## htsjdk.samtools.metrics.StringHeader # MarkDuplicates TAG_DUPLICATE_SET_MEMBERS=true TAGGING_POLICY=All INPUT=[two.sorted.bam] OUTPUT=two.markdup.bam METRICS_FILE=two.markdup_metrics.txt REMOVE_DUPLICATES=false OPTICAL_DUPLICATE_PIXEL_DISTANCE=2500 TMP_DIR=[/tmp/nxf.a1OFT5tvei] VALIDATION_STRINGENCY=SILENT MAX_RECORDS_IN_RAM=250000 CREATE_INDEX=true MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false FLOW_MODE=false FLOW_DUP_STRATEGY=FLOW_QUALITY_SUM_STRATEGY FLOW_USE_END_IN_UNPAIRED_READS=false FLOW_USE_UNPAIRED_CLIPPED_END=false FLOW_UNPAIRED_END_UNCERTAINTY=0 FLOW_UNPAIRED_START_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= MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false COMPRESSION_LEVEL=5 CREATE_MD5_FILE=false USE_JDK_DEFLATER=false USE_JDK_INFLATER=false ## htsjdk.samtools.metrics.StringHeader # Started on: Mon Jun 08 19:34:50 UTC 2026 ## 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 two 6 878864 0 2410 5 700137 4560 0.796639 180131 ## HISTOGRAM java.lang.Double BIN CoverageMult all_sets optical_sets non_optical_sets 1.0 1.000191 48752 0 48981 2.0 1.007797 45388 4132 45595 3.0 1.007855 23405 185 23321 4.0 1.007856 14500 18 14442 5.0 1.007856 9603 1 9557 6.0 1.007856 6620 0 6557 7.0 1.007856 4818 0 4788 8.0 1.007856 3577 0 3575 9.0 1.007856 2919 0 2904 10.0 1.007856 2430 0 2409 11.0 1.007856 1841 0 1836 12.0 1.007856 1499 0 1476 13.0 1.007856 1320 0 1331 14.0 1.007856 1097 0 1078 15.0 1.007856 903 0 894 16.0 1.007856 853 0 846 17.0 1.007856 786 0 773 18.0 1.007856 597 0 603 19.0 1.007856 576 0 577 20.0 1.007856 491 0 483 21.0 1.007856 431 0 443 22.0 1.007856 399 0 369 23.0 1.007856 325 0 336 24.0 1.007856 342 0 350 25.0 1.007856 286 0 281 26.0 1.007856 257 0 245 27.0 1.007856 270 0 280 28.0 1.007856 234 0 224 29.0 1.007856 204 0 199 30.0 1.007856 187 0 192 31.0 1.007856 212 0 210 32.0 1.007856 158 0 148 33.0 1.007856 184 0 189 34.0 1.007856 148 0 153 35.0 1.007856 135 0 120 36.0 1.007856 120 0 126 37.0 1.007856 149 0 149 38.0 1.007856 110 0 111 39.0 1.007856 122 0 120 40.0 1.007856 111 0 119 41.0 1.007856 142 0 134 42.0 1.007856 76 0 81 43.0 1.007856 116 0 120 44.0 1.007856 100 0 84 45.0 1.007856 88 0 95 46.0 1.007856 72 0 73 47.0 1.007856 69 0 67 48.0 1.007856 76 0 82 49.0 1.007856 85 0 85 50.0 1.007856 71 0 64 51.0 1.007856 53 0 47 52.0 1.007856 47 0 43 53.0 1.007856 35 0 39 54.0 1.007856 51 0 50 55.0 1.007856 41 0 47 56.0 1.007856 65 0 62 57.0 1.007856 35 0 31 58.0 1.007856 34 0 39 59.0 1.007856 37 0 34 60.0 1.007856 46 0 44 61.0 1.007856 37 0 37 62.0 1.007856 45 0 53 63.0 1.007856 47 0 41 64.0 1.007856 35 0 32 65.0 1.007856 42 0 41 66.0 1.007856 33 0 32 67.0 1.007856 25 0 24 68.0 1.007856 33 0 38 69.0 1.007856 27 0 32 70.0 1.007856 44 0 40 71.0 1.007856 35 0 29 72.0 1.007856 34 0 35 73.0 1.007856 31 0 31 74.0 1.007856 33 0 33 75.0 1.007856 26 0 19 76.0 1.007856 23 0 37 77.0 1.007856 31 0 30 78.0 1.007856 20 0 12 79.0 1.007856 15 0 21 80.0 1.007856 29 0 22 81.0 1.007856 19 0 16 82.0 1.007856 16 0 25 83.0 1.007856 29 0 27 84.0 1.007856 29 0 26 85.0 1.007856 18 0 21 86.0 1.007856 13 0 18 87.0 1.007856 29 0 28 88.0 1.007856 24 0 20 89.0 1.007856 22 0 21 90.0 1.007856 16 0 18 91.0 1.007856 26 0 22 92.0 1.007856 19 0 19 93.0 1.007856 13 0 11 94.0 1.007856 10 0 11 95.0 1.007856 12 0 14 96.0 1.007856 18 0 15 97.0 1.007856 17 0 20 98.0 1.007856 16 0 14 99.0 1.007856 15 0 13 100.0 1.007856 7 0 7 101.0 0 3 0 2 102.0 0 3 0 1 103.0 0 2 0 1 104.0 0 1 0 0 106.0 0 0 0 1 109.0 0 1 0 1 110.0 0 2 0 1 112.0 0 1 0 1 114.0 0 0 0 1 115.0 0 1 0 1 116.0 0 1 0 0 125.0 0 1 0 1