## htsjdk.samtools.metrics.StringHeader # MarkDuplicates INPUT=[/project/berglandlab/DEST/dest_mapped/DESTv1/UA_Kie_Cho_1_2016-09-05/UA_Kie_Cho_1_2016-09-05.sorted_merged.bam] OUTPUT=/project/berglandlab/DEST/dest_mapped/DESTv1/UA_Kie_Cho_1_2016-09-05/UA_Kie_Cho_1_2016-09-05.dedup.bam METRICS_FILE=/project/berglandlab/DEST/dest_mapped/DESTv1/UA_Kie_Cho_1_2016-09-05/UA_Kie_Cho_1_2016-09-05.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 15:08:51 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 38983100 14094156 0 0 11484115 1217214 0 0.207209 76829338 ## HISTOGRAM java.lang.Double BIN VALUE all_sets non_optical_sets 1.0 1 11641617 11641617 2.0 1.832396 775133 775133 3.0 2.525278 60367 60367 4.0 3.10203 7417 7417 5.0 3.582116 2569 2569 6.0 3.981737 1546 1546 7.0 4.31438 1063 1063 8.0 4.591271 783 783 9.0 4.821753 603 603 10.0 5.013606 494 494 11.0 5.173303 393 393 12.0 5.306234 294 294 13.0 5.416885 246 246 14.0 5.508991 226 226 15.0 5.585659 184 184 16.0 5.649478 184 184 17.0 5.7026 151 151 18.0 5.746819 145 145 19.0 5.783626 122 122 20.0 5.814264 121 121 21.0 5.839768 100 100 22.0 5.860996 109 109 23.0 5.878667 109 109 24.0 5.893376 100 100 25.0 5.90562 91 91 26.0 5.915811 68 68 27.0 5.924295 81 81 28.0 5.931356 99 99 29.0 5.937234 75 75 30.0 5.942127 73 73 31.0 5.9462 72 72 32.0 5.94959 68 68 33.0 5.952412 51 51 34.0 5.954761 67 67 35.0 5.956716 67 67 36.0 5.958344 57 57 37.0 5.959699 47 47 38.0 5.960827 44 44 39.0 5.961765 56 56 40.0 5.962547 55 55 41.0 5.963197 40 40 42.0 5.963738 42 42 43.0 5.964189 34 34 44.0 5.964564 27 27 45.0 5.964876 32 32 46.0 5.965136 38 38 47.0 5.965353 26 26 48.0 5.965533 32 32 49.0 5.965683 30 30 50.0 5.965808 29 29 51.0 5.965911 28 28 52.0 5.965998 17 17 53.0 5.96607 24 24 54.0 5.96613 28 28 55.0 5.96618 20 20 56.0 5.966221 23 23 57.0 5.966256 25 25 58.0 5.966284 17 17 59.0 5.966308 22 22 60.0 5.966328 14 14 61.0 5.966345 15 15 62.0 5.966359 13 13 63.0 5.96637 16 16 64.0 5.96638 14 14 65.0 5.966388 14 14 66.0 5.966394 18 18 67.0 5.9664 12 12 68.0 5.966404 13 13 69.0 5.966408 18 18 70.0 5.966411 15 15 71.0 5.966414 18 18 72.0 5.966416 7 7 73.0 5.966418 11 11 74.0 5.96642 14 14 75.0 5.966421 12 12 76.0 5.966422 13 13 77.0 5.966423 18 18 78.0 5.966424 9 9 79.0 5.966424 11 11 80.0 5.966425 10 10 81.0 5.966425 7 7 82.0 5.966426 10 10 83.0 5.966426 12 12 84.0 5.966426 7 7 85.0 5.966426 13 13 86.0 5.966426 7 7 87.0 5.966427 10 10 88.0 5.966427 6 6 89.0 5.966427 11 11 90.0 5.966427 11 11 91.0 5.966427 9 9 92.0 5.966427 17 17 93.0 5.966427 5 5 94.0 5.966427 9 9 95.0 5.966427 8 8 96.0 5.966427 8 8 97.0 5.966427 11 11 98.0 5.966427 9 9 99.0 5.966427 7 7 100.0 5.966427 8 8 101.0 0 9 9 102.0 0 8 8 103.0 0 13 13 104.0 0 8 8 105.0 0 7 7 106.0 0 6 6 107.0 0 5 5 108.0 0 9 9 109.0 0 7 7 110.0 0 7 7 111.0 0 5 5 112.0 0 10 10 113.0 0 9 9 114.0 0 10 10 115.0 0 6 6 116.0 0 8 8 117.0 0 8 8 118.0 0 6 6 119.0 0 9 9 120.0 0 5 5 121.0 0 6 6 122.0 0 7 7 123.0 0 3 3 124.0 0 7 7 125.0 0 3 3 126.0 0 6 6 127.0 0 5 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227.0 0 2 2 229.0 0 1 1 230.0 0 1 1 233.0 0 1 1 235.0 0 1 1 238.0 0 1 1 242.0 0 1 1 243.0 0 4 4 245.0 0 4 4 246.0 0 1 1 248.0 0 2 2 252.0 0 1 1 255.0 0 1 1 258.0 0 1 1 261.0 0 2 2 262.0 0 3 3 263.0 0 1 1 264.0 0 1 1 267.0 0 1 1 268.0 0 1 1 269.0 0 2 2 272.0 0 2 2 273.0 0 2 2 277.0 0 1 1 280.0 0 1 1 283.0 0 1 1 284.0 0 4 4 285.0 0 1 1 291.0 0 1 1 292.0 0 1 1 296.0 0 1 1 297.0 0 1 1 299.0 0 2 2 300.0 0 2 2 305.0 0 1 1 311.0 0 1 1 316.0 0 1 1 317.0 0 2 2 319.0 0 1 1 321.0 0 1 1 323.0 0 2 2 326.0 0 1 1 327.0 0 1 1 329.0 0 1 1 332.0 0 1 1 333.0 0 1 1 334.0 0 1 1 343.0 0 1 1 347.0 0 2 2 349.0 0 1 1 351.0 0 1 1 355.0 0 1 1 356.0 0 1 1 359.0 0 1 1 362.0 0 1 1 365.0 0 1 1 370.0 0 1 1 376.0 0 2 2 379.0 0 1 1 380.0 0 1 1 383.0 0 1 1 384.0 0 1 1 387.0 0 1 1 389.0 0 1 1 394.0 0 2 2 398.0 0 1 1 399.0 0 1 1 406.0 0 1 1 413.0 0 1 1 417.0 0 1 1 432.0 0 1 1 434.0 0 1 1 442.0 0 2 2 443.0 0 2 2 444.0 0 1 1 448.0 0 1 1 450.0 0 1 1 464.0 0 1 1 465.0 0 1 1 466.0 0 1 1 467.0 0 1 1 469.0 0 1 1 470.0 0 1 1 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