## htsjdk.samtools.metrics.StringHeader # MarkDuplicates TAG_DUPLICATE_SET_MEMBERS=true TAGGING_POLICY=All INPUT=[four.sorted.bam] OUTPUT=four.markdup.bam METRICS_FILE=four.markdup_metrics.txt REMOVE_DUPLICATES=false OPTICAL_DUPLICATE_PIXEL_DISTANCE=2500 TMP_DIR=[/tmp/nxf.ei2XOLkBkk] 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 19:30:54 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 four 16 874761 0 2404 16 696440 4515 0.796151 179739 ## HISTOGRAM java.lang.Double BIN CoverageMult all_sets optical_sets non_optical_sets 1.0 1.000193 48949 0 49178 2.0 1.007892 45804 4056 46003 3.0 1.007951 23047 200 22989 4.0 1.007952 14087 17 13996 5.0 1.007952 9238 2 9201 6.0 1.007952 6625 0 6607 7.0 1.007952 4840 0 4794 8.0 1.007952 3813 0 3793 9.0 1.007952 2913 0 2879 10.0 1.007952 2301 0 2283 11.0 1.007952 1978 0 1974 12.0 1.007952 1473 0 1465 13.0 1.007952 1206 0 1196 14.0 1.007952 1082 0 1087 15.0 1.007952 973 0 968 16.0 1.007952 798 0 788 17.0 1.007952 797 0 775 18.0 1.007952 654 0 653 19.0 1.007952 564 0 580 20.0 1.007952 510 0 493 21.0 1.007952 454 0 451 22.0 1.007952 430 0 420 23.0 1.007952 348 0 341 24.0 1.007952 282 0 298 25.0 1.007952 344 0 343 26.0 1.007952 289 0 282 27.0 1.007952 241 0 228 28.0 1.007952 193 0 202 29.0 1.007952 214 0 217 30.0 1.007952 198 0 194 31.0 1.007952 205 0 203 32.0 1.007952 168 0 162 33.0 1.007952 133 0 123 34.0 1.007952 166 0 182 35.0 1.007952 175 0 165 36.0 1.007952 120 0 127 37.0 1.007952 109 0 108 38.0 1.007952 95 0 83 39.0 1.007952 120 0 123 40.0 1.007952 119 0 124 41.0 1.007952 63 0 58 42.0 1.007952 83 0 86 43.0 1.007952 94 0 89 44.0 1.007952 102 0 102 45.0 1.007952 78 0 76 46.0 1.007952 48 0 58 47.0 1.007952 54 0 45 48.0 1.007952 65 0 62 49.0 1.007952 53 0 55 50.0 1.007952 60 0 51 51.0 1.007952 33 0 36 52.0 1.007952 38 0 45 53.0 1.007952 48 0 52 54.0 1.007952 58 0 66 55.0 1.007952 63 0 57 56.0 1.007952 54 0 46 57.0 1.007952 22 0 17 58.0 1.007952 52 0 66 59.0 1.007952 73 0 67 60.0 1.007952 40 0 43 61.0 1.007952 47 0 40 62.0 1.007952 38 0 40 63.0 1.007952 43 0 44 64.0 1.007952 41 0 44 65.0 1.007952 47 0 42 66.0 1.007952 32 0 34 67.0 1.007952 31 0 36 68.0 1.007952 45 0 46 69.0 1.007952 40 0 34 70.0 1.007952 45 0 49 71.0 1.007952 44 0 48 72.0 1.007952 33 0 27 73.0 1.007952 27 0 21 74.0 1.007952 41 0 41 75.0 1.007952 20 0 17 76.0 1.007952 20 0 20 77.0 1.007952 24 0 27 78.0 1.007952 19 0 18 79.0 1.007952 22 0 19 80.0 1.007952 18 0 21 81.0 1.007952 17 0 19 82.0 1.007952 17 0 13 83.0 1.007952 21 0 23 84.0 1.007952 18 0 29 85.0 1.007952 31 0 22 86.0 1.007952 21 0 22 87.0 1.007952 26 0 28 88.0 1.007952 26 0 23 89.0 1.007952 20 0 30 90.0 1.007952 33 0 28 91.0 1.007952 24 0 17 92.0 1.007952 23 0 17 93.0 1.007952 14 0 19 94.0 1.007952 14 0 12 95.0 1.007952 19 0 20 96.0 1.007952 10 0 11 97.0 1.007952 12 0 10 98.0 1.007952 14 0 12 99.0 1.007952 7 0 9 100.0 1.007952 17 0 19 101.0 0 11 0 5 102.0 0 3 0 1 103.0 0 2 0 1 105.0 0 1 0 1 107.0 0 2 0 2 109.0 0 1 0 1 114.0 0 0 0 1 115.0 0 2 0 1 117.0 0 1 0 1 121.0 0 0 0 1 122.0 0 1 0 0