## htsjdk.samtools.metrics.StringHeader # MarkDuplicates INPUT=[/project/berglandlab/DEST/dest_mapped/DESTv1/UA_Kie_Cho_2_2016-09-04/UA_Kie_Cho_2_2016-09-04.sorted_merged.bam] OUTPUT=/project/berglandlab/DEST/dest_mapped/DESTv1/UA_Kie_Cho_2_2016-09-04/UA_Kie_Cho_2_2016-09-04.dedup.bam METRICS_FILE=/project/berglandlab/DEST/dest_mapped/DESTv1/UA_Kie_Cho_2_2016-09-04/UA_Kie_Cho_2_2016-09-04.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 15:22:41 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 34127866 10024125 0 0 8169844 886906 0 0.183543 53254982 ## HISTOGRAM java.lang.Double BIN VALUE all_sets non_optical_sets 1.0 1 8254225 8254225 2.0 1.828425 543465 543465 3.0 2.514713 44092 44092 4.0 3.083252 5830 5830 5.0 3.554243 2000 2000 6.0 3.944424 1212 1212 7.0 4.26766 823 823 8.0 4.535436 569 569 9.0 4.757269 444 444 10.0 4.941041 355 355 11.0 5.093282 312 312 12.0 5.219403 261 261 13.0 5.323884 196 196 14.0 5.410439 181 181 15.0 5.482144 171 171 16.0 5.541545 127 127 17.0 5.590755 137 137 18.0 5.631522 120 120 19.0 5.665294 120 120 20.0 5.693272 134 134 21.0 5.716449 99 99 22.0 5.73565 93 93 23.0 5.751556 86 86 24.0 5.764733 89 89 25.0 5.77565 97 97 26.0 5.784693 78 78 27.0 5.792185 79 79 28.0 5.798391 74 74 29.0 5.803533 83 83 30.0 5.807792 60 60 31.0 5.811321 61 61 32.0 5.814244 67 67 33.0 5.816665 59 59 34.0 5.818672 52 52 35.0 5.820333 41 41 36.0 5.82171 38 38 37.0 5.822851 45 45 38.0 5.823796 44 44 39.0 5.824578 43 43 40.0 5.825227 40 40 41.0 5.825764 42 42 42.0 5.826209 27 27 43.0 5.826578 39 39 44.0 5.826883 36 36 45.0 5.827136 20 20 46.0 5.827346 38 38 47.0 5.827519 27 27 48.0 5.827663 36 36 49.0 5.827782 19 19 50.0 5.827881 17 17 51.0 5.827963 13 13 52.0 5.828031 19 19 53.0 5.828087 14 14 54.0 5.828133 21 21 55.0 5.828172 19 19 56.0 5.828204 18 18 57.0 5.82823 5 5 58.0 5.828252 13 13 59.0 5.82827 17 17 60.0 5.828285 13 13 61.0 5.828298 9 9 62.0 5.828308 24 24 63.0 5.828317 15 15 64.0 5.828324 10 10 65.0 5.82833 16 16 66.0 5.828334 9 9 67.0 5.828338 10 10 68.0 5.828342 11 11 69.0 5.828345 12 12 70.0 5.828347 6 6 71.0 5.828349 8 8 72.0 5.82835 11 11 73.0 5.828352 10 10 74.0 5.828353 7 7 75.0 5.828354 7 7 76.0 5.828354 12 12 77.0 5.828355 11 11 78.0 5.828355 7 7 79.0 5.828356 18 18 80.0 5.828356 10 10 81.0 5.828356 7 7 82.0 5.828357 7 7 83.0 5.828357 14 14 84.0 5.828357 8 8 85.0 5.828357 11 11 86.0 5.828357 9 9 87.0 5.828357 4 4 88.0 5.828357 6 6 89.0 5.828358 9 9 90.0 5.828358 14 14 91.0 5.828358 9 9 92.0 5.828358 7 7 93.0 5.828358 5 5 94.0 5.828358 12 12 95.0 5.828358 8 8 96.0 5.828358 8 8 97.0 5.828358 8 8 98.0 5.828358 7 7 99.0 5.828358 7 7 100.0 5.828358 9 9 101.0 0 7 7 102.0 0 6 6 103.0 0 6 6 104.0 0 7 7 105.0 0 13 13 106.0 0 7 7 107.0 0 3 3 108.0 0 10 10 109.0 0 6 6 110.0 0 7 7 111.0 0 3 3 112.0 0 7 7 113.0 0 6 6 114.0 0 6 6 115.0 0 9 9 116.0 0 7 7 117.0 0 7 7 118.0 0 2 2 119.0 0 3 3 120.0 0 11 11 121.0 0 4 4 122.0 0 9 9 124.0 0 5 5 125.0 0 5 5 127.0 0 4 4 128.0 0 2 2 129.0 0 4 4 130.0 0 3 3 131.0 0 5 5 132.0 0 1 1 133.0 0 2 2 135.0 0 6 6 136.0 0 3 3 137.0 0 4 4 138.0 0 2 2 139.0 0 3 3 140.0 0 2 2 141.0 0 2 2 142.0 0 5 5 143.0 0 2 2 144.0 0 4 4 145.0 0 1 1 146.0 0 1 1 147.0 0 6 6 148.0 0 2 2 149.0 0 2 2 150.0 0 2 2 151.0 0 1 1 152.0 0 1 1 153.0 0 4 4 154.0 0 1 1 155.0 0 3 3 156.0 0 6 6 157.0 0 7 7 158.0 0 1 1 160.0 0 1 1 161.0 0 5 5 162.0 0 1 1 163.0 0 1 1 164.0 0 2 2 165.0 0 4 4 166.0 0 3 3 168.0 0 2 2 169.0 0 2 2 170.0 0 1 1 171.0 0 1 1 172.0 0 3 3 173.0 0 1 1 174.0 0 1 1 175.0 0 2 2 176.0 0 1 1 177.0 0 1 1 178.0 0 1 1 179.0 0 4 4 181.0 0 1 1 182.0 0 2 2 183.0 0 3 3 185.0 0 1 1 186.0 0 2 2 188.0 0 1 1 189.0 0 4 4 190.0 0 2 2 192.0 0 2 2 193.0 0 1 1 194.0 0 2 2 195.0 0 1 1 197.0 0 2 2 198.0 0 1 1 199.0 0 1 1 202.0 0 2 2 204.0 0 1 1 205.0 0 1 1 206.0 0 1 1 207.0 0 2 2 208.0 0 2 2 210.0 0 2 2 211.0 0 1 1 212.0 0 2 2 213.0 0 1 1 215.0 0 1 1 217.0 0 2 2 218.0 0 2 2 219.0 0 1 1 220.0 0 2 2 221.0 0 3 3 222.0 0 1 1 223.0 0 2 2 225.0 0 1 1 229.0 0 2 2 233.0 0 1 1 235.0 0 1 1 238.0 0 1 1 239.0 0 1 1 240.0 0 1 1 242.0 0 1 1 243.0 0 1 1 244.0 0 3 3 245.0 0 1 1 248.0 0 1 1 251.0 0 1 1 252.0 0 1 1 253.0 0 1 1 255.0 0 1 1 257.0 0 1 1 260.0 0 1 1 261.0 0 1 1 265.0 0 1 1 266.0 0 1 1 267.0 0 1 1 273.0 0 2 2 276.0 0 1 1 277.0 0 1 1 280.0 0 1 1 282.0 0 1 1 283.0 0 1 1 286.0 0 2 2 288.0 0 1 1 292.0 0 2 2 293.0 0 1 1 298.0 0 1 1 302.0 0 3 3 304.0 0 1 1 306.0 0 1 1 307.0 0 1 1 309.0 0 1 1 314.0 0 1 1 316.0 0 1 1 317.0 0 1 1 318.0 0 1 1 323.0 0 1 1 325.0 0 1 1 327.0 0 1 1 329.0 0 2 2 339.0 0 1 1 341.0 0 1 1 342.0 0 3 3 345.0 0 1 1 348.0 0 1 1 351.0 0 1 1 352.0 0 1 1 357.0 0 1 1 369.0 0 1 1 370.0 0 1 1 375.0 0 1 1 379.0 0 1 1 380.0 0 1 1 381.0 0 1 1 384.0 0 1 1 390.0 0 2 2 391.0 0 1 1 398.0 0 1 1 399.0 0 1 1 403.0 0 1 1 406.0 0 1 1 410.0 0 1 1 414.0 0 1 1 422.0 0 2 2 430.0 0 1 1 436.0 0 1 1 459.0 0 1 1 463.0 0 1 1 464.0 0 1 1 467.0 0 1 1 468.0 0 1 1 475.0 0 1 1 486.0 0 1 1 497.0 0 1 1 573.0 0 1 1 588.0 0 1 1 604.0 0 1 1 638.0 0 1 1 657.0 0 1 1 672.0 0 1 1 695.0 0 1 1 707.0 0 1 1 718.0 0 1 1 830.0 0 1 1 838.0 0 1 1 1063.0 0 1 1 1091.0 0 1 1 1174.0 0 1 1 1246.0 0 1 1 1887.0 0 1 1 3368.0 0 1 1