## htsjdk.samtools.metrics.StringHeader # MarkDuplicates --INPUT H3K27ac_R1.target.filtered.sorted.bam --OUTPUT H3K27ac_R1.target.markdup.bam --METRICS_FILE H3K27ac_R1.target.markdup.MarkDuplicates.metrics.txt --REMOVE_DUPLICATES false --ASSUME_SORT_ORDER coordinate --TMP_DIR tmp --VALIDATION_STRINGENCY LENIENT --REFERENCE_SEQUENCE GCA_000001405.15_GRCh38_no_alt_plus_hs38d1_analysis_set.fna --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --TAGGING_POLICY DontTag --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_QUALITY_SUM_STRATEGY false --USE_END_IN_UNPAIRED_READS false --USE_UNPAIRED_CLIPPED_END false --UNPAIRED_END_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --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 --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --GA4GH_CLIENT_SECRETS client_secrets.json --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false ## htsjdk.samtools.metrics.StringHeader # Started on: Fri May 26 22:03:58 GMT 2023 ## 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 13644545 0 0 0 454477 3000 0.033308 201519454 ## HISTOGRAM java.lang.Double BIN CoverageMult all_sets optical_sets non_optical_sets 1.0 1.000213 12748440 0 12751150 2.0 1.934944 429168 2996 426738 3.0 2.808482 12086 2 11816 4.0 3.624832 365 0 355 5.0 4.387737 7 0 7 6.0 5.100698 0 0 0 7.0 5.766983 1 0 1 8.0 6.389649 0 0 0 9.0 6.97155 1 0 1 10.0 7.515356 0 0 0 11.0 8.023561 0 0 0 12.0 8.498495 0 0 0 13.0 8.942337 0 0 0 14.0 9.357122 0 0 0 15.0 9.744752 0 0 0 16.0 10.107005 0 0 0 17.0 10.445542 0 0 0 18.0 10.761916 0 0 0 19.0 11.057579 0 0 0 20.0 11.333885 0 0 0 21.0 11.592102 0 0 0 22.0 11.833415 0 0 0 23.0 12.058929 0 0 0 24.0 12.26968 0 0 0 25.0 12.466634 0 0 0 26.0 12.650693 0 0 0 27.0 12.822703 0 0 0 28.0 12.983452 0 0 0 29.0 13.133677 0 0 0 30.0 13.274067 0 0 0 31.0 13.405267 0 0 0 32.0 13.527877 0 0 0 33.0 13.64246 0 0 0 34.0 13.749542 0 0 0 35.0 13.849613 0 0 0 36.0 13.943133 0 0 0 37.0 14.030531 0 0 0 38.0 14.112207 0 0 0 39.0 14.188536 0 0 0 40.0 14.259868 0 0 0 41.0 14.32653 0 0 0 42.0 14.388827 0 0 0 43.0 14.447047 0 0 0 44.0 14.501455 0 0 0 45.0 14.552301 0 0 0 46.0 14.599818 0 0 0 47.0 14.644224 0 0 0 48.0 14.685724 0 0 0 49.0 14.724506 0 0 0 50.0 14.76075 0 0 0 51.0 14.79462 0 0 0 52.0 14.826274 0 0 0 53.0 14.855855 0 0 0 54.0 14.883499 0 0 0 55.0 14.909334 0 0 0 56.0 14.933477 0 0 0 57.0 14.95604 0 0 0 58.0 14.977126 0 0 0 59.0 14.996831 0 0 0 60.0 15.015246 0 0 0 61.0 15.032456 0 0 0 62.0 15.048539 0 0 0 63.0 15.063569 0 0 0 64.0 15.077615 0 0 0 65.0 15.090741 0 0 0 66.0 15.103009 0 0 0 67.0 15.114473 0 0 0 68.0 15.125186 0 0 0 69.0 15.135198 0 0 0 70.0 15.144555 0 0 0 71.0 15.153299 0 0 0 72.0 15.161471 0 0 0 73.0 15.169108 0 0 0 74.0 15.176244 0 0 0 75.0 15.182914 0 0 0 76.0 15.189147 0 0 0 77.0 15.194972 0 0 0 78.0 15.200415 0 0 0 79.0 15.205502 0 0 0 80.0 15.210257 0 0 0 81.0 15.214699 0 0 0 82.0 15.218851 0 0 0 83.0 15.222732 0 0 0 84.0 15.226358 0 0 0 85.0 15.229747 0 0 0 86.0 15.232914 0 0 0 87.0 15.235873 0 0 0 88.0 15.238639 0 0 0 89.0 15.241224 0 0 0 90.0 15.243639 0 0 0 91.0 15.245897 0 0 0 92.0 15.248006 0 0 0 93.0 15.249978 0 0 0 94.0 15.25182 0 0 0 95.0 15.253542 0 0 0 96.0 15.255151 0 0 0 97.0 15.256655 0 0 0 98.0 15.25806 0 0 0 99.0 15.259374 0 0 0 100.0 15.260601 0 0 0