## htsjdk.samtools.metrics.StringHeader # MarkDuplicates INPUT=[/project/berglandlab/DEST/dest_mapped/DESTv1/UA_Che_Uma_1_2016-09-11/UA_Che_Uma_1_2016-09-11.sorted_merged.bam] OUTPUT=/project/berglandlab/DEST/dest_mapped/DESTv1/UA_Che_Uma_1_2016-09-11/UA_Che_Uma_1_2016-09-11.dedup.bam METRICS_FILE=/project/berglandlab/DEST/dest_mapped/DESTv1/UA_Che_Uma_1_2016-09-11/UA_Che_Uma_1_2016-09-11.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 08:45:53 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 24883191 7096547 0 0 5138730 600311 0 0.16223 39545279 ## HISTOGRAM java.lang.Double BIN VALUE all_sets non_optical_sets 1.0 1 5890506 5890506 2.0 1.835727 355488 355488 3.0 2.534166 27376 27376 4.0 3.11787 3901 3901 5.0 3.605687 1503 1503 6.0 4.013368 942 942 7.0 4.354079 660 660 8.0 4.63882 473 473 9.0 4.876785 374 374 10.0 5.075659 290 290 11.0 5.241864 200 200 12.0 5.380765 199 199 13.0 5.496849 187 187 14.0 5.593863 178 178 15.0 5.67494 162 162 16.0 5.742699 155 155 17.0 5.799326 142 142 18.0 5.846651 124 124 19.0 5.886202 117 117 20.0 5.919256 117 117 21.0 5.94688 101 101 22.0 5.969966 91 91 23.0 5.98926 88 88 24.0 6.005384 90 90 25.0 6.018859 76 76 26.0 6.030121 61 61 27.0 6.039533 66 66 28.0 6.047398 56 56 29.0 6.053972 49 49 30.0 6.059466 53 53 31.0 6.064057 51 51 32.0 6.067894 55 55 33.0 6.0711 37 37 34.0 6.07378 44 44 35.0 6.07602 35 35 36.0 6.077892 27 27 37.0 6.079456 25 25 38.0 6.080763 23 23 39.0 6.081856 23 23 40.0 6.082769 37 37 41.0 6.083532 22 22 42.0 6.08417 27 27 43.0 6.084703 22 22 44.0 6.085148 14 14 45.0 6.08552 15 15 46.0 6.085831 15 15 47.0 6.086091 23 23 48.0 6.086309 15 15 49.0 6.08649 15 15 50.0 6.086642 20 20 51.0 6.086769 19 19 52.0 6.086875 12 12 53.0 6.086964 14 14 54.0 6.087038 14 14 55.0 6.087099 15 15 56.0 6.087151 23 23 57.0 6.087194 13 13 58.0 6.08723 12 12 59.0 6.087261 18 18 60.0 6.087286 13 13 61.0 6.087307 16 16 62.0 6.087325 15 15 63.0 6.087339 11 11 64.0 6.087352 12 12 65.0 6.087362 11 11 66.0 6.08737 16 16 67.0 6.087378 11 11 68.0 6.087384 10 10 69.0 6.087389 9 9 70.0 6.087393 10 10 71.0 6.087396 8 8 72.0 6.087399 8 8 73.0 6.087402 11 11 74.0 6.087404 10 10 75.0 6.087405 6 6 76.0 6.087407 11 11 77.0 6.087408 11 11 78.0 6.087409 7 7 79.0 6.08741 6 6 80.0 6.087411 14 14 81.0 6.087411 10 10 82.0 6.087412 10 10 83.0 6.087412 7 7 84.0 6.087412 6 6 85.0 6.087413 8 8 86.0 6.087413 5 5 87.0 6.087413 9 9 88.0 6.087413 5 5 89.0 6.087413 3 3 90.0 6.087414 6 6 91.0 6.087414 8 8 92.0 6.087414 8 8 93.0 6.087414 7 7 94.0 6.087414 7 7 95.0 6.087414 5 5 96.0 6.087414 5 5 97.0 6.087414 6 6 98.0 6.087414 8 8 99.0 6.087414 1 1 100.0 6.087414 3 3 101.0 0 7 7 102.0 0 3 3 103.0 0 6 6 104.0 0 10 10 105.0 0 7 7 106.0 0 4 4 107.0 0 3 3 108.0 0 5 5 109.0 0 6 6 110.0 0 2 2 111.0 0 2 2 112.0 0 8 8 113.0 0 3 3 114.0 0 2 2 115.0 0 5 5 116.0 0 4 4 117.0 0 2 2 118.0 0 3 3 119.0 0 2 2 120.0 0 1 1 121.0 0 2 2 122.0 0 2 2 123.0 0 3 3 124.0 0 1 1 125.0 0 1 1 126.0 0 2 2 127.0 0 2 2 128.0 0 4 4 129.0 0 2 2 130.0 0 1 1 131.0 0 2 2 132.0 0 4 4 133.0 0 4 4 134.0 0 1 1 135.0 0 4 4 136.0 0 2 2 137.0 0 2 2 138.0 0 1 1 140.0 0 1 1 141.0 0 1 1 142.0 0 4 4 143.0 0 2 2 144.0 0 1 1 145.0 0 1 1 147.0 0 1 1 148.0 0 3 3 149.0 0 1 1 150.0 0 1 1 151.0 0 3 3 152.0 0 1 1 153.0 0 1 1 154.0 0 1 1 155.0 0 2 2 156.0 0 2 2 157.0 0 2 2 158.0 0 2 2 159.0 0 3 3 160.0 0 1 1 161.0 0 1 1 162.0 0 1 1 163.0 0 1 1 165.0 0 3 3 166.0 0 1 1 167.0 0 1 1 169.0 0 2 2 170.0 0 3 3 171.0 0 1 1 172.0 0 2 2 174.0 0 2 2 176.0 0 2 2 177.0 0 2 2 179.0 0 1 1 182.0 0 1 1 183.0 0 1 1 184.0 0 1 1 185.0 0 1 1 186.0 0 1 1 190.0 0 1 1 193.0 0 1 1 195.0 0 3 3 196.0 0 1 1 198.0 0 1 1 199.0 0 2 2 200.0 0 1 1 203.0 0 1 1 204.0 0 6 6 207.0 0 1 1 210.0 0 1 1 211.0 0 3 3 213.0 0 2 2 215.0 0 2 2 217.0 0 2 2 219.0 0 1 1 221.0 0 1 1 223.0 0 1 1 226.0 0 1 1 228.0 0 1 1 232.0 0 1 1 233.0 0 2 2 234.0 0 1 1 237.0 0 1 1 241.0 0 1 1 246.0 0 1 1 248.0 0 2 2 251.0 0 1 1 253.0 0 1 1 255.0 0 2 2 256.0 0 1 1 257.0 0 1 1 258.0 0 2 2 259.0 0 2 2 266.0 0 1 1 269.0 0 2 2 270.0 0 1 1 272.0 0 1 1 274.0 0 1 1 280.0 0 1 1 282.0 0 1 1 289.0 0 2 2 290.0 0 1 1 292.0 0 1 1 294.0 0 1 1 301.0 0 1 1 304.0 0 1 1 305.0 0 1 1 313.0 0 1 1 318.0 0 1 1 321.0 0 1 1 322.0 0 2 2 330.0 0 1 1 333.0 0 1 1 334.0 0 1 1 335.0 0 1 1 342.0 0 1 1 347.0 0 2 2 354.0 0 1 1 364.0 0 1 1 383.0 0 1 1 419.0 0 1 1 480.0 0 1 1 492.0 0 2 2 507.0 0 1 1 512.0 0 1 1 558.0 0 1 1 560.0 0 1 1 565.0 0 1 1 583.0 0 1 1 627.0 0 1 1 685.0 0 1 1 695.0 0 1 1 857.0 0 1 1 861.0 0 1 1 905.0 0 1 1 1012.0 0 1 1 1694.0 0 1 1 2989.0 0 1 1