## htsjdk.samtools.metrics.StringHeader # MarkDuplicates INPUT=[/project/berglandlab/DEST/dest_mapped/DESTv1/US_Pen_Lin_1_2010-07-15/US_Pen_Lin_1_2010-07-15.sorted_merged.bam] OUTPUT=/project/berglandlab/DEST/dest_mapped/DESTv1/US_Pen_Lin_1_2010-07-15/US_Pen_Lin_1_2010-07-15.dedup.bam METRICS_FILE=/project/berglandlab/DEST/dest_mapped/DESTv1/US_Pen_Lin_1_2010-07-15/US_Pen_Lin_1_2010-07-15.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 17:14:34 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 7020737 13313773 0 0 1763852 124940 0 0.059847 704921801 ## HISTOGRAM java.lang.Double BIN VALUE all_sets non_optical_sets 1.0 1 12938148 12938148 2.0 1.98129 20939 20939 3.0 2.944221 1314 1314 4.0 3.889136 479 479 5.0 4.816371 265 265 6.0 5.726259 175 175 7.0 6.619123 100 100 8.0 7.495281 106 106 9.0 8.355047 59 59 10.0 9.198727 53 53 11.0 10.026622 54 54 12.0 10.839028 50 50 13.0 11.636234 30 30 14.0 12.418524 41 41 15.0 13.186178 27 27 16.0 13.939469 34 34 17.0 14.678667 21 21 18.0 15.404034 30 30 19.0 16.11583 23 23 20.0 16.814309 19 19 21.0 17.499719 25 25 22.0 18.172306 17 17 23.0 18.832308 22 22 24.0 19.479963 11 11 25.0 20.1155 14 14 26.0 20.739146 17 17 27.0 21.351124 15 15 28.0 21.951652 11 11 29.0 22.540945 15 15 30.0 23.119212 9 9 31.0 23.68666 15 15 32.0 24.243491 9 9 33.0 24.789904 15 15 34.0 25.326094 9 9 35.0 25.852251 12 12 36.0 26.368565 10 10 37.0 26.875219 8 8 38.0 27.372393 7 7 39.0 27.860265 8 8 40.0 28.33901 5 5 41.0 28.808797 10 10 42.0 29.269795 12 12 43.0 29.722168 6 6 44.0 30.166077 5 5 45.0 30.60168 4 4 46.0 31.029134 6 6 47.0 31.44859 8 8 48.0 31.860198 10 10 49.0 32.264105 8 8 50.0 32.660455 8 8 51.0 33.04939 7 7 52.0 33.431048 4 4 53.0 33.805565 12 12 54.0 34.173075 9 9 55.0 34.533709 5 5 56.0 34.887596 6 6 57.0 35.234862 5 5 58.0 35.57563 5 5 59.0 35.910023 8 8 60.0 36.238159 9 9 61.0 36.560156 7 7 62.0 36.876129 5 5 63.0 37.18619 5 5 64.0 37.49045 7 7 65.0 37.789017 2 2 66.0 38.081998 6 6 67.0 38.369497 3 3 68.0 38.651618 7 7 69.0 38.92846 4 4 70.0 39.200123 4 4 71.0 39.466702 4 4 72.0 39.728295 4 4 73.0 39.984993 3 3 74.0 40.236888 5 5 75.0 40.48407 5 5 76.0 40.726628 3 3 77.0 40.964647 7 7 78.0 41.198213 3 3 79.0 41.42741 4 4 80.0 41.652318 7 7 81.0 41.873018 3 3 82.0 42.089589 2 2 83.0 42.302108 6 6 84.0 42.510651 2 2 85.0 42.715292 4 4 86.0 42.916104 3 3 87.0 43.113159 5 5 88.0 43.306527 5 5 89.0 43.496278 3 3 90.0 43.682478 3 3 91.0 43.865195 5 5 92.0 44.044493 3 3 93.0 44.220436 2 2 94.0 44.393088 4 4 95.0 44.562509 2 2 96.0 44.728761 1 1 97.0 44.891902 6 6 98.0 45.05199 3 3 99.0 45.209084 0 0 100.0 45.363238 3 3 101.0 0 2 2 103.0 0 4 4 104.0 0 1 1 106.0 0 6 6 107.0 0 5 5 108.0 0 3 3 109.0 0 1 1 110.0 0 1 1 111.0 0 1 1 112.0 0 3 3 113.0 0 5 5 114.0 0 2 2 115.0 0 1 1 116.0 0 2 2 117.0 0 1 1 118.0 0 1 1 119.0 0 3 3 120.0 0 1 1 121.0 0 2 2 122.0 0 1 1 123.0 0 1 1 124.0 0 1 1 125.0 0 4 4 126.0 0 4 4 127.0 0 2 2 128.0 0 5 5 129.0 0 2 2 130.0 0 3 3 131.0 0 1 1 132.0 0 3 3 133.0 0 1 1 134.0 0 3 3 135.0 0 4 4 136.0 0 3 3 137.0 0 1 1 138.0 0 5 5 139.0 0 2 2 140.0 0 4 4 141.0 0 2 2 142.0 0 2 2 144.0 0 1 1 145.0 0 2 2 146.0 0 1 1 148.0 0 2 2 149.0 0 1 1 150.0 0 4 4 151.0 0 2 2 152.0 0 2 2 153.0 0 1 1 154.0 0 4 4 157.0 0 1 1 158.0 0 1 1 159.0 0 2 2 160.0 0 2 2 161.0 0 1 1 163.0 0 2 2 164.0 0 4 4 166.0 0 2 2 167.0 0 1 1 168.0 0 1 1 170.0 0 1 1 171.0 0 1 1 172.0 0 1 1 174.0 0 1 1 176.0 0 1 1 177.0 0 1 1 179.0 0 1 1 180.0 0 3 3 181.0 0 4 4 183.0 0 2 2 184.0 0 2 2 185.0 0 1 1 188.0 0 1 1 189.0 0 1 1 192.0 0 2 2 193.0 0 1 1 196.0 0 1 1 199.0 0 2 2 200.0 0 2 2 201.0 0 2 2 202.0 0 2 2 203.0 0 3 3 205.0 0 1 1 208.0 0 1 1 209.0 0 1 1 210.0 0 1 1 213.0 0 2 2 214.0 0 1 1 216.0 0 2 2 217.0 0 2 2 218.0 0 1 1 219.0 0 1 1 221.0 0 1 1 222.0 0 1 1 225.0 0 1 1 229.0 0 1 1 232.0 0 1 1 234.0 0 1 1 235.0 0 1 1 236.0 0 3 3 237.0 0 1 1 238.0 0 3 3 241.0 0 2 2 242.0 0 1 1 244.0 0 3 3 245.0 0 2 2 246.0 0 1 1 248.0 0 1 1 249.0 0 1 1 250.0 0 1 1 253.0 0 1 1 256.0 0 2 2 257.0 0 1 1 259.0 0 1 1 262.0 0 1 1 268.0 0 1 1 269.0 0 1 1 273.0 0 1 1 277.0 0 2 2 282.0 0 1 1 290.0 0 1 1 301.0 0 3 3 303.0 0 1 1 304.0 0 1 1 306.0 0 1 1 307.0 0 1 1 308.0 0 2 2 313.0 0 1 1 319.0 0 1 1 320.0 0 1 1 322.0 0 1 1 325.0 0 2 2 326.0 0 1 1 335.0 0 1 1 338.0 0 2 2 343.0 0 1 1 346.0 0 1 1 348.0 0 1 1 355.0 0 1 1 360.0 0 1 1 363.0 0 1 1 371.0 0 1 1 378.0 0 1 1 387.0 0 1 1 399.0 0 1 1 400.0 0 2 2 402.0 0 1 1 417.0 0 1 1 420.0 0 1 1 424.0 0 1 1 427.0 0 1 1 432.0 0 1 1 440.0 0 1 1 453.0 0 1 1 456.0 0 1 1 460.0 0 1 1 465.0 0 3 3 496.0 0 1 1 503.0 0 1 1 522.0 0 1 1 538.0 0 1 1 543.0 0 1 1 559.0 0 2 2 609.0 0 1 1 633.0 0 1 1 637.0 0 1 1 774.0 0 1 1 926.0 0 1 1 989.0 0 1 1 1004.0 0 1 1 1033.0 0 1 1 1277.0 0 1 1