193.0 0 1 1 195.0 0 1 1 196.0 0 2 2 197.0 0 1 1 201.0 0 1 1 204.0 0 1 1 211.0 0 2 2 216.0 0 1 1 221.0 0 1 1 223.0 0 1 1 224.0 0 1 1 227.0 0 2 2 228.0 0 1 1 230.0 0 1 1 231.0 0 1 1 235.0 0 1 1 241.0 0 1 1 242.0 0 1 1 252.0 0 1 1 257.0 0 1 1 263.0 0 1 1 276.0 0 1 1 292.0 0 1 1 302.0 0 1 1 322.0 0 1 1 324.0 0 1 1 325.0 0 1 1 345.0 0 1 1 360.0 0 1 1 374.0 0 1 1 398.0 0 1 1 421.0 0 1 1 427.0 0 1 1 452.0 0 1 1 458.0 0 1 1 721.0 0 1 1 1289.0 0 1 1