## htsjdk.samtools.metrics.StringHeader # MarkDuplicates INPUT=[/project/berglandlab/DEST/dest_mapped/DESTv1/AT_Nie_Mau_1_2015-07-20/AT_Nie_Mau_1_2015-07-20.sorted_merged.bam] OUTPUT=/project/berglandlab/DEST/dest_mapped/DESTv1/AT_Nie_Mau_1_2015-07-20/AT_Nie_Mau_1_2015-07-20.dedup.bam METRICS_FILE=/project/berglandlab/DEST/dest_mapped/DESTv1/AT_Nie_Mau_1_2015-07-20/AT_Nie_Mau_1_2015-07-20.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 09:22:57 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 14173720 36372629 0 0 5452100 3970085 0 0.154078 154258479 ## HISTOGRAM java.lang.Double BIN VALUE all_sets non_optical_sets 1.0 1 28491696 28491696 2.0 1.789946 3188046 3188046 3.0 2.413962 312650 312650 4.0 2.906901 30272 30272 5.0 3.296296 3733 3733 6.0 3.603897 934 934 7.0 3.846886 459 459 8.0 4.038834 270 270 9.0 4.190462 186 186 10.0 4.310241 154 154 11.0 4.404859 125 125 12.0 4.479603 109 109 13.0 4.538646 80 80 14.0 4.585287 69 69 15.0 4.622131 62 62 16.0 4.651236 50 50 17.0 4.674227 41 41 18.0 4.692389 47 47 19.0 4.706736 36 36 20.0 4.718069 23 23 21.0 4.727022 32 32 22.0 4.734094 32 32 23.0 4.739681 22 22 24.0 4.744094 26 26 25.0 4.74758 25 25 26.0 4.750334 19 19 27.0 4.752509 21 21 28.0 4.754228 15 15 29.0 4.755585 19 19 30.0 4.756658 15 15 31.0 4.757505 9 9 32.0 4.758174 18 18 33.0 4.758702 11 11 34.0 4.75912 14 14 35.0 4.75945 14 14 36.0 4.75971 13 13 37.0 4.759916 6 6 38.0 4.760079 11 11 39.0 4.760207 11 11 40.0 4.760309 5 5 41.0 4.760389 3 3 42.0 4.760452 9 9 43.0 4.760502 8 8 44.0 4.760542 1 1 45.0 4.760573 8 8 46.0 4.760598 5 5 47.0 4.760617 4 4 48.0 4.760633 10 10 49.0 4.760645 1 1 50.0 4.760654 4 4 51.0 4.760662 2 2 52.0 4.760668 7 7 53.0 4.760673 3 3 54.0 4.760676 3 3 55.0 4.760679 3 3 56.0 4.760682 5 5 57.0 4.760683 2 2 58.0 4.760685 6 6 59.0 4.760686 4 4 60.0 4.760687 3 3 61.0 4.760688 4 4 62.0 4.760688 4 4 63.0 4.760689 0 0 64.0 4.760689 4 4 65.0 4.760689 0 0 66.0 4.76069 3 3 67.0 4.76069 3 3 68.0 4.76069 3 3 69.0 4.76069 0 0 70.0 4.76069 2 2 71.0 4.76069 0 0 72.0 4.76069 2 2 73.0 4.76069 0 0 74.0 4.76069 4 4 75.0 4.76069 1 1 76.0 4.76069 1 1 77.0 4.76069 2 2 78.0 4.76069 2 2 79.0 4.76069 1 1 80.0 4.76069 1 1 81.0 4.76069 1 1 82.0 4.76069 1 1 83.0 4.76069 1 1 84.0 4.76069 2 2 85.0 4.76069 0 0 86.0 4.76069 1 1 87.0 4.76069 0 0 88.0 4.76069 1 1 89.0 4.76069 2 2 90.0 4.76069 2 2 91.0 4.76069 1 1 92.0 4.76069 1 1 93.0 4.76069 0 0 94.0 4.76069 0 0 95.0 4.76069 1 1 96.0 4.76069 1 1 97.0 4.76069 4 4 98.0 4.76069 2 2 99.0 4.76069 1 1 100.0 4.76069 1 1 102.0 0 1 1 103.0 0 1 1 104.0 0 2 2 105.0 0 1 1 106.0 0 1 1 108.0 0 2 2 109.0 0 2 2 110.0 0 1 1 112.0 0 1 1 113.0 0 2 2 115.0 0 1 1 118.0 0 2 2 119.0 0 1 1 125.0 0 1 1 126.0 0 1 1 129.0 0 2 2 133.0 0 1 1 134.0 0 1 1 139.0 0 1 1 142.0 0 1 1 147.0 0 1 1 148.0 0 1 1 150.0 0 1 1 153.0 0 1 1 157.0 0 2 2 161.0 0 1 1 162.0 0 1 1 166.0 0 1 1 170.0 0 1 1 174.0 0 1 1 177.0 0 1 1 181.0 0 1 1 190.0 0 2 2 196.0 0 1 1 198.0 0 1 1 204.0 0 2 2 205.0 0 1 1 206.0 0 1 1 212.0 0 2 2 231.0 0 2 2 233.0 0 1 1 242.0 0 1 1 260.0 0 1 1 272.0 0 1 1 286.0 0 1 1 299.0 0 1 1 305.0 0 1 1 357.0 0 1 1 413.0 0 2 2 420.0 0 1 1 465.0 0 1 1 618.0 0 1 1