## htsjdk.samtools.metrics.StringHeader # MarkDuplicates INPUT=[/project/berglandlab/DEST/dest_mapped/DESTv1/US_New_Ith_1_2012-09-23/US_New_Ith_1_2012-09-23.sorted_merged.bam] OUTPUT=/project/berglandlab/DEST/dest_mapped/DESTv1/US_New_Ith_1_2012-09-23/US_New_Ith_1_2012-09-23.dedup.bam METRICS_FILE=/project/berglandlab/DEST/dest_mapped/DESTv1/US_New_Ith_1_2012-09-23/US_New_Ith_1_2012-09-23.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 17:24:36 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 1852184 23210135 0 0 377185 147368 0 0.013919 1820027611 ## HISTOGRAM java.lang.Double BIN VALUE all_sets non_optical_sets 1.0 1 22755951 22755951 2.0 1.987328 68778 68778 3.0 2.962146 5625 5625 4.0 3.92461 1107 1107 5.0 4.874879 415 415 6.0 5.813106 216 216 7.0 6.739444 142 142 8.0 7.654045 112 112 9.0 8.557055 72 72 10.0 9.448623 74 74 11.0 10.328893 62 62 12.0 11.198009 54 54 13.0 12.056112 31 31 14.0 12.903341 29 29 15.0 13.739834 33 33 16.0 14.565728 25 25 17.0 15.381156 28 28 18.0 16.186251 15 15 19.0 16.981144 11 11 20.0 17.765965 19 19 21.0 18.540841 14 14 22.0 19.305898 6 6 23.0 20.06126 16 16 24.0 20.807051 7 7 25.0 21.543391 11 11 26.0 22.2704 5 5 27.0 22.988197 4 4 28.0 23.696899 9 9 29.0 24.39662 2 2 30.0 25.087474 5 5 31.0 25.769574 4 4 32.0 26.443031 4 4 33.0 27.107954 1 1 34.0 27.764451 5 5 35.0 28.41263 9 9 36.0 29.052595 1 1 37.0 29.68445 1 1 38.0 30.308299 6 6 39.0 30.924242 5 5 40.0 31.532381 6 6 41.0 32.132814 2 2 42.0 32.725637 5 5 43.0 33.310949 1 1 44.0 33.888844 2 2 45.0 34.459417 3 3 46.0 35.022759 1 1 47.0 35.578962 6 6 48.0 36.128118 3 3 49.0 36.670315 3 3 50.0 37.205641 3 3 51.0 37.734184 1 1 52.0 38.256029 3 3 53.0 38.771262 2 2 54.0 39.279966 5 5 55.0 39.782223 1 1 56.0 40.278117 1 1 57.0 40.767726 3 3 58.0 41.251132 1 1 59.0 41.728411 5 5 60.0 42.199643 0 0 61.0 42.664904 5 5 62.0 43.124269 0 0 63.0 43.577813 1 1 64.0 44.02561 1 1 65.0 44.467732 1 1 66.0 44.904252 1 1 67.0 45.335241 0 0 68.0 45.760768 3 3 69.0 46.180903 1 1 70.0 46.595715 0 0 71.0 47.00527 0 0 72.0 47.409635 1 1 73.0 47.808877 2 2 74.0 48.203059 2 2 75.0 48.592246 1 1 76.0 48.976502 1 1 77.0 49.355888 2 2 78.0 49.730467 1 1 79.0 50.1003 2 2 80.0 50.465446 3 3 81.0 50.825965 0 0 82.0 51.181916 3 3 83.0 51.533356 0 0 84.0 51.880343 0 0 85.0 52.222933 0 0 86.0 52.561182 0 0 87.0 52.895145 0 0 88.0 53.224876 1 1 89.0 53.550428 1 1 90.0 53.871856 3 3 91.0 54.18921 1 1 92.0 54.502543 2 2 93.0 54.811905 0 0 94.0 55.117347 2 2 95.0 55.418919 0 0 96.0 55.71667 3 3 97.0 56.010647 0 0 98.0 56.300899 3 3 99.0 56.587474 1 1 100.0 56.870417 0 0 101.0 0 3 3 102.0 0 1 1 104.0 0 1 1 105.0 0 1 1 107.0 0 2 2 109.0 0 1 1 110.0 0 2 2 111.0 0 1 1 112.0 0 1 1 116.0 0 1 1 118.0 0 1 1 121.0 0 2 2 126.0 0 1 1 129.0 0 1 1 131.0 0 1 1 134.0 0 1 1 135.0 0 1 1 142.0 0 3 3 144.0 0 1 1 145.0 0 1 1 146.0 0 1 1 149.0 0 2 2 151.0 0 1 1 152.0 0 1 1 160.0 0 1 1 167.0 0 1 1 170.0 0 2 2 173.0 0 1 1 181.0 0 1 1 186.0 0 1 1 193.0 0 1 1 196.0 0 1 1 197.0 0 1 1 199.0 0 1 1 212.0 0 1 1 217.0 0 1 1 224.0 0 1 1 247.0 0 1 1 249.0 0 1 1 252.0 0 1 1 257.0 0 1 1 258.0 0 1 1 261.0 0 1 1 263.0 0 1 1 268.0 0 1 1 282.0 0 1 1 291.0 0 1 1 293.0 0 1 1 295.0 0 1 1 304.0 0 1 1 310.0 0 1 1 324.0 0 1 1 325.0 0 1 1 329.0 0 1 1 345.0 0 1 1 346.0 0 1 1 356.0 0 1 1 364.0 0 1 1 381.0 0 1 1 383.0 0 1 1 407.0 0 1 1 409.0 0 1 1 421.0 0 1 1 427.0 0 1 1 432.0 0 1 1 444.0 0 1 1 454.0 0 1 1 465.0 0 1 1 471.0 0 1 1 494.0 0 1 1 498.0 0 1 1 504.0 0 1 1 517.0 0 1 1 552.0 0 1 1 561.0 0 1 1 562.0 0 1 1 610.0 0 1 1 1108.0 0 1 1 1238.0 0 1 1 1353.0 0 1 1 1387.0 0 1 1 1762.0 0 1 1 1781.0 0 1 1 2742.0 0 1 1 11647.0 0 1 1