## htsjdk.samtools.metrics.StringHeader # MarkDuplicates INPUT=[/project/berglandlab/DEST/dest_mapped/DESTv1/US_Flo_Hom_1_2010-12-16/US_Flo_Hom_1_2010-12-16.sorted_merged.bam] OUTPUT=/project/berglandlab/DEST/dest_mapped/DESTv1/US_Flo_Hom_1_2010-12-16/US_Flo_Hom_1_2010-12-16.dedup.bam METRICS_FILE=/project/berglandlab/DEST/dest_mapped/DESTv1/US_Flo_Hom_1_2010-12-16/US_Flo_Hom_1_2010-12-16.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 17:09:25 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 4569658 20852275 0 0 1043203 197675 0 0.031088 1092867146 ## HISTOGRAM java.lang.Double BIN VALUE all_sets non_optical_sets 1.0 1 20173998 20173998 2.0 1.981101 50977 50977 3.0 2.943659 3067 3067 4.0 3.888025 1106 1106 5.0 4.814544 591 591 6.0 5.723551 322 322 7.0 6.615379 203 203 8.0 7.490352 146 146 9.0 8.348789 103 103 10.0 9.191001 82 82 11.0 10.017296 67 67 12.0 10.827975 67 67 13.0 11.623332 56 56 14.0 12.403657 37 37 15.0 13.169235 42 42 16.0 13.920343 38 38 17.0 14.657256 17 17 18.0 15.380242 28 28 19.0 16.089564 24 24 20.0 16.78548 20 20 21.0 17.468243 27 27 22.0 18.138103 15 15 23.0 18.795302 16 16 24.0 19.440081 26 26 25.0 20.072674 13 13 26.0 20.693311 18 18 27.0 21.302219 10 10 28.0 21.899619 13 13 29.0 22.485728 12 12 30.0 23.060759 19 19 31.0 23.624923 20 20 32.0 24.178425 10 10 33.0 24.721466 11 11 34.0 25.254244 17 17 35.0 25.776952 9 9 36.0 26.289781 18 18 37.0 26.792919 9 9 38.0 27.286547 13 13 39.0 27.770846 12 12 40.0 28.245992 11 11 41.0 28.712158 13 13 42.0 29.169514 11 11 43.0 29.618226 2 2 44.0 30.058457 9 9 45.0 30.490368 11 11 46.0 30.914117 9 9 47.0 31.329857 7 7 48.0 31.737739 7 7 49.0 32.137913 6 6 50.0 32.530524 7 7 51.0 32.915715 10 10 52.0 33.293625 4 4 53.0 33.664394 5 5 54.0 34.028155 9 9 55.0 34.385041 5 5 56.0 34.735182 5 5 57.0 35.078706 10 10 58.0 35.415737 13 13 59.0 35.746399 7 7 60.0 36.070811 6 6 61.0 36.389093 5 5 62.0 36.701358 6 6 63.0 37.007722 6 6 64.0 37.308296 3 3 65.0 37.60319 3 3 66.0 37.89251 3 3 67.0 38.176362 4 4 68.0 38.454849 2 2 69.0 38.728073 8 8 70.0 38.996133 6 6 71.0 39.259128 1 1 72.0 39.517151 1 1 73.0 39.770298 4 4 74.0 40.018661 4 4 75.0 40.26233 2 2 76.0 40.501394 5 5 77.0 40.735939 9 9 78.0 40.966052 4 4 79.0 41.191816 6 6 80.0 41.413312 3 3 81.0 41.630623 4 4 82.0 41.843827 3 3 83.0 42.053001 7 7 84.0 42.258222 4 4 85.0 42.459564 1 1 86.0 42.657101 3 3 87.0 42.850905 5 5 88.0 43.041046 5 5 89.0 43.227594 5 5 90.0 43.410615 5 5 91.0 43.590178 0 0 92.0 43.766347 1 1 93.0 43.939187 3 3 94.0 44.10876 7 7 95.0 44.275128 4 4 96.0 44.438352 2 2 97.0 44.598491 5 5 98.0 44.755604 2 2 99.0 44.909747 2 2 100.0 45.060977 1 1 101.0 0 1 1 102.0 0 4 4 103.0 0 4 4 105.0 0 3 3 106.0 0 1 1 107.0 0 3 3 108.0 0 2 2 109.0 0 3 3 110.0 0 2 2 111.0 0 1 1 112.0 0 4 4 113.0 0 4 4 114.0 0 2 2 115.0 0 2 2 116.0 0 1 1 117.0 0 2 2 118.0 0 4 4 119.0 0 3 3 120.0 0 3 3 121.0 0 1 1 122.0 0 3 3 123.0 0 3 3 124.0 0 3 3 125.0 0 2 2 126.0 0 1 1 127.0 0 2 2 128.0 0 7 7 129.0 0 3 3 130.0 0 2 2 131.0 0 1 1 132.0 0 3 3 133.0 0 2 2 134.0 0 2 2 135.0 0 4 4 136.0 0 3 3 137.0 0 3 3 138.0 0 4 4 139.0 0 1 1 140.0 0 3 3 142.0 0 3 3 145.0 0 3 3 146.0 0 1 1 147.0 0 2 2 151.0 0 6 6 152.0 0 1 1 153.0 0 1 1 154.0 0 3 3 155.0 0 1 1 156.0 0 2 2 157.0 0 1 1 158.0 0 1 1 159.0 0 3 3 160.0 0 4 4 161.0 0 1 1 162.0 0 1 1 164.0 0 1 1 165.0 0 2 2 166.0 0 1 1 167.0 0 2 2 168.0 0 2 2 170.0 0 1 1 171.0 0 2 2 172.0 0 3 3 173.0 0 1 1 175.0 0 2 2 176.0 0 2 2 177.0 0 5 5 178.0 0 3 3 179.0 0 3 3 180.0 0 2 2 181.0 0 1 1 182.0 0 1 1 183.0 0 1 1 184.0 0 1 1 186.0 0 3 3 187.0 0 2 2 190.0 0 1 1 191.0 0 2 2 192.0 0 3 3 193.0 0 2 2 194.0 0 1 1 195.0 0 1 1 197.0 0 1 1 198.0 0 2 2 199.0 0 5 5 200.0 0 1 1 202.0 0 2 2 203.0 0 3 3 204.0 0 1 1 206.0 0 1 1 207.0 0 1 1 208.0 0 3 3 209.0 0 2 2 210.0 0 1 1 211.0 0 1 1 212.0 0 2 2 213.0 0 2 2 216.0 0 2 2 218.0 0 3 3 219.0 0 1 1 221.0 0 2 2 225.0 0 1 1 226.0 0 2 2 227.0 0 1 1 228.0 0 3 3 230.0 0 1 1 231.0 0 1 1 232.0 0 1 1 233.0 0 1 1 235.0 0 1 1 237.0 0 3 3 240.0 0 2 2 242.0 0 1 1 243.0 0 3 3 244.0 0 2 2 247.0 0 1 1 250.0 0 1 1 251.0 0 1 1 253.0 0 1 1 256.0 0 1 1 259.0 0 2 2 260.0 0 1 1 261.0 0 1 1 262.0 0 2 2 263.0 0 3 3 265.0 0 2 2 266.0 0 1 1 269.0 0 2 2 274.0 0 1 1 275.0 0 1 1 278.0 0 2 2 280.0 0 1 1 281.0 0 1 1 283.0 0 3 3 284.0 0 1 1 287.0 0 1 1 288.0 0 1 1 295.0 0 2 2 296.0 0 1 1 298.0 0 2 2 299.0 0 1 1 300.0 0 1 1 301.0 0 2 2 302.0 0 1 1 303.0 0 1 1 304.0 0 3 3 305.0 0 1 1 307.0 0 1 1 309.0 0 1 1 310.0 0 2 2 311.0 0 2 2 312.0 0 1 1 313.0 0 2 2 315.0 0 1 1 317.0 0 2 2 318.0 0 1 1 319.0 0 3 3 320.0 0 1 1 324.0 0 1 1 326.0 0 1 1 327.0 0 1 1 328.0 0 1 1 329.0 0 1 1 330.0 0 1 1 332.0 0 1 1 333.0 0 1 1 334.0 0 1 1 338.0 0 1 1 340.0 0 1 1 352.0 0 2 2 353.0 0 1 1 355.0 0 1 1 357.0 0 1 1 358.0 0 1 1 359.0 0 1 1 361.0 0 1 1 377.0 0 2 2 378.0 0 1 1 381.0 0 1 1 386.0 0 1 1 393.0 0 2 2 394.0 0 1 1 407.0 0 1 1 408.0 0 1 1 422.0 0 1 1 427.0 0 1 1 429.0 0 1 1 435.0 0 1 1 442.0 0 1 1 445.0 0 1 1 452.0 0 1 1 453.0 0 1 1 467.0 0 1 1 469.0 0 1 1 472.0 0 1 1 473.0 0 1 1 479.0 0 1 1 480.0 0 1 1 481.0 0 1 1 486.0 0 1 1 487.0 0 1 1 491.0 0 2 2 498.0 0 1 1 502.0 0 1 1 511.0 0 1 1 520.0 0 2 2 531.0 0 1 1 534.0 0 1 1 541.0 0 1 1 564.0 0 1 1 577.0 0 1 1 578.0 0 1 1 582.0 0 1 1 587.0 0 1 1 594.0 0 1 1 610.0 0 1 1 616.0 0 1 1 625.0 0 1 1 635.0 0 1 1 736.0 0 1 1 859.0 0 1 1 945.0 0 1 1 962.0 0 1 1 1078.0 0 1 1 1133.0 0 1 1 1185.0 0 1 1 1191.0 0 1 1 1268.0 0 1 1