## htsjdk.samtools.metrics.StringHeader # MarkDuplicates INPUT=[/project/berglandlab/DEST/dest_mapped/DESTv1/US_Pen_Lin_1_2012-10-10/US_Pen_Lin_1_2012-10-10.sorted_merged.bam] OUTPUT=/project/berglandlab/DEST/dest_mapped/DESTv1/US_Pen_Lin_1_2012-10-10/US_Pen_Lin_1_2012-10-10.dedup.bam METRICS_FILE=/project/berglandlab/DEST/dest_mapped/DESTv1/US_Pen_Lin_1_2012-10-10/US_Pen_Lin_1_2012-10-10.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 17:22:12 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 1219531 19614579 0 0 260667 281793 0 0.020378 676095545 ## HISTOGRAM java.lang.Double BIN VALUE all_sets non_optical_sets 1.0 1 18846756 18846756 2.0 1.971405 125000 125000 3.0 2.915033 8513 8513 4.0 3.831679 964 964 5.0 4.722113 375 375 6.0 5.587085 203 203 7.0 6.427324 148 148 8.0 7.243536 126 126 9.0 8.036409 134 134 10.0 8.80661 116 116 11.0 9.554787 94 94 12.0 10.28157 73 73 13.0 10.987571 69 69 14.0 11.673384 64 64 15.0 12.339587 60 60 16.0 12.986739 54 54 17.0 13.615387 61 61 18.0 14.226058 47 47 19.0 14.819267 47 47 20.0 15.395514 35 35 21.0 15.955283 39 39 22.0 16.499046 37 37 23.0 17.02726 28 28 24.0 17.540369 28 28 25.0 18.038807 17 17 26.0 18.522991 17 17 27.0 18.993331 19 19 28.0 19.450221 11 11 29.0 19.894047 12 12 30.0 20.325182 17 17 31.0 20.743988 7 7 32.0 21.150819 14 14 33.0 21.546016 11 11 34.0 21.929913 5 5 35.0 22.302833 6 6 36.0 22.665089 3 3 37.0 23.016986 7 7 38.0 23.358821 6 6 39.0 23.690881 5 5 40.0 24.013447 0 0 41.0 24.326788 5 5 42.0 24.631169 7 7 43.0 24.926847 7 7 44.0 25.21407 6 6 45.0 25.49308 5 5 46.0 25.764112 6 6 47.0 26.027393 5 5 48.0 26.283146 5 5 49.0 26.531586 4 4 50.0 26.772922 3 3 51.0 27.007357 7 7 52.0 27.235088 4 4 53.0 27.456307 6 6 54.0 27.671201 5 5 55.0 27.87995 5 5 56.0 28.08273 4 4 57.0 28.279711 2 2 58.0 28.471059 5 5 59.0 28.656936 4 4 60.0 28.837498 2 2 61.0 29.012897 3 3 62.0 29.183281 6 6 63.0 29.348792 1 1 64.0 29.50957 5 5 65.0 29.665751 5 5 66.0 29.817467 3 3 67.0 29.964843 1 1 68.0 30.108006 8 8 69.0 30.247075 4 4 70.0 30.382167 4 4 71.0 30.513397 4 4 72.0 30.640874 2 2 73.0 30.764705 2 2 74.0 30.884996 4 4 75.0 31.001847 4 4 76.0 31.115357 1 1 77.0 31.225621 3 3 78.0 31.332732 6 6 79.0 31.43678 5 5 80.0 31.537853 1 1 81.0 31.636036 0 0 82.0 31.731412 2 2 83.0 31.82406 3 3 84.0 31.914058 3 3 85.0 32.001484 5 5 86.0 32.086409 2 2 87.0 32.168906 1 1 88.0 32.249044 3 3 89.0 32.326891 2 2 90.0 32.402511 1 1 91.0 32.475969 2 2 92.0 32.547327 2 2 93.0 32.616644 0 0 94.0 32.683979 1 1 95.0 32.749389 5 5 96.0 32.812928 1 1 97.0 32.874651 1 1 98.0 32.934608 1 1 99.0 32.992851 0 0 100.0 33.049429 2 2 102.0 0 2 2 104.0 0 1 1 105.0 0 3 3 107.0 0 2 2 110.0 0 2 2 111.0 0 3 3 112.0 0 2 2 115.0 0 3 3 120.0 0 2 2 121.0 0 2 2 123.0 0 1 1 126.0 0 1 1 128.0 0 2 2 129.0 0 1 1 130.0 0 1 1 132.0 0 1 1 133.0 0 2 2 135.0 0 1 1 136.0 0 1 1 139.0 0 2 2 142.0 0 2 2 144.0 0 2 2 146.0 0 1 1 147.0 0 2 2 149.0 0 2 2 150.0 0 3 3 151.0 0 1 1 153.0 0 1 1 154.0 0 2 2 155.0 0 1 1 156.0 0 2 2 158.0 0 1 1 159.0 0 1 1 160.0 0 1 1 161.0 0 1 1 163.0 0 2 2 165.0 0 1 1 168.0 0 2 2 171.0 0 1 1 172.0 0 1 1 173.0 0 1 1 175.0 0 1 1 177.0 0 1 1 179.0 0 1 1 182.0 0 1 1 184.0 0 1 1 185.0 0 1 1 186.0 0 2 2 188.0 0 2 2 189.0 0 1 1 191.0 0 1 1 193.0 0 1 1 194.0 0 4 4 195.0 0 2 2 198.0 0 1 1 199.0 0 1 1 201.0 0 3 3 202.0 0 1 1 203.0 0 2 2 205.0 0 1 1 206.0 0 1 1 210.0 0 1 1 212.0 0 1 1 214.0 0 1 1 218.0 0 1 1 220.0 0 1 1 222.0 0 2 2 223.0 0 1 1 225.0 0 2 2 227.0 0 1 1 228.0 0 1 1 231.0 0 1 1 233.0 0 1 1 234.0 0 1 1 238.0 0 2 2 239.0 0 1 1 240.0 0 1 1 243.0 0 3 3 249.0 0 1 1 251.0 0 1 1 253.0 0 1 1 268.0 0 1 1 273.0 0 1 1 276.0 0 1 1 277.0 0 1 1 283.0 0 1 1 286.0 0 2 2 289.0 0 1 1 290.0 0 1 1 296.0 0 1 1 303.0 0 1 1 309.0 0 1 1 317.0 0 1 1 324.0 0 1 1 326.0 0 1 1 334.0 0 1 1 343.0 0 1 1 350.0 0 1 1 352.0 0 1 1 358.0 0 1 1 372.0 0 1 1 373.0 0 2 2 381.0 0 1 1 386.0 0 1 1 388.0 0 1 1 391.0 0 1 1 399.0 0 1 1 402.0 0 1 1 408.0 0 1 1 413.0 0 1 1 415.0 0 1 1 417.0 0 1 1 419.0 0 1 1 433.0 0 1 1 435.0 0 1 1 436.0 0 1 1 441.0 0 1 1 442.0 0 1 1 452.0 0 1 1 457.0 0 1 1 460.0 0 1 1 467.0 0 1 1 475.0 0 1 1 496.0 0 1 1 498.0 0 1 1 501.0 0 1 1 504.0 0 1 1 508.0 0 1 1 509.0 0 2 2 522.0 0 1 1 539.0 0 1 1 563.0 0 1 1 585.0 0 1 1 588.0 0 1 1 593.0 0 1 1 599.0 0 1 1 620.0 0 1 1 636.0 0 1 1 662.0 0 2 2 665.0 0 1 1 694.0 0 1 1 700.0 0 1 1 711.0 0 1 1 730.0 0 1 1 804.0 0 1 1 811.0 0 1 1 894.0 0 1 1 1005.0 0 1 1 1010.0 0 1 1 1030.0 0 1 1 1061.0 0 1 1 1070.0 0 1 1 1138.0 0 1 1 1152.0 0 1 1 1167.0 0 1 1 1174.0 0 1 1 1250.0 0 1 1 1309.0 0 1 1 1335.0 0 1 1 1365.0 0 1 1 1394.0 0 1 1 1395.0 0 1 1 1407.0 0 1 1 1425.0 0 1 1 1530.0 0 1 1 1565.0 0 1 1 1639.0 0 1 1 1676.0 0 1 1 1955.0 0 1 1 2253.0 0 1 1 2777.0 0 1 1 3478.0 0 1 1 11821.0 0 1 1