## htsjdk.samtools.metrics.StringHeader # MarkDuplicates --INPUT H1-H3K4me1_R1.target.filtered.sorted.bam --OUTPUT H1-H3K4me1_R1.target.markdup.bam --METRICS_FILE H1-H3K4me1_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: Thu Jun 15 14:29:31 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 7198839 0 0 0 152069 1157 0.021124 169237444 ## HISTOGRAM java.lang.Double BIN CoverageMult all_sets optical_sets non_optical_sets 1.0 1.000157 6897198 0 6898302 2.0 1.958663 147121 1157 146068 3.0 2.877252 2409 0 2360 4.0 3.757587 40 0 38 5.0 4.60126 1 0 1 6.0 5.409798 0 0 0 7.0 6.184665 1 0 1 8.0 6.927262 0 0 0 9.0 7.638934 0 0 0 10.0 8.320969 0 0 0 11.0 8.9746 0 0 0 12.0 9.601011 0 0 0 13.0 10.201335 0 0 0 14.0 10.776659 0 0 0 15.0 11.328023 0 0 0 16.0 11.856426 0 0 0 17.0 12.362823 0 0 0 18.0 12.848132 0 0 0 19.0 13.31323 0 0 0 20.0 13.758959 0 0 0 21.0 14.186126 0 0 0 22.0 14.595503 0 0 0 23.0 14.987832 0 0 0 24.0 15.363822 0 0 0 25.0 15.724155 0 0 0 26.0 16.069481 0 0 0 27.0 16.400426 0 0 0 28.0 16.717589 0 0 0 29.0 17.021544 0 0 0 30.0 17.312841 0 0 0 31.0 17.592006 0 0 0 32.0 17.859546 0 0 0 33.0 18.115944 0 0 0 34.0 18.361664 0 0 0 35.0 18.597152 0 0 0 36.0 18.822832 0 0 0 37.0 19.039115 0 0 0 38.0 19.24639 0 0 0 39.0 19.445033 0 0 0 40.0 19.635403 0 0 0 41.0 19.817846 0 0 0 42.0 19.992691 0 0 0 43.0 20.160254 0 0 0 44.0 20.32084 0 0 0 45.0 20.474737 0 0 0 46.0 20.622226 0 0 0 47.0 20.763573 0 0 0 48.0 20.899033 0 0 0 49.0 21.028852 0 0 0 50.0 21.153264 0 0 0 51.0 21.272496 0 0 0 52.0 21.386762 0 0 0 53.0 21.496269 0 0 0 54.0 21.601216 0 0 0 55.0 21.701793 0 0 0 56.0 21.798181 0 0 0 57.0 21.890555 0 0 0 58.0 21.979082 0 0 0 59.0 22.063922 0 0 0 60.0 22.14523 0 0 0 61.0 22.223151 0 0 0 62.0 22.297827 0 0 0 63.0 22.369393 0 0 0 64.0 22.437979 0 0 0 65.0 22.503709 0 0 0 66.0 22.566701 0 0 0 67.0 22.62707 0 0 0 68.0 22.684925 0 0 0 69.0 22.740371 0 0 0 70.0 22.793507 0 0 0 71.0 22.844431 0 0 0 72.0 22.893234 0 0 0 73.0 22.940004 0 0 0 74.0 22.984827 0 0 0 75.0 23.027784 0 0 0 76.0 23.068951 0 0 0 77.0 23.108404 0 0 0 78.0 23.146214 0 0 0 79.0 23.182449 0 0 0 80.0 23.217175 0 0 0 81.0 23.250455 0 0 0 82.0 23.282349 0 0 0 83.0 23.312915 0 0 0 84.0 23.342208 0 0 0 85.0 23.370281 0 0 0 86.0 23.397185 0 0 0 87.0 23.422969 0 0 0 88.0 23.447679 0 0 0 89.0 23.471359 0 0 0 90.0 23.494054 0 0 0 91.0 23.515804 0 0 0 92.0 23.536647 0 0 0 93.0 23.556623 0 0 0 94.0 23.575767 0 0 0 95.0 23.594113 0 0 0 96.0 23.611696 0 0 0 97.0 23.628546 0 0 0 98.0 23.644695 0 0 0 99.0 23.660171 0 0 0 100.0 23.675002 0 0 0