## htsjdk.samtools.metrics.StringHeader # MarkDuplicates INPUT=[/project/berglandlab/DEST/dest_mapped/DESTv1/FR_Ess_Vil_1_2015-10-14/FR_Ess_Vil_1_2015-10-14.sorted_merged.bam] OUTPUT=/project/berglandlab/DEST/dest_mapped/DESTv1/FR_Ess_Vil_1_2015-10-14/FR_Ess_Vil_1_2015-10-14.dedup.bam METRICS_FILE=/project/berglandlab/DEST/dest_mapped/DESTv1/FR_Ess_Vil_1_2015-10-14/FR_Ess_Vil_1_2015-10-14.mark_duplicates_report.txt REMOVE_DUPLICATES=true VALIDATION_STRINGENCY=SILENT 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 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 USE_JDK_DEFLATER=false USE_JDK_INFLATER=false ## htsjdk.samtools.metrics.StringHeader # Started on: Fri Jan 20 08:51:06 UTC 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 lib1 6710499 33025796 0 0 2454615 3062372 0 0.11791 166893732 ## HISTOGRAM java.lang.Double BIN VALUE all_sets non_optical_sets 1.0 1 26872636 26872636 2.0 1.820464 2475915 2475915 3.0 2.493625 196414 196414 4.0 3.04593 15909 15909 5.0 3.499076 2053 2053 6.0 3.870866 758 758 7.0 4.175906 527 527 8.0 4.426181 404 404 9.0 4.631523 271 271 10.0 4.799998 239 239 11.0 4.938226 198 198 12.0 5.051637 168 168 13.0 5.144686 189 189 14.0 5.22103 171 171 15.0 5.283668 144 144 16.0 5.335059 122 122 17.0 5.377224 139 139 18.0 5.411819 119 119 19.0 5.440203 118 118 20.0 5.463491 124 124 21.0 5.482598 95 95 22.0 5.498275 102 102 23.0 5.511137 64 64 24.0 5.52169 76 76 25.0 5.530348 71 71 26.0 5.537452 70 70 27.0 5.54328 61 61 28.0 5.548062 76 76 29.0 5.551985 56 56 30.0 5.555204 46 46 31.0 5.557846 51 51 32.0 5.560013 51 51 33.0 5.56179 40 40 34.0 5.563249 41 41 35.0 5.564446 45 45 36.0 5.565428 34 34 37.0 5.566234 32 32 38.0 5.566895 33 33 39.0 5.567437 25 25 40.0 5.567882 40 40 41.0 5.568247 29 29 42.0 5.568546 21 21 43.0 5.568792 24 24 44.0 5.568994 22 22 45.0 5.569159 22 22 46.0 5.569295 13 13 47.0 5.569406 23 23 48.0 5.569498 19 19 49.0 5.569573 24 24 50.0 5.569634 15 15 51.0 5.569685 15 15 52.0 5.569726 18 18 53.0 5.56976 18 18 54.0 5.569788 18 18 55.0 5.569811 11 11 56.0 5.56983 13 13 57.0 5.569845 17 17 58.0 5.569858 19 19 59.0 5.569868 9 9 60.0 5.569876 12 12 61.0 5.569883 8 8 62.0 5.569889 15 15 63.0 5.569894 12 12 64.0 5.569898 17 17 65.0 5.569901 10 10 66.0 5.569903 15 15 67.0 5.569906 11 11 68.0 5.569907 10 10 69.0 5.569909 14 14 70.0 5.56991 10 10 71.0 5.569911 8 8 72.0 5.569912 7 7 73.0 5.569912 9 9 74.0 5.569913 11 11 75.0 5.569913 13 13 76.0 5.569914 8 8 77.0 5.569914 9 9 78.0 5.569914 5 5 79.0 5.569914 11 11 80.0 5.569914 13 13 81.0 5.569915 10 10 82.0 5.569915 7 7 83.0 5.569915 7 7 84.0 5.569915 7 7 85.0 5.569915 9 9 86.0 5.569915 14 14 87.0 5.569915 7 7 88.0 5.569915 4 4 89.0 5.569915 10 10 90.0 5.569915 5 5 91.0 5.569915 5 5 92.0 5.569915 6 6 93.0 5.569915 6 6 94.0 5.569915 4 4 95.0 5.569915 6 6 96.0 5.569915 8 8 97.0 5.569915 4 4 98.0 5.569915 6 6 99.0 5.569915 4 4 100.0 5.569915 1 1 101.0 0 3 3 102.0 0 3 3 103.0 0 3 3 104.0 0 7 7 105.0 0 3 3 106.0 0 5 5 107.0 0 8 8 108.0 0 4 4 109.0 0 4 4 110.0 0 3 3 111.0 0 1 1 112.0 0 2 2 113.0 0 2 2 114.0 0 3 3 115.0 0 4 4 116.0 0 4 4 117.0 0 3 3 118.0 0 2 2 120.0 0 3 3 121.0 0 2 2 123.0 0 1 1 124.0 0 3 3 125.0 0 1 1 126.0 0 2 2 127.0 0 4 4 128.0 0 4 4 129.0 0 2 2 130.0 0 5 5 131.0 0 4 4 132.0 0 2 2 133.0 0 1 1 134.0 0 3 3 135.0 0 1 1 136.0 0 3 3 137.0 0 1 1 138.0 0 6 6 140.0 0 2 2 142.0 0 1 1 143.0 0 1 1 144.0 0 1 1 146.0 0 2 2 147.0 0 3 3 148.0 0 1 1 149.0 0 2 2 152.0 0 1 1 154.0 0 1 1 157.0 0 1 1 158.0 0 2 2 159.0 0 1 1 161.0 0 1 1 162.0 0 1 1 165.0 0 2 2 166.0 0 1 1 169.0 0 1 1 171.0 0 1 1 172.0 0 1 1 174.0 0 1 1 175.0 0 1 1 178.0 0 3 3 179.0 0 1 1 182.0 0 1 1 183.0 0 1 1 185.0 0 1 1 186.0 0 1 1 188.0 0 1 1 192.0 0 1 1 196.0 0 1 1 199.0 0 1 1 201.0 0 1 1 202.0 0 1 1 203.0 0 1 1 207.0 0 1 1 210.0 0 1 1 212.0 0 1 1 213.0 0 1 1 215.0 0 1 1 216.0 0 1 1 219.0 0 1 1 221.0 0 1 1 222.0 0 1 1 233.0 0 1 1 239.0 0 1 1 243.0 0 1 1 245.0 0 1 1 247.0 0 1 1 253.0 0 1 1 262.0 0 3 3 264.0 0 1 1 265.0 0 1 1 268.0 0 1 1 282.0 0 1 1 288.0 0 1 1 289.0 0 1 1 297.0 0 1 1 300.0 0 1 1 310.0 0 1 1 365.0 0 1 1 379.0 0 1 1 501.0 0 1 1